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# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for SearchIO BlastIO parsers."""
import os
import sys
import unittest
import warnings
from Bio import BiopythonParserWarning
from Bio import BiopythonExperimentalWarning
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonExperimentalWarning)
from Bio.SearchIO import parse
# test case files are in the Blast directory
TEST_DIR = 'Blast'
FMT = 'blast-xml'
REFERENCE = (u'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Sch\xe4ffer, '
u'Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), '
u'"Gapped BLAST and PSI-BLAST: a new generation of protein database '
u'search programs", Nucleic Acids Res. 25:3389-3402.')
def get_file(filename):
"""Returns the path of a test file."""
return os.path.join(TEST_DIR, filename)
class BlastnXmlCases(unittest.TestCase):
def test_xml_2212L_blastn_001(self):
xml_file = get_file('xml_2212L_blastn_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.12', qresult.version)
self.assertEqual(REFERENCE, qresult.reference)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual(1, qresult.param_score_match)
self.assertEqual(-3, qresult.param_score_mismatch)
self.assertEqual(5, qresult.param_gap_open)
self.assertEqual(2, qresult.param_gap_extend)
# test parsed values of qresult
self.assertEqual('gi|1348916|gb|G26684.1|G26684', qresult.id)
self.assertEqual('human STS STS_D11570, sequence tagged site',
qresult.description)
self.assertEqual(285, qresult.seq_len)
self.assertEqual(371021, qresult.stat_db_num)
self.assertEqual(1233631384, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.710603, qresult.stat_kappa)
self.assertEqual(1.37406, qresult.stat_lambda)
self.assertEqual(1.30725, qresult.stat_entropy)
self.assertEqual(2, len(qresult))
hit = qresult[0]
self.assertEqual('gi|9950606|gb|AE004854.1|', hit.id)
self.assertEqual('Pseudomonas aeruginosa PAO1, section 415 of 529 of the complete genome', hit.description)
self.assertEqual(11884, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(38.1576, hsp.bitscore)
self.assertEqual(19, hsp.bitscore_raw)
self.assertEqual(1.0598, hsp.evalue)
self.assertEqual(67, hsp.query_start)
self.assertEqual(86, hsp.query_end)
self.assertEqual(6011, hsp.hit_start)
self.assertEqual(6030, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(19, hsp.ident_num)
self.assertEqual(19, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(19, hsp.aln_span)
self.assertEqual('CAGGCCAGCGACTTCTGGG', str(hsp.query.seq))
self.assertEqual('CAGGCCAGCGACTTCTGGG', str(hsp.hit.seq))
self.assertEqual('|||||||||||||||||||', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# parse last hit
hit = qresult[-1]
self.assertEqual('gi|15073988|emb|AL591786.1|SME591786', hit.id)
self.assertEqual('Sinorhizobium meliloti 1021 complete chromosome; segment 5/12', hit.description)
self.assertEqual(299350, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(36.1753, hsp.bitscore)
self.assertEqual(18, hsp.bitscore_raw)
self.assertEqual(4.18768, hsp.evalue)
self.assertEqual(203, hsp.query_start)
self.assertEqual(224, hsp.query_end)
self.assertEqual(83627, hsp.hit_start)
self.assertEqual(83648, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(-1, hsp.hit_frame)
self.assertEqual(20, hsp.ident_num)
self.assertEqual(20, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(21, hsp.aln_span)
self.assertEqual('TGAAAGGAAATNAAAATGGAA', str(hsp.query.seq))
self.assertEqual('TGAAAGGAAATCAAAATGGAA', str(hsp.hit.seq))
self.assertEqual('||||||||||| |||||||||', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_blastn_001(self):
xml_file = get_file('xml_2226_blastn_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Zheng Zhang, Scott Schwartz, Lukas Wagner, and '
'Webb Miller (2000), \"A greedy algorithm for aligning DNA '
'sequences\", J Comput Biol 2000; 7(1-2):203-14.',
qresult.reference)
self.assertEqual(1.0, qresult.param_score_match)
self.assertEqual(-2.0, qresult.param_score_mismatch)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;m;', qresult.param_filter)
self.assertEqual(0.0, qresult.param_gap_open)
self.assertEqual(0.0, qresult.param_gap_extend)
self.assertEqual('blastn', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(128, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(7616765.0, qresult.stat_eff_space)
self.assertEqual(0.46, qresult.stat_kappa)
self.assertEqual(1.28, qresult.stat_lambda)
self.assertEqual(0.85, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|356995852:1-490', qresult.id)
self.assertEqual('Mus musculus POU domain, class 5, transcription factor 1 (Pou5f1), transcript variant 1, mRNA', qresult.description)
self.assertEqual(490, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(31860807.0, qresult.stat_eff_space)
self.assertEqual(0.46, qresult.stat_kappa)
self.assertEqual(1.28, qresult.stat_lambda)
self.assertEqual(0.85, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|356995852|ref|NM_013633.3|', hit.id)
self.assertEqual('Mus musculus POU '
'domain, class 5, transcription factor 1 (Pou5f1), '
'transcript variant 1, mRNA', hit.description)
self.assertEqual(1353, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(905.979, hsp.bitscore)
self.assertEqual(490, hsp.bitscore_raw)
self.assertEqual(0, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(490, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(490, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(490, hsp.ident_num)
self.assertEqual(490, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(490, hsp.aln_span)
self.assertEqual('GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA', str(hsp.query.seq))
self.assertEqual('GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA', str(hsp.hit.seq))
self.assertEqual('||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# test parsed values of the third qresult
qresult = next(qresults)
counter += 1
self.assertEqual('hg19_dna', qresult.id)
self.assertEqual('range=chr1:1207307-1207372 5\'pad=0 3\'pad=0 strand=+ repeatMasking=none', qresult.description)
self.assertEqual(66, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(3506256.0, qresult.stat_eff_space)
self.assertEqual(0.46, qresult.stat_kappa)
self.assertEqual(1.28, qresult.stat_lambda)
self.assertEqual(0.85, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|94721341|ref|NM_001040441.1|', hit.id)
self.assertEqual('Homo sapiens zinc '
'finger and BTB domain containing 8A (ZBTB8A), mRNA',
hit.description)
self.assertEqual(7333, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(115.613, hsp.bitscore)
self.assertEqual(62, hsp.bitscore_raw)
self.assertEqual(5.52066e-29, hsp.evalue)
self.assertEqual(4, hsp.query_start)
self.assertEqual(66, hsp.query_end)
self.assertEqual(3676, hsp.hit_start)
self.assertEqual(3738, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(62, hsp.ident_num)
self.assertEqual(62, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(62, hsp.aln_span)
self.assertEqual('GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.query.seq))
self.assertEqual('GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.hit.seq))
self.assertEqual('||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(98.9927, hsp.bitscore)
self.assertEqual(53, hsp.bitscore_raw)
self.assertEqual(5.55986e-24, hsp.evalue)
self.assertEqual(5, hsp.query_start)
self.assertEqual(58, hsp.query_end)
self.assertEqual(2823, hsp.hit_start)
self.assertEqual(2876, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(53, hsp.ident_num)
self.assertEqual(53, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(53, hsp.aln_span)
self.assertEqual('CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA', str(hsp.query.seq))
self.assertEqual('CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA', str(hsp.hit.seq))
self.assertEqual('|||||||||||||||||||||||||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|332865372|ref|XM_003318468.1|', hit.id)
self.assertEqual('PREDICTED: Pan '
'troglodytes zinc finger protein 273, transcript variant 1 '
'(ZNF273), mRNA', hit.description)
self.assertEqual(4430, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(111.919, hsp.bitscore)
self.assertEqual(60, hsp.bitscore_raw)
self.assertEqual(7.14143e-28, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(66, hsp.query_end)
self.assertEqual(2734, hsp.hit_start)
self.assertEqual(2800, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(-1, hsp.hit_frame)
self.assertEqual(64, hsp.ident_num)
self.assertEqual(64, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(66, hsp.aln_span)
self.assertEqual('TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.query.seq))
self.assertEqual('TCACGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.hit.seq))
self.assertEqual('||| |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(3, counter)
def test_xml_2226_blastn_002(self):
xml_file = get_file('xml_2226_blastn_002.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Zheng Zhang, Scott Schwartz, Lukas Wagner, and '
'Webb Miller (2000), \"A greedy algorithm for aligning DNA '
'sequences\", J Comput Biol 2000; 7(1-2):203-14.',
qresult.reference)
self.assertEqual(1.0, qresult.param_score_match)
self.assertEqual(-2.0, qresult.param_score_mismatch)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;m;', qresult.param_filter)
self.assertEqual(0.0, qresult.param_gap_open)
self.assertEqual(0.0, qresult.param_gap_extend)
self.assertEqual('blastn', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(128, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(7616765.0, qresult.stat_eff_space)
self.assertEqual(0.46, qresult.stat_kappa)
self.assertEqual(1.28, qresult.stat_lambda)
self.assertEqual(0.85, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
self.assertEqual([], list(qresult.hits))
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_blastn_003(self):
xml_file = get_file('xml_2226_blastn_003.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Zheng Zhang, Scott Schwartz, Lukas Wagner, and '
'Webb Miller (2000), \"A greedy algorithm for aligning DNA '
'sequences\", J Comput Biol 2000; 7(1-2):203-14.',
qresult.reference)
self.assertEqual(1.0, qresult.param_score_match)
self.assertEqual(-2.0, qresult.param_score_mismatch)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;m;', qresult.param_filter)
self.assertEqual(0.0, qresult.param_gap_open)
self.assertEqual(0.0, qresult.param_gap_extend)
self.assertEqual('blastn', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
self.assertEqual('gi|356995852:1-490', qresult.id)
self.assertEqual('Mus musculus POU domain, class 5, transcription '
'factor 1 (Pou5f1), transcript variant 1, mRNA',
qresult.description)
self.assertEqual(490, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(31860807.0, qresult.stat_eff_space)
self.assertEqual(0.46, qresult.stat_kappa)
self.assertEqual(1.28, qresult.stat_lambda)
self.assertEqual(0.85, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|356995852|ref|NM_013633.3|', hit.id)
self.assertEqual('Mus musculus POU '
'domain, class 5, transcription factor 1 (Pou5f1), '
'transcript variant 1, mRNA', hit.description)
self.assertEqual(1353, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(905.979, hsp.bitscore)
self.assertEqual(490, hsp.bitscore_raw)
self.assertEqual(0, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(490, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(490, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(490, hsp.ident_num)
self.assertEqual(490, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(490, hsp.aln_span)
self.assertEqual('GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA', str(hsp.query.seq))
self.assertEqual('GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA', str(hsp.hit.seq))
self.assertEqual('||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_blastn_004(self):
xml_file = get_file('xml_2226_blastn_004.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('hg19_dna', qresult.id)
self.assertEqual('range=chr1:1207307-1207372 5\'pad=0 3\'pad=0 '
'strand=+ repeatMasking=none',
qresult.description)
self.assertEqual(66, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(3506256.0, qresult.stat_eff_space)
self.assertEqual(0.46, qresult.stat_kappa)
self.assertEqual(1.28, qresult.stat_lambda)
self.assertEqual(0.85, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|94721341|ref|NM_001040441.1|', hit.id)
self.assertEqual('Homo sapiens zinc '
'finger and BTB domain containing 8A (ZBTB8A), mRNA',
hit.description)
self.assertEqual(7333, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(115.613, hsp.bitscore)
self.assertEqual(62, hsp.bitscore_raw)
self.assertEqual(5.52066e-29, hsp.evalue)
self.assertEqual(4, hsp.query_start)
self.assertEqual(66, hsp.query_end)
self.assertEqual(3676, hsp.hit_start)
self.assertEqual(3738, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(62, hsp.ident_num)
self.assertEqual(62, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(62, hsp.aln_span)
self.assertEqual('GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.query.seq))
self.assertEqual('GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.hit.seq))
self.assertEqual('||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(98.9927, hsp.bitscore)
self.assertEqual(53, hsp.bitscore_raw)
self.assertEqual(5.55986e-24, hsp.evalue)
self.assertEqual(5, hsp.query_start)
self.assertEqual(58, hsp.query_end)
self.assertEqual(2823, hsp.hit_start)
self.assertEqual(2876, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(53, hsp.ident_num)
self.assertEqual(53, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(53, hsp.aln_span)
self.assertEqual('CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA', str(hsp.query.seq))
self.assertEqual('CCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAA', str(hsp.hit.seq))
self.assertEqual('|||||||||||||||||||||||||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|332865372|ref|XM_003318468.1|', hit.id)
self.assertEqual('PREDICTED: Pan '
'troglodytes zinc finger protein 273, transcript variant 1 '
'(ZNF273), mRNA', hit.description)
self.assertEqual(4430, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(111.919, hsp.bitscore)
self.assertEqual(60, hsp.bitscore_raw)
self.assertEqual(7.14143e-28, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(66, hsp.query_end)
self.assertEqual(2734, hsp.hit_start)
self.assertEqual(2800, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(-1, hsp.hit_frame)
self.assertEqual(64, hsp.ident_num)
self.assertEqual(64, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(66, hsp.aln_span)
self.assertEqual('TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.query.seq))
self.assertEqual('TCACGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.hit.seq))
self.assertEqual('||| |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_blastn_005(self):
xml_file = get_file('xml_2226_blastn_005.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Zheng Zhang, Scott Schwartz, Lukas Wagner, and '
'Webb Miller (2000), \"A greedy algorithm for aligning DNA '
'sequences\", J Comput Biol 2000; 7(1-2):203-14.',
qresult.reference)
self.assertEqual(1.0, qresult.param_score_match)
self.assertEqual(-2.0, qresult.param_score_mismatch)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;m;', qresult.param_filter)
self.assertEqual(0.0, qresult.param_gap_open)
self.assertEqual(0.0, qresult.param_gap_extend)
self.assertEqual('blastn', qresult.program)
self.assertEqual('refseq_rna', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(128, qresult.seq_len)
self.assertEqual(2933984, qresult.stat_db_num)
self.assertEqual(4726730735, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.46, qresult.stat_kappa)
self.assertEqual(1.28, qresult.stat_lambda)
self.assertEqual(0.85, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|356995852:1-490', qresult.id)
self.assertEqual('Mus musculus POU domain, class 5, transcription '
'factor 1 (Pou5f1), transcript variant 1, mRNA',
qresult.description)
self.assertEqual(490, qresult.seq_len)
self.assertEqual(2933984, qresult.stat_db_num)
self.assertEqual(4726730735, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.46, qresult.stat_kappa)
self.assertEqual(1.28, qresult.stat_lambda)
self.assertEqual(0.85, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|356995852|ref|NM_013633.3|', hit.id)
self.assertEqual('Mus musculus POU '
'domain, class 5, transcription factor 1 (Pou5f1), '
'transcript variant 1, mRNA', hit.description)
self.assertEqual(1353, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(905.979, hsp.bitscore)
self.assertEqual(490, hsp.bitscore_raw)
self.assertEqual(0, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(490, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(490, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(490, hsp.ident_num)
self.assertEqual(490, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(490, hsp.aln_span)
self.assertEqual('GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA', str(hsp.query.seq))
self.assertEqual('GAGGTGAAACCGTCCCTAGGTGAGCCGTCTTTCCACCAGGCCCCCGGCTCGGGGTGCCCACCTTCCCCATGGCTGGACACCTGGCTTCAGACTTCGCCTTCTCACCCCCACCAGGTGGGGGTGATGGGTCAGCAGGGCTGGAGCCGGGCTGGGTGGATCCTCGAACCTGGCTAAGCTTCCAAGGGCCTCCAGGTGGGCCTGGAATCGGACCAGGCTCAGAGGTATTGGGGATCTCCCCATGTCCGCCCGCATACGAGTTCTGCGGAGGGATGGCATACTGTGGACCTCAGGTTGGACTGGGCCTAGTCCCCCAAGTTGGCGTGGAGACTTTGCAGCCTGAGGGCCAGGCAGGAGCACGAGTGGAAAGCAACTCAGAGGGAACCTCCTCTGAGCCCTGTGCCGACCGCCCCAATGCCGTGAAGTTGGAGAAGGTGGAACCAACTCCCGAGGAGTCCCAGGACATGAAAGCCCTGCAGAAGGAGCTAGAACA', str(hsp.hit.seq))
self.assertEqual('||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# test parsed values of the third qresult
qresult = next(qresults)
counter += 1
self.assertEqual('hg19_dna', qresult.id)
self.assertEqual('range=chr1:1207307-1207372 5\'pad=0 3\'pad=0 '
'strand=+ repeatMasking=none', qresult.description)
self.assertEqual(66, qresult.seq_len)
self.assertEqual(2933984, qresult.stat_db_num)
self.assertEqual(4726730735, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.46, qresult.stat_kappa)
self.assertEqual(1.28, qresult.stat_lambda)
self.assertEqual(0.85, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|332237160|ref|XM_003267724.1|', hit.id)
self.assertEqual('PREDICTED: Nomascus leucogenys ATG14 autophagy '
'related 14 homolog (S. cerevisiae) (ATG14), mRNA', hit.description)
self.assertEqual(4771, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(115.613, hsp.bitscore)
self.assertEqual(62, hsp.bitscore_raw)
self.assertEqual(3.35972e-23, hsp.evalue)
self.assertEqual(4, hsp.query_start)
self.assertEqual(66, hsp.query_end)
self.assertEqual(2864, hsp.hit_start)
self.assertEqual(2926, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(62, hsp.ident_num)
self.assertEqual(62, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(62, hsp.aln_span)
self.assertEqual('GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.query.seq))
self.assertEqual('GCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.hit.seq))
self.assertEqual('||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|332254616|ref|XM_003276378.1|', hit.id)
self.assertEqual('PREDICTED: Nomascus leucogenys S100P binding '
'protein, transcript variant 2 (S100PBP), mRNA', hit.description)
self.assertEqual(4345, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(111.919, hsp.bitscore)
self.assertEqual(60, hsp.bitscore_raw)
self.assertEqual(4.34607e-22, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(66, hsp.query_end)
self.assertEqual(2791, hsp.hit_start)
self.assertEqual(2857, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(-1, hsp.hit_frame)
self.assertEqual(64, hsp.ident_num)
self.assertEqual(64, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(66, hsp.aln_span)
self.assertEqual('TCAAGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.query.seq))
self.assertEqual('TCATGCCACTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCGTCTCAAAAAAAAAAAAAAAAAA', str(hsp.hit.seq))
self.assertEqual('||| |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(3, counter)
class BlastpXmlCases(unittest.TestCase):
def test_xml_2212L_blastp_001(self):
xml_file = get_file('xml_2212L_blastp_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.12', qresult.version)
self.assertEqual(REFERENCE, qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastp', qresult.program)
self.assertEqual('nr', qresult.target)
self.assertEqual('gi|49176427|ref|NP_418280.3|', qresult.id)
self.assertEqual('component of Sec-independent translocase [Escherichia coli K12]',
qresult.description)
self.assertEqual(103, qresult.seq_len)
self.assertEqual(2934173, qresult.stat_db_num)
self.assertEqual(1011751523, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(212, len(qresult))
# check for alternative ID results
self.assertEqual(qresult['gi|49176427|ref|NP_418280.3|'],
qresult['gi|26250604|ref|NP_756644.1|'])
self.assertEqual(qresult['gi|49176427|ref|NP_418280.3|'],
qresult['gi|30064867|ref|NP_839038.1|'])
self.assertEqual(qresult['gi|49176427|ref|NP_418280.3|'],
qresult['gi|24115132|ref|NP_709642.1|'])
self.assertEqual(qresult['gi|49176427|ref|NP_418280.3|'],
qresult['gi|24054404|gb|AAN45349.1|'])
self.assertEqual(qresult['gi|49176427|ref|NP_418280.3|'],
qresult['gi|2367310|gb|AAC76839.1|'])
self.assertEqual(qresult['gi|49176427|ref|NP_418280.3|'],
qresult['gi|30043127|gb|AAP18849.1|'])
self.assertEqual(qresult['gi|49176427|ref|NP_418280.3|'],
qresult['gi|26111035|gb|AAN83218.1|'])
self.assertEqual(qresult['gi|49176427|ref|NP_418280.3|'],
qresult['gi|3193217|gb|AAC19240.1|'])
self.assertEqual(qresult['gi|49176427|ref|NP_418280.3|'],
qresult['gi|7444818|pir||E65188'])
hit = qresult[0]
self.assertEqual('gi|49176427|ref|NP_418280.3|', hit.id)
self.assertEqual('component of Sec-independent translocase '
'[Escherichia coli K12]', hit.description)
self.assertEqual(10, len(hit.id_all))
self.assertEqual(10, len(hit.description_all))
self.assertEqual(103, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(185.267, hsp.bitscore)
self.assertEqual(469, hsp.bitscore_raw)
self.assertEqual(4.20576e-46, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(103, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(103, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(103, hsp.ident_num)
self.assertEqual(103, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(103, hsp.aln_span)
self.assertEqual('MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV', str(hsp.query.seq))
self.assertEqual('MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV', str(hsp.hit.seq))
self.assertEqual('MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# parse last hit
hit = qresult[-1]
self.assertEqual('gi|39593039|emb|CAE64508.1|', hit.id)
self.assertEqual('Hypothetical protein CBG09238 [Caenorhabditis briggsae]', hit.description)
self.assertEqual(960, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(31.5722, hsp.bitscore)
self.assertEqual(70, hsp.bitscore_raw)
self.assertEqual(7.7721, hsp.evalue)
self.assertEqual(54, hsp.query_start)
self.assertEqual(102, hsp.query_end)
self.assertEqual(409, hsp.hit_start)
self.assertEqual(459, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(19, hsp.ident_num)
self.assertEqual(33, hsp.pos_num)
self.assertEqual(4, hsp.gap_num)
self.assertEqual(51, hsp.aln_span)
self.assertEqual('KAMSDDEPKQD---KTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ', str(hsp.query.seq))
self.assertEqual('KKEADDKAKKDLEAKTKKEADEKAKKEADEKA-KKEAEAKTKEAEAKTKKE', str(hsp.hit.seq))
self.assertEqual('K +DD+ K+D KT ++AD AK AD++A + +AKT++A+ K++', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2218_blastp_001(self):
xml_file = get_file('xml_2218_blastp_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.18+', qresult.version)
self.assertEqual(REFERENCE, qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastp', qresult.program)
self.assertEqual('nr', qresult.target)
self.assertEqual('31493', qresult.id)
self.assertEqual('unnamed protein product', qresult.description)
self.assertEqual(70, qresult.seq_len)
self.assertEqual(15287, qresult.stat_db_num)
self.assertEqual(7033566, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(10, len(qresult))
hit = qresult[0]
self.assertEqual('gi|151942244|gb|EDN60600.1|', hit.id)
self.assertEqual('cytosolic iron-sulfur protein assembly protein [Saccharomyces cerevisiae YJM789]', hit.description)
self.assertEqual(330, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(33.113, hsp.bitscore)
self.assertEqual(74, hsp.bitscore_raw)
self.assertEqual(0.0185319, hsp.evalue)
self.assertEqual(14, hsp.query_start)
self.assertEqual(62, hsp.query_end)
self.assertEqual(113, hsp.hit_start)
self.assertEqual(163, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(16, hsp.ident_num)
self.assertEqual(27, hsp.pos_num)
self.assertEqual(2, hsp.gap_num)
self.assertEqual(50, hsp.aln_span)
self.assertEqual('AWNKDRTQIAICPNNHEVHIYE--KSGAKWNKVHELKEHNGQVTGIDWAP', str(hsp.query.seq))
self.assertEqual('AWSNDGYYLATCSRDKSVWIWETDESGEEYECISVLQEHSQDVKHVIWHP', str(hsp.hit.seq))
self.assertEqual('AW+ D +A C + V I+E +SG ++ + L+EH+ V + W P', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# parse last hit
hit = qresult[-1]
self.assertEqual('gi|151567870|pdb|2PM9|B', hit.id)
self.assertEqual('Chain B, Crystal Structure Of Yeast Sec1331 VERTEX ELEMENT OF THE Copii Vesicular Coat', hit.description)
self.assertEqual(297, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(30.8018, hsp.bitscore)
self.assertEqual(68, hsp.bitscore_raw)
self.assertEqual(0.0919731, hsp.evalue)
self.assertEqual(20, hsp.query_start)
self.assertEqual(62, hsp.query_end)
self.assertEqual(67, hsp.hit_start)
self.assertEqual(109, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(11, hsp.ident_num)
self.assertEqual(23, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(42, hsp.aln_span)
self.assertEqual('TQIAICPNNHEVHIYEKSGAKWNKVHELKEHNGQVTGIDWAP', str(hsp.query.seq))
self.assertEqual('TILASCSYDGKVMIWKEENGRWSQIAVHAVHSASVNSVQWAP', str(hsp.hit.seq))
self.assertEqual('T +A C + +V I+++ +W+++ H+ V + WAP', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2218_blastp_002(self):
xml_file = get_file('xml_2218_blastp_002.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.18+', qresult.version)
self.assertEqual(REFERENCE, qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(0.01, qresult.param_evalue_threshold)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('m L; R -d repeat/repeat_9606;', qresult.param_filter)
self.assertEqual('blastp', qresult.program)
self.assertEqual('gpipe/9606/Previous/protein', qresult.target)
# test parsed values of the first qresult
self.assertEqual('gi|585505|sp|Q08386|MOPB_RHOCA', qresult.id)
self.assertEqual('Molybdenum-pterin-binding protein mopB >gi|310278|gb|AAA71913.1| molybdenum-pterin-binding protein', qresult.description)
self.assertEqual(270, qresult.seq_len)
self.assertEqual(27252, qresult.stat_db_num)
self.assertEqual(13958303, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|129628|sp|P07175.1|PARA_AGRTU', qresult.id)
self.assertEqual('Protein parA', qresult.description)
self.assertEqual(222, qresult.seq_len)
self.assertEqual(27252, qresult.stat_db_num)
self.assertEqual(13958303, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(2, counter)
def test_xml_2218L_blastp_001(self):
xml_file = get_file('xml_2218L_blastp_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.18', qresult.version)
self.assertEqual('~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(1e-05, qresult.param_evalue_threshold)
self.assertEqual('F', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastp', qresult.program)
self.assertEqual('/Users/pjcock/Downloads/Software/blast-2.2.18/data/nr', qresult.target)
# test parsed values of the first qresult
self.assertEqual('Fake', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(9, qresult.seq_len)
self.assertEqual(6589360, qresult.stat_db_num)
self.assertEqual(2253133281, qresult.stat_db_len)
self.assertEqual(2.02782e+10, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2222_blastp_001(self):
xml_file = get_file('xml_2222_blastp_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.22+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(1e-06, qresult.param_evalue_threshold)
self.assertEqual('F', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastp', qresult.program)
self.assertEqual('nr', qresult.target)
self.assertEqual('1', qresult.id)
self.assertEqual('gi|3298468|dbj|BAA31520.1| SAMIPF', qresult.description)
self.assertEqual(107, qresult.seq_len)
self.assertEqual(8994603, qresult.stat_db_num)
self.assertEqual(-1216159329, qresult.stat_db_len)
self.assertEqual(76934807744, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(10, len(qresult))
hit = qresult[0]
self.assertEqual('gi|3298468|dbj|BAA31520.1|', hit.id)
self.assertEqual('SAMIPF [Aster tripolium]', hit.description)
self.assertEqual(107, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(204.912011757068, hsp.bitscore)
self.assertEqual(520, hsp.bitscore_raw)
self.assertEqual(1.77242652875017e-51, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(107, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(107, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(107, hsp.ident_num)
self.assertEqual(107, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(107, hsp.aln_span)
self.assertEqual('GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVGVTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI', str(hsp.query.seq))
self.assertEqual('GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVGVTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI', str(hsp.hit.seq))
self.assertEqual('GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVGVTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# parse last hit
hit = qresult[-1]
self.assertEqual('gi|162809290|dbj|BAF95576.1|', hit.id)
self.assertEqual('tonoplast intrinsic protein [Nicotiana tabacum]', hit.description)
self.assertEqual(251, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(177.948041442853, hsp.bitscore)
self.assertEqual(450, hsp.bitscore_raw)
self.assertEqual(2.0302699895292e-43, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(107, hsp.query_end)
self.assertEqual(80, hsp.hit_start)
self.assertEqual(187, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(91, hsp.ident_num)
self.assertEqual(95, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(107, hsp.aln_span)
self.assertEqual('GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVGVTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI', str(hsp.query.seq))
self.assertEqual('GGHVNPAVTFGAFVGGNITLFRGILYIIAQLLGSTVACFLLEFATGGMSTGAFALSAGVSVWNAFVFEIVMTFGLVYTVYATAIDPKKGDLGVIAPIAIGFIVGANI', str(hsp.hit.seq))
self.assertEqual('GGHVNPAVTFGAFVGGNITL RGI+YIIAQLLGSTVAC LL+F T M+ G F+LSAGV V NA VFEIVMTFGLVYTVYATAIDPKKG LG IAPIAIGFIVGANI', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# def test_xml_2218L_rpsblast_001(self):
# PSI-blast, handle later
def test_xml_2226_blastp_001(self):
xml_file = get_file('xml_2226_blastp_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb '
'Miller, and David J. Lipman (1997), \"Gapped BLAST and '
'PSI-BLAST: a new generation of protein database search '
'programs\", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('F', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastp', qresult.program)
self.assertEqual('db/minirefseq_prot', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(32, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(156650.0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|16080617|ref|NP_391444.1|', qresult.id)
self.assertEqual('membrane bound lipoprotein [Bacillus subtilis '
'subsp. subtilis str. 168]', qresult.description)
self.assertEqual(102, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(361344, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|308175296|ref|YP_003922001.1|', hit.id)
self.assertEqual('membrane bound '
'lipoprotein [Bacillus amyloliquefaciens DSM 7]',
hit.description)
self.assertEqual(100, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(139.428, hsp.bitscore)
self.assertEqual(350, hsp.bitscore_raw)
self.assertEqual(1.99275e-46, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(102, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(100, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(69, hsp.ident_num)
self.assertEqual(81, hsp.pos_num)
self.assertEqual(2, hsp.gap_num)
self.assertEqual(102, hsp.aln_span)
self.assertEqual('MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN', str(hsp.query.seq))
self.assertEqual('MKKIFGCLFFILLLAGCGVTNEKSQGEDAG--EKLVTKEGTYVGLADTHTIEVTVDHEPVSFDITEESADDVKNLNNGEKVTVKYQKNSKGQLVLKDIEPAN', str(hsp.hit.seq))
self.assertEqual('MKK LFFILLL+GCGV ++KSQGED + TKEGTYVGLADTHTIEVTVD+EPVS DITEES D+ N+G+KVT+ Y+KN +GQL+LKDIE AN', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# test parsed values of the third qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|11464971:4-101', qresult.id)
self.assertEqual('pleckstrin [Mus musculus]', qresult.description)
self.assertEqual(98, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(345626, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|11464971|ref|NP_062422.1|', hit.id)
self.assertEqual('pleckstrin [Mus musculus]', hit.description)
self.assertEqual(350, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(205.682, hsp.bitscore)
self.assertEqual(522, hsp.bitscore_raw)
self.assertEqual(2.24956e-69, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(3, hsp.hit_start)
self.assertEqual(101, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(98, hsp.ident_num)
self.assertEqual(98, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(43.5134, hsp.bitscore)
self.assertEqual(101, hsp.bitscore_raw)
self.assertEqual(2.90061e-09, hsp.evalue)
self.assertEqual(2, hsp.query_start)
self.assertEqual(96, hsp.query_end)
self.assertEqual(245, hsp.hit_start)
self.assertEqual(345, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(29, hsp.ident_num)
self.assertEqual(48, hsp.pos_num)
self.assertEqual(6, hsp.gap_num)
self.assertEqual(100, hsp.aln_span)
self.assertEqual('IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTS--PCQDFGK--RMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA', str(hsp.query.seq))
self.assertEqual('IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAVHLRGCVVTSVESSHDVKKSDEENLFEIITADEVHYYLQAATSKERTEWIKAIQVA', str(hsp.hit.seq))
self.assertEqual('I++G L+K+G WK +L ED + +Y P G + L+G +TS D K + +I T + ++ QAA +ER W++ I+ A', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|350596020|ref|XP_003360649.2|', hit.id)
self.assertEqual('PREDICTED: pleckstrin-like [Sus scrofa]', hit.description)
self.assertEqual(228, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(199.519, hsp.bitscore)
self.assertEqual(506, hsp.bitscore_raw)
self.assertEqual(1.97058e-68, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(3, hsp.hit_start)
self.assertEqual(101, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(94, hsp.ident_num)
self.assertEqual(96, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(3, counter)
def test_xml_2226_blastp_002(self):
xml_file = get_file('xml_2226_blastp_002.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb '
'Miller, and David J. Lipman (1997), \"Gapped BLAST and '
'PSI-BLAST: a new generation of protein database search '
'programs\", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('F', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastp', qresult.program)
self.assertEqual('db/minirefseq_prot', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(32, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(156650.0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_blastp_003(self):
xml_file = get_file('xml_2226_blastp_003.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb '
'Miller, and David J. Lipman (1997), \"Gapped BLAST and '
'PSI-BLAST: a new generation of protein database search '
'programs\", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('F', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastp', qresult.program)
self.assertEqual('db/minirefseq_prot', qresult.target)
self.assertEqual('gi|16080617|ref|NP_391444.1|', qresult.id)
self.assertEqual('membrane bound lipoprotein [Bacillus subtilis '
'subsp. subtilis str. 168]', qresult.description)
self.assertEqual(102, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(361344, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|308175296|ref|YP_003922001.1|', hit.id)
self.assertEqual('membrane bound lipoprotein [Bacillus amyloliquefaciens DSM 7]', hit.description)
self.assertEqual(100, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(139.428, hsp.bitscore)
self.assertEqual(350, hsp.bitscore_raw)
self.assertEqual(1.99275e-46, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(102, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(100, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(69, hsp.ident_num)
self.assertEqual(81, hsp.pos_num)
self.assertEqual(2, hsp.gap_num)
self.assertEqual(102, hsp.aln_span)
self.assertEqual('MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN', str(hsp.query.seq))
self.assertEqual('MKKIFGCLFFILLLAGCGVTNEKSQGEDAG--EKLVTKEGTYVGLADTHTIEVTVDHEPVSFDITEESADDVKNLNNGEKVTVKYQKNSKGQLVLKDIEPAN', str(hsp.hit.seq))
self.assertEqual('MKK LFFILLL+GCGV ++KSQGED + TKEGTYVGLADTHTIEVTVD+EPVS DITEES D+ N+G+KVT+ Y+KN +GQL+LKDIE AN', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_blastp_004(self):
xml_file = get_file('xml_2226_blastp_004.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb '
'Miller, and David J. Lipman (1997), \"Gapped BLAST and '
'PSI-BLAST: a new generation of protein database search '
'programs\", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('F', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastp', qresult.program)
self.assertEqual('db/minirefseq_prot', qresult.target)
self.assertEqual('gi|11464971:4-101', qresult.id)
self.assertEqual('pleckstrin [Mus musculus]', qresult.description)
self.assertEqual(98, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(345626, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|11464971|ref|NP_062422.1|', hit.id)
self.assertEqual('pleckstrin [Mus musculus]', hit.description)
self.assertEqual(350, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(205.682, hsp.bitscore)
self.assertEqual(522, hsp.bitscore_raw)
self.assertEqual(2.24956e-69, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(3, hsp.hit_start)
self.assertEqual(101, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(98, hsp.ident_num)
self.assertEqual(98, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(43.5134, hsp.bitscore)
self.assertEqual(101, hsp.bitscore_raw)
self.assertEqual(2.90061e-09, hsp.evalue)
self.assertEqual(2, hsp.query_start)
self.assertEqual(96, hsp.query_end)
self.assertEqual(245, hsp.hit_start)
self.assertEqual(345, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(29, hsp.ident_num)
self.assertEqual(48, hsp.pos_num)
self.assertEqual(6, hsp.gap_num)
self.assertEqual(100, hsp.aln_span)
self.assertEqual('IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTS--PCQDFGK--RMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA', str(hsp.query.seq))
self.assertEqual('IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAVHLRGCVVTSVESSHDVKKSDEENLFEIITADEVHYYLQAATSKERTEWIKAIQVA', str(hsp.hit.seq))
self.assertEqual('I++G L+K+G WK +L ED + +Y P G + L+G +TS D K + +I T + ++ QAA +ER W++ I+ A', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|350596020|ref|XP_003360649.2|', hit.id)
self.assertEqual('PREDICTED: pleckstrin-like [Sus scrofa]', hit.description)
self.assertEqual(228, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(199.519, hsp.bitscore)
self.assertEqual(506, hsp.bitscore_raw)
self.assertEqual(1.97058e-68, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(3, hsp.hit_start)
self.assertEqual(101, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(94, hsp.ident_num)
self.assertEqual(96, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_blastp_005(self):
xml_file = get_file('xml_2226_blastp_005.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb '
'Miller, and David J. Lipman (1997), \"Gapped BLAST and '
'PSI-BLAST: a new generation of protein database search '
'programs\", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('F', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastp', qresult.program)
self.assertEqual('refseq_protein', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(32, qresult.seq_len)
self.assertEqual(12646943, qresult.stat_db_num)
self.assertEqual(4397139428, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|16080617|ref|NP_391444.1|', qresult.id)
self.assertEqual('membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]', qresult.description)
self.assertEqual(102, qresult.seq_len)
self.assertEqual(12646943, qresult.stat_db_num)
self.assertEqual(4397139428, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
# check for alternative ID results
self.assertEqual(qresult['gi|16080617|ref|NP_391444.1|'],
qresult['gi|221311516|ref|ZP_03593363.1|'])
self.assertEqual(qresult['gi|16080617|ref|NP_391444.1|'],
qresult['gi|221315843|ref|ZP_03597648.1|'])
self.assertEqual(qresult['gi|16080617|ref|NP_391444.1|'],
qresult['gi|221320757|ref|ZP_03602051.1|'])
self.assertEqual(qresult['gi|16080617|ref|NP_391444.1|'],
qresult['gi|221325043|ref|ZP_03606337.1|'])
self.assertEqual(qresult['gi|16080617|ref|NP_391444.1|'],
qresult['gi|321313111|ref|YP_004205398.1|'])
hit = qresult[0]
self.assertEqual('gi|16080617|ref|NP_391444.1|', hit.id)
self.assertEqual('membrane bound lipoprotein [Bacillus '
'subtilis subsp. subtilis str. 168]', hit.description)
self.assertEqual(6, len(hit.id_all))
self.assertEqual(6, len(hit.description_all))
self.assertEqual(102, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(205.297, hsp.bitscore)
self.assertEqual(521, hsp.bitscore_raw)
self.assertEqual(1.45285e-66, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(102, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(102, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(102, hsp.ident_num)
self.assertEqual(102, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(102, hsp.aln_span)
self.assertEqual('MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN', str(hsp.query.seq))
self.assertEqual('MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN', str(hsp.hit.seq))
self.assertEqual('MKKFIALLFFILLLSGCGVNSQKSQGEDVSPDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLLLKDIERAN', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# test parsed values of the third qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|11464971:4-101', qresult.id)
self.assertEqual('pleckstrin [Mus musculus]', qresult.description)
self.assertEqual(98, qresult.seq_len)
self.assertEqual(12646943, qresult.stat_db_num)
self.assertEqual(4397139428, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|11464971|ref|NP_062422.1|', hit.id)
self.assertEqual('pleckstrin [Mus musculus]', hit.description)
self.assertEqual(350, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(205.682, hsp.bitscore)
self.assertEqual(522, hsp.bitscore_raw)
self.assertEqual(1.54412e-63, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(3, hsp.hit_start)
self.assertEqual(101, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(98, hsp.ident_num)
self.assertEqual(98, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(43.5134, hsp.bitscore)
self.assertEqual(101, hsp.bitscore_raw)
self.assertEqual(0.00199101, hsp.evalue)
self.assertEqual(2, hsp.query_start)
self.assertEqual(96, hsp.query_end)
self.assertEqual(245, hsp.hit_start)
self.assertEqual(345, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(29, hsp.ident_num)
self.assertEqual(48, hsp.pos_num)
self.assertEqual(6, hsp.gap_num)
self.assertEqual(100, hsp.aln_span)
self.assertEqual('IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTS--PCQDFGK--RMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA', str(hsp.query.seq))
self.assertEqual('IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAVHLRGCVVTSVESSHDVKKSDEENLFEIITADEVHYYLQAATSKERTEWIKAIQVA', str(hsp.hit.seq))
self.assertEqual('I++G L+K+G WK +L ED + +Y P G + L+G +TS D K + +I T + ++ QAA +ER W++ I+ A', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|350596020|ref|XP_003360649.2|', hit.id)
self.assertEqual('PREDICTED: pleckstrin-like [Sus scrofa]', hit.description)
self.assertEqual(228, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(199.519, hsp.bitscore)
self.assertEqual(506, hsp.bitscore_raw)
self.assertEqual(1.35263e-62, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(3, hsp.hit_start)
self.assertEqual(101, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(94, hsp.ident_num)
self.assertEqual(96, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(3, counter)
class BlastxXmlCases(unittest.TestCase):
def test_xml_2212L_blastx_001(self):
xml_file = get_file('xml_2212L_blastx_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.12', qresult.version)
self.assertEqual(REFERENCE, qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastx', qresult.program)
self.assertEqual('nr', qresult.target)
# test parsed values of the first qresult
self.assertEqual('gi|1347369|gb|G25137.1|G25137', qresult.id)
self.assertEqual('human STS EST48004, sequence tagged site', qresult.description)
self.assertEqual(556, qresult.seq_len)
self.assertEqual(2934173, qresult.stat_db_num)
self.assertEqual(1011751523, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
# test parsed values of the first hit
hit = qresult[0]
self.assertEqual('gi|12654095|gb|AAH00859.1|', hit.id)
self.assertEqual('Unknown (protein for IMAGE:3459481) [Homo sapiens]', hit.description)
self.assertEqual(319, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(247.284, hsp.bitscore)
self.assertEqual(630, hsp.bitscore_raw)
self.assertEqual(1.69599e-64, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(399, hsp.query_end)
self.assertEqual(155, hsp.hit_start)
self.assertEqual(288, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(122, hsp.ident_num)
self.assertEqual(123, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(133, hsp.aln_span)
self.assertEqual('DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE', str(hsp.query.seq))
self.assertEqual('DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK', str(hsp.hit.seq))
self.assertEqual('DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+', hsp.aln_annotation['similarity'])
# test parsed values of last hit
hit = qresult[-1]
self.assertEqual('gi|72081091|ref|XP_800619.1|', hit.id)
self.assertEqual('PREDICTED: hypothetical protein XP_795526 [Strongylocentrotus purpuratus]', hit.description)
self.assertEqual(337, hit.seq_len)
hsp = hit.hsps[0]
self.assertEqual(32.3426, hsp.bitscore)
self.assertEqual(72, hsp.bitscore_raw)
self.assertEqual(8.57476, hsp.evalue)
self.assertEqual(39, hsp.query_start)
self.assertEqual(231, hsp.query_end)
self.assertEqual(105, hsp.hit_start)
self.assertEqual(172, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(21, hsp.ident_num)
self.assertEqual(37, hsp.pos_num)
self.assertEqual(3, hsp.gap_num)
self.assertEqual('AGTNSRWEVIANYMNI--HSSSGVKRT-AKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQ', str(hsp.query.seq))
self.assertEqual('SSSNSSSKASASSSNVGASSSSGTKKSDSKSSNESSKSKRDKEDHKEGSINRSKDEKVSKEHRVVKE', str(hsp.hit.seq))
self.assertEqual('+ +NS + A+ N+ SSSG K++ +K +KS + + H++ IN+ +K KEH VV +', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2222_blastx_001(self):
xml_file = get_file('xml_2222_blastx_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.22+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(0.0001, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastx', qresult.program)
self.assertEqual('nr', qresult.target)
# test parsed values of the first qresult
self.assertEqual('1', qresult.id)
self.assertEqual('gi|4104054|gb|AH007193.1|SEG_CVIGS Centaurea vallesiaca 18S ribosomal RNA gene, partial sequence', qresult.description)
self.assertEqual(1002, qresult.seq_len)
self.assertEqual(8994603, qresult.stat_db_num)
self.assertEqual(-1216159329, qresult.stat_db_len)
self.assertEqual(367397307882, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
# test parsed values of the first hit
hit = qresult[0]
self.assertEqual('gi|149390769|gb|ABR25402.1|', hit.id)
self.assertEqual('unknown [Oryza sativa (indica cultivar-group)]', hit.description)
self.assertEqual(26, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(54.2989775733826, hsp.bitscore)
self.assertEqual(129, hsp.bitscore_raw)
self.assertEqual(1.83262460293058e-05, hsp.evalue)
self.assertEqual(910, hsp.query_start)
self.assertEqual(988, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(26, hsp.hit_end)
self.assertEqual(2, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(24, hsp.ident_num)
self.assertEqual(25, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(26, hsp.aln_span)
self.assertEqual('HMLVSKIKPCMCKYEQIQTVKLRMAH', str(hsp.query.seq))
self.assertEqual('HMLVSKIKPCMCKYELIRTVKLRMAH', str(hsp.hit.seq))
self.assertEqual('HMLVSKIKPCMCKYE I+TVKLRMAH', hsp.aln_annotation['similarity'])
def test_xml_2226_blastx_001(self):
xml_file = get_file('xml_2226_blastx_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb '
'Miller, and David J. Lipman (1997), "Gapped BLAST '
'and PSI-BLAST: a new generation of protein database search '
'programs", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastx', qresult.program)
self.assertEqual('db/minirefseq_prot', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(128, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(-1, qresult.stat_kappa)
self.assertEqual(-1, qresult.stat_lambda)
self.assertEqual(-1, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the third qresult
qresult = next(qresults)
counter += 1
self.assertEqual('hg19_dna', qresult.id)
self.assertEqual('range=chr1:1207057-1207541 5\'pad=0 3\'pad=0 '
'strand=+ repeatMasking=none', qresult.description)
self.assertEqual(485, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(662354, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|332258565|ref|XP_003278367.1|', hit.id)
self.assertEqual('PREDICTED: UPF0764 protein C16orf89-like [Nomascus leucogenys]', hit.description)
self.assertEqual(132, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(121.709, hsp.bitscore)
self.assertEqual(304, hsp.bitscore_raw)
self.assertEqual(2.9522e-38, hsp.evalue)
self.assertEqual(15, hsp.query_start)
self.assertEqual(300, hsp.query_end)
self.assertEqual(24, hsp.hit_start)
self.assertEqual(119, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(69, hsp.ident_num)
self.assertEqual(74, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(95, hsp.aln_span)
self.assertEqual('LRRSFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQP', str(hsp.query.seq))
self.assertEqual('LRRSFALVAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLANFLFLVEMGFLHVGQAGLELVTSGDPPTLTSQSAGIIGVSHCAQP', str(hsp.hit.seq))
self.assertEqual('LRRSFALVAQ VQW +LG PQPPPPGFK FSCLS SSW+YRH+PP L NF+FLVE GF HVGQAGLE SG+ P SQS GI GVSH AQP', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(51.6026, hsp.bitscore)
self.assertEqual(122, hsp.bitscore_raw)
self.assertEqual(2.73605e-12, hsp.evalue)
self.assertEqual(243, hsp.query_start)
self.assertEqual(459, hsp.query_end)
self.assertEqual(31, hsp.hit_start)
self.assertEqual(98, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(34, hsp.ident_num)
self.assertEqual(41, hsp.pos_num)
self.assertEqual(5, hsp.gap_num)
self.assertEqual(72, hsp.aln_span)
self.assertEqual('VGPARVQ*HDLSSLQPPAPEFK*FSHLSLQSSWDCRCPPPHPANXXXXXXXXFLRRSFALVAQAGVQWLDLG', str(hsp.query.seq))
self.assertEqual('VAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLAN-----FLFLVEMGFLHVGQAGLELVTSG', str(hsp.hit.seq))
self.assertEqual('V RVQ ++L S QPP P FK FS LSL SSW+ R PPH AN F F + F V QAG++ + G', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|33188429|ref|NP_872601.1|', hit.id)
self.assertEqual('histone demethylase UTY isoform 1 [Homo sapiens]', hit.description)
self.assertEqual(1079, hit.seq_len)
self.assertEqual(6, len(hit))
hsp = hit.hsps[0]
self.assertEqual(104.375, hsp.bitscore)
self.assertEqual(259, hsp.bitscore_raw)
self.assertEqual(6.31914e-29, hsp.evalue)
self.assertEqual(18, hsp.query_start)
self.assertEqual(291, hsp.query_end)
self.assertEqual(988, hsp.hit_start)
self.assertEqual(1079, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(59, hsp.ident_num)
self.assertEqual(66, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(91, hsp.aln_span)
self.assertEqual('SFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQ', str(hsp.query.seq))
self.assertEqual('SFQESLRAGMQWCDLSSLQPPPPGFKRFSHLSLPNSWNYRHLPSCPTNFCIFVETGFHHVGQACLELLTSGGLLASASQSAGITGVSHHAR', str(hsp.hit.seq))
self.assertEqual('SF +AG+QW DL QPPPPGFK FS LS P+SW+YRH+P C NF VETGF+HVGQA LE SG L A ASQS GITGVSHHA+', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(2, counter)
def test_xml_2226_blastx_002(self):
xml_file = get_file('xml_2226_blastx_002.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb '
'Miller, and David J. Lipman (1997), "Gapped BLAST '
'and PSI-BLAST: a new generation of protein database search '
'programs", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastx', qresult.program)
self.assertEqual('db/minirefseq_prot', qresult.target)
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(128, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(-1, qresult.stat_kappa)
self.assertEqual(-1, qresult.stat_lambda)
self.assertEqual(-1, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_blastx_003(self):
xml_file = get_file('xml_2226_blastx_003.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb '
'Miller, and David J. Lipman (1997), "Gapped BLAST '
'and PSI-BLAST: a new generation of protein database search '
'programs", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastx', qresult.program)
self.assertEqual('db/minirefseq_prot', qresult.target)
self.assertEqual('hg19_dna', qresult.id)
self.assertEqual('range=chr1:1207057-1207541 5\'pad=0 3\'pad=0 strand=+ repeatMasking=none', qresult.description)
self.assertEqual(485, qresult.seq_len)
self.assertEqual(20, qresult.stat_db_num)
self.assertEqual(6406, qresult.stat_db_len)
self.assertEqual(662354, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|332258565|ref|XP_003278367.1|', hit.id)
self.assertEqual('PREDICTED: UPF0764 protein C16orf89-like [Nomascus leucogenys]', hit.description)
self.assertEqual(132, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(121.709, hsp.bitscore)
self.assertEqual(304, hsp.bitscore_raw)
self.assertEqual(2.9522e-38, hsp.evalue)
self.assertEqual(15, hsp.query_start)
self.assertEqual(300, hsp.query_end)
self.assertEqual(24, hsp.hit_start)
self.assertEqual(119, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(69, hsp.ident_num)
self.assertEqual(74, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(95, hsp.aln_span)
self.assertEqual('LRRSFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQP', str(hsp.query.seq))
self.assertEqual('LRRSFALVAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLANFLFLVEMGFLHVGQAGLELVTSGDPPTLTSQSAGIIGVSHCAQP', str(hsp.hit.seq))
self.assertEqual('LRRSFALVAQ VQW +LG PQPPPPGFK FSCLS SSW+YRH+PP L NF+FLVE GF HVGQAGLE SG+ P SQS GI GVSH AQP', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(51.6026, hsp.bitscore)
self.assertEqual(122, hsp.bitscore_raw)
self.assertEqual(2.73605e-12, hsp.evalue)
self.assertEqual(243, hsp.query_start)
self.assertEqual(459, hsp.query_end)
self.assertEqual(31, hsp.hit_start)
self.assertEqual(98, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(34, hsp.ident_num)
self.assertEqual(41, hsp.pos_num)
self.assertEqual(5, hsp.gap_num)
self.assertEqual(72, hsp.aln_span)
self.assertEqual('VGPARVQ*HDLSSLQPPAPEFK*FSHLSLQSSWDCRCPPPHPANXXXXXXXXFLRRSFALVAQAGVQWLDLG', str(hsp.query.seq))
self.assertEqual('VAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLAN-----FLFLVEMGFLHVGQAGLELVTSG', str(hsp.hit.seq))
self.assertEqual('V RVQ ++L S QPP P FK FS LSL SSW+ R PPH AN F F + F V QAG++ + G', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|33188429|ref|NP_872601.1|', hit.id)
self.assertEqual('histone demethylase UTY isoform 1 [Homo sapiens]', hit.description)
self.assertEqual(1079, hit.seq_len)
self.assertEqual(6, len(hit))
hsp = hit.hsps[0]
self.assertEqual(104.375, hsp.bitscore)
self.assertEqual(259, hsp.bitscore_raw)
self.assertEqual(6.31914e-29, hsp.evalue)
self.assertEqual(18, hsp.query_start)
self.assertEqual(291, hsp.query_end)
self.assertEqual(988, hsp.hit_start)
self.assertEqual(1079, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(59, hsp.ident_num)
self.assertEqual(66, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(91, hsp.aln_span)
self.assertEqual('SFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQ', str(hsp.query.seq))
self.assertEqual('SFQESLRAGMQWCDLSSLQPPPPGFKRFSHLSLPNSWNYRHLPSCPTNFCIFVETGFHHVGQACLELLTSGGLLASASQSAGITGVSHHAR', str(hsp.hit.seq))
self.assertEqual('SF +AG+QW DL QPPPPGFK FS LS P+SW+YRH+P C NF VETGF+HVGQA LE SG L A ASQS GITGVSHHA+', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_blastx_004(self):
xml_file = get_file('xml_2226_blastx_004.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb '
'Miller, and David J. Lipman (1997), "Gapped BLAST '
'and PSI-BLAST: a new generation of protein database search '
'programs", Nucleic Acids Res. 25:3389-3402.',
qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('blastx', qresult.program)
self.assertEqual('refseq_protein', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(128, qresult.seq_len)
self.assertEqual(12646943, qresult.stat_db_num)
self.assertEqual(4397139428, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('hg19_dna', qresult.id)
self.assertEqual('range=chr1:1207057-1207541 5\'pad=0 3\'pad=0 '
'strand=+ repeatMasking=none', qresult.description)
self.assertEqual(485, qresult.seq_len)
self.assertEqual(12646943, qresult.stat_db_num)
self.assertEqual(4397139428, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|332258565|ref|XP_003278367.1|', hit.id)
self.assertEqual('PREDICTED: UPF0764 protein C16orf89-like [Nomascus '
'leucogenys]', hit.description)
self.assertEqual(132, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(121.709, hsp.bitscore)
self.assertEqual(304, hsp.bitscore_raw)
self.assertEqual(2.02642e-32, hsp.evalue)
self.assertEqual(15, hsp.query_start)
self.assertEqual(300, hsp.query_end)
self.assertEqual(24, hsp.hit_start)
self.assertEqual(119, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(69, hsp.ident_num)
self.assertEqual(74, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(95, hsp.aln_span)
self.assertEqual('LRRSFALVAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQP', str(hsp.query.seq))
self.assertEqual('LRRSFALVAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLANFLFLVEMGFLHVGQAGLELVTSGDPPTLTSQSAGIIGVSHCAQP', str(hsp.hit.seq))
self.assertEqual('LRRSFALVAQ VQW +LG PQPPPPGFK FSCLS SSW+YRH+PP L NF+FLVE GF HVGQAGLE SG+ P SQS GI GVSH AQP', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(51.6026, hsp.bitscore)
self.assertEqual(122, hsp.bitscore_raw)
self.assertEqual(1.87805e-06, hsp.evalue)
self.assertEqual(243, hsp.query_start)
self.assertEqual(459, hsp.query_end)
self.assertEqual(31, hsp.hit_start)
self.assertEqual(98, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(34, hsp.ident_num)
self.assertEqual(41, hsp.pos_num)
self.assertEqual(5, hsp.gap_num)
self.assertEqual(72, hsp.aln_span)
self.assertEqual('VGPARVQ*HDLSSLQPPAPEFK*FSHLSLQSSWDCRCPPPHPANXXXXXXXXFLRRSFALVAQAGVQWLDLG', str(hsp.query.seq))
self.assertEqual('VAQTRVQWYNLGSPQPPPPGFKRFSCLSLLSSWEYRHVPPHLAN-----FLFLVEMGFLHVGQAGLELVTSG', str(hsp.hit.seq))
self.assertEqual('V RVQ ++L S QPP P FK FS LSL SSW+ R PPH AN F F + F V QAG++ + G', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|332815399|ref|XP_003309509.1|', hit.id)
self.assertEqual('PREDICTED: histone demethylase UTY-like [Pan troglodytes]', hit.description)
self.assertEqual(101, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(97.0561, hsp.bitscore)
self.assertEqual(240, hsp.bitscore_raw)
self.assertEqual(2.76414e-23, hsp.evalue)
self.assertEqual(6, hsp.query_start)
self.assertEqual(279, hsp.query_end)
self.assertEqual(9, hsp.hit_start)
self.assertEqual(100, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(0, hsp.hit_frame)
self.assertEqual(56, hsp.ident_num)
self.assertEqual(62, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(91, hsp.aln_span)
self.assertEqual('VAQAGVQWLDLGXXXXXXPGFK*FSCLSHPSSWDYRHMPPCLINFVFLVETGFYHVGQAGLEPPISGNLPAWASQSVGITGVSHHAQPLCE', str(hsp.query.seq))
self.assertEqual('VPHAGVQWHNLSSLQPPPSRFKPFSYLSLLSSWDQRRPPPCLVTFVFLIETGFRHVGQAGLKLLTSGDPSASASQSAGIRGVSHCTWPECQ', str(hsp.hit.seq))
self.assertEqual('V AGVQW +L QPPP FK FS LS SSWD R PPCL+ FVFL+ETGF HVGQAGL+ SG+ A ASQS GI GVSH P C+', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(2, counter)
class TblastnXmlCases(unittest.TestCase):
def test_xml_2212L_tblastn_001(self):
xml_file = get_file('xml_2212L_tblastn_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.12', qresult.version)
self.assertEqual(REFERENCE, qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(0.001, qresult.param_evalue_threshold)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual('tblastn', qresult.program)
self.assertEqual('nr', qresult.target)
# test parsed values of qresult
self.assertEqual('gi|729325|sp|P39483|DHG2_BACME', qresult.id)
self.assertEqual('Glucose 1-dehydrogenase II (GLCDH-II)', qresult.description)
self.assertEqual(261, qresult.seq_len)
self.assertEqual(251887, qresult.stat_db_num)
self.assertEqual(438542399, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(100, len(qresult))
hit = qresult[0]
self.assertEqual('gi|58264321|ref|XM_569317.1|', hit.id)
self.assertEqual('Filobasidiella neoformans glucose 1-dehydrogenase, putative (CNB05760) mRNA, complete cds', hit.description)
self.assertEqual(904, hit.seq_len)
self.assertEqual(1, len(hit))
self.assertRaises(IndexError, hit.__getitem__, 1)
hsp = hit.hsps[0]
self.assertEqual(148.288, hsp.bitscore)
self.assertEqual(373, hsp.bitscore_raw)
self.assertEqual(1.46834e-35, hsp.evalue)
self.assertEqual(4, hsp.query_start)
self.assertEqual(250, hsp.query_end)
self.assertEqual(15, hsp.hit_start)
self.assertEqual(762, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(84, hsp.ident_num)
self.assertEqual(143, hsp.pos_num)
self.assertEqual(9, hsp.gap_num)
self.assertEqual(252, hsp.aln_span)
self.assertEqual('LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSH---ELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKG-NVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM', str(hsp.query.seq))
self.assertEqual('LQGKVVAITGCSTGIGRAIAIGAAKNGANVVLHHLGDSTASDIAQVQEECKQAGAKTVVVPGDIAEAKTANEIVSAAVSSFSRIDVLISNAGI---CPFHSFLDLPHPLWKRVQDVNLNGSFYVVQAVANQMAKQEPKGGSIVAVSSISALMGGGEQCHYTPTKAGIKSLMESCAIALGPMGIRCNSVLPGTIETNINKEDLSNPEKRADQIRRVPLGRLGKPEDLVGPTLFFASDLSNYCTGASVLVDGGM', str(hsp.hit.seq))
self.assertEqual('L+ KVV +TG S G+GRA+A+ + + VV+++ + + + + E +AG + ++V GD+ + + +V AV F +DV+I+NAG+ P H +L W +V D NL G+F + + + KG +++ +SS+ ++ HY +K G+K + E+ A+ P GIR N++ PG I+T IN E ++PE+RAD +P+G +GKPE++ F AS ++Y TG ++ DGGM', hsp.aln_annotation['similarity'])
# parse last hit
hit = qresult[-1]
self.assertEqual('gi|450259|gb|L27825.1|EMEVERA1AA', hit.id)
self.assertEqual('Emericella nidulans (verA) gene, complete cds, ORF 1 gene, complete cds, and ORF 2 gene, 5\' end', hit.description)
self.assertEqual(4310, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(91.2781, hsp.bitscore)
self.assertEqual(225, hsp.bitscore_raw)
self.assertEqual(1.31998e-20, hsp.evalue)
self.assertEqual(4, hsp.query_start)
self.assertEqual(204, hsp.query_end)
self.assertEqual(578, hsp.hit_start)
self.assertEqual(1253, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(3, hsp.hit_frame)
self.assertEqual(76, hsp.ident_num)
self.assertEqual(113, hsp.pos_num)
self.assertEqual(31, hsp.gap_num)
self.assertEqual(228, hsp.aln_span)
self.assertEqual('LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV-----------ENPVPS-HELSLE-----NWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPW-PLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPE', str(hsp.query.seq))
self.assertEqual('LDGKVALVTGAGRGIGAAIAVALGQPGAKVVVNYANSREAAEKVVDEIKSNAQSAISIQADVGDPDAVTKLMDQAVEHFGYLDIVSSNAGIVSFGHVKDVTPDVCVPSPYESPVEL*PQQEFDRVFRVNTRGQFFVAREAYRHLREG---GRIILTSSNTASVKGVPRHAVYSGSKGAIDTFVRCLAIDCGDKKITVNAVAPGAIKTDMFLSVSREYIPNGETFTDEQ', str(hsp.hit.seq))
self.assertEqual('L KV +VTG +G+G A+AV GQ +KVVVNY ++ E A +V EI+ AI ++ DV + V L++ AV+ FG LD++ +NAG+ + VPS +E +E +++V N G F +REA ++ E G +I SS + P Y+ SKG + LA++ K I VN + PGAI T + N E F D +', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_tblastn_001(self):
xml_file = get_file('xml_2226_tblastn_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, '
'and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a '
'new generation of protein database search programs", '
'Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastn', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(32, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(-1, qresult.stat_kappa)
self.assertEqual(-1, qresult.stat_lambda)
self.assertEqual(-1, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|16080617|ref|NP_391444.1|', qresult.id)
self.assertEqual('membrane bound lipoprotein [Bacillus subtilis '
'subsp. subtilis str. 168]', qresult.description)
self.assertEqual(102, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(1205400.0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(3, len(qresult))
hit = qresult[0]
self.assertEqual('gi|145479850|ref|XM_001425911.1|', hit.id)
self.assertEqual('Paramecium tetraurelia hypothetical protein (GSPATT00004923001) partial mRNA', hit.description)
self.assertEqual(4632, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(34.6538, hsp.bitscore)
self.assertEqual(78, hsp.bitscore_raw)
self.assertEqual(1.08241e-05, hsp.evalue)
self.assertEqual(30, hsp.query_start)
self.assertEqual(73, hsp.query_end)
self.assertEqual(1743, hsp.hit_start)
self.assertEqual(1872, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(15, hsp.ident_num)
self.assertEqual(26, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(43, hsp.aln_span)
self.assertEqual('PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD', str(hsp.query.seq))
self.assertEqual('PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID', str(hsp.hit.seq))
self.assertEqual('P + TK+GT +GL HTI + + +SL++ E++ D+D', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# test parsed values of the third qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|11464971:4-101', qresult.id)
self.assertEqual('pleckstrin [Mus musculus]', qresult.description)
self.assertEqual(98, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(1119300.0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|350596019|ref|XM_003360601.2|', hit.id)
self.assertEqual('PREDICTED: Sus scrofa pleckstrin-like (LOC100626968), mRNA', hit.description)
self.assertEqual(772, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(199.519, hsp.bitscore)
self.assertEqual(506, hsp.bitscore_raw)
self.assertEqual(1.57249e-67, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(94, hsp.hit_start)
self.assertEqual(388, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(2, hsp.hit_frame)
self.assertEqual(94, hsp.ident_num)
self.assertEqual(96, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(32.7278, hsp.bitscore)
self.assertEqual(73, hsp.bitscore_raw)
self.assertEqual(4.07518e-05, hsp.evalue)
self.assertEqual(29, hsp.query_start)
self.assertEqual(96, hsp.query_end)
self.assertEqual(541, hsp.hit_start)
self.assertEqual(754, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(2, hsp.hit_frame)
self.assertEqual(21, hsp.ident_num)
self.assertEqual(33, hsp.pos_num)
self.assertEqual(4, hsp.gap_num)
self.assertEqual(71, hsp.aln_span)
self.assertEqual('IEFYKKKSDNSPKGMIPLKGSTLTS-PCQDFGKRMFVLK---ITTTKQQDHFFQAAFLEERDAWVRDIKKA', str(hsp.query.seq))
self.assertEqual('LHYYDPAGGEDPLGAIHLRGCVVTSVESNTDGKNGFLWERAXXITADEVHYFLQAANPKERTEWIKAIQVA', str(hsp.hit.seq))
self.assertEqual('+ +Y P G I L+G +TS GK F+ + T + +F QAA +ER W++ I+ A', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|365982352|ref|XM_003667962.1|', hit.id)
self.assertEqual('Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA', hit.description)
self.assertEqual(4932, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(19.631, hsp.bitscore)
self.assertEqual(39, hsp.bitscore_raw)
self.assertEqual(1.65923, hsp.evalue)
self.assertEqual(11, hsp.query_start)
self.assertEqual(54, hsp.query_end)
self.assertEqual(3180, hsp.hit_start)
self.assertEqual(3336, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(16, hsp.ident_num)
self.assertEqual(23, hsp.pos_num)
self.assertEqual(9, hsp.gap_num)
self.assertEqual(52, hsp.aln_span)
self.assertEqual('GSVFNTWKPMWVVLL---------EDGIEFYKKKSDNSPKGMIPLKGSTLTS', str(hsp.query.seq))
self.assertEqual('GSCFPTWDLIFIEVLNPFLKEKLWEADNEEISKFVDLTLKGLVDLYPSHFTS', str(hsp.hit.seq))
self.assertEqual('GS F TW +++ +L E E K D + KG++ L S TS', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(3, counter)
def test_xml_2226_tblastn_002(self):
xml_file = get_file('xml_2226_tblastn_002.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, '
'and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a '
'new generation of protein database search programs", '
'Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastn', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(32, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(-1, qresult.stat_kappa)
self.assertEqual(-1, qresult.stat_lambda)
self.assertEqual(-1, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_tblastn_003(self):
xml_file = get_file('xml_2226_tblastn_003.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, '
'and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a '
'new generation of protein database search programs", '
'Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastn', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
self.assertEqual('gi|16080617|ref|NP_391444.1|', qresult.id)
self.assertEqual('membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]', qresult.description)
self.assertEqual(102, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(1205400.0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(3, len(qresult))
hit = qresult[0]
self.assertEqual('gi|145479850|ref|XM_001425911.1|', hit.id)
self.assertEqual('Paramecium tetraurelia hypothetical protein (GSPATT00004923001) partial mRNA', hit.description)
self.assertEqual(4632, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(34.6538, hsp.bitscore)
self.assertEqual(78, hsp.bitscore_raw)
self.assertEqual(1.08241e-05, hsp.evalue)
self.assertEqual(30, hsp.query_start)
self.assertEqual(73, hsp.query_end)
self.assertEqual(1743, hsp.hit_start)
self.assertEqual(1872, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(15, hsp.ident_num)
self.assertEqual(26, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(43, hsp.aln_span)
self.assertEqual('PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD', str(hsp.query.seq))
self.assertEqual('PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID', str(hsp.hit.seq))
self.assertEqual('P + TK+GT +GL HTI + + +SL++ E++ D+D', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_tblastn_004(self):
xml_file = get_file('xml_2226_tblastn_004.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, '
'and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a '
'new generation of protein database search programs", '
'Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastn', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
self.assertEqual('gi|11464971:4-101', qresult.id)
self.assertEqual('pleckstrin [Mus musculus]', qresult.description)
self.assertEqual(98, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(1119300.0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|350596019|ref|XM_003360601.2|', hit.id)
self.assertEqual('PREDICTED: Sus scrofa pleckstrin-like (LOC100626968), mRNA', hit.description)
self.assertEqual(772, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(199.519, hsp.bitscore)
self.assertEqual(506, hsp.bitscore_raw)
self.assertEqual(1.57249e-67, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(94, hsp.hit_start)
self.assertEqual(388, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(2, hsp.hit_frame)
self.assertEqual(94, hsp.ident_num)
self.assertEqual(96, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGS+FNTWKPMWV+LLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERD WVRDIKKAIK', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(32.7278, hsp.bitscore)
self.assertEqual(73, hsp.bitscore_raw)
self.assertEqual(4.07518e-05, hsp.evalue)
self.assertEqual(29, hsp.query_start)
self.assertEqual(96, hsp.query_end)
self.assertEqual(541, hsp.hit_start)
self.assertEqual(754, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(2, hsp.hit_frame)
self.assertEqual(21, hsp.ident_num)
self.assertEqual(33, hsp.pos_num)
self.assertEqual(4, hsp.gap_num)
self.assertEqual(71, hsp.aln_span)
self.assertEqual('IEFYKKKSDNSPKGMIPLKGSTLTS-PCQDFGKRMFVLK---ITTTKQQDHFFQAAFLEERDAWVRDIKKA', str(hsp.query.seq))
self.assertEqual('LHYYDPAGGEDPLGAIHLRGCVVTSVESNTDGKNGFLWERAXXITADEVHYFLQAANPKERTEWIKAIQVA', str(hsp.hit.seq))
self.assertEqual('+ +Y P G I L+G +TS GK F+ + T + +F QAA +ER W++ I+ A', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|365982352|ref|XM_003667962.1|', hit.id)
self.assertEqual('Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA', hit.description)
self.assertEqual(4932, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(19.631, hsp.bitscore)
self.assertEqual(39, hsp.bitscore_raw)
self.assertEqual(1.65923, hsp.evalue)
self.assertEqual(11, hsp.query_start)
self.assertEqual(54, hsp.query_end)
self.assertEqual(3180, hsp.hit_start)
self.assertEqual(3336, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(16, hsp.ident_num)
self.assertEqual(23, hsp.pos_num)
self.assertEqual(9, hsp.gap_num)
self.assertEqual(52, hsp.aln_span)
self.assertEqual('GSVFNTWKPMWVVLL---------EDGIEFYKKKSDNSPKGMIPLKGSTLTS', str(hsp.query.seq))
self.assertEqual('GSCFPTWDLIFIEVLNPFLKEKLWEADNEEISKFVDLTLKGLVDLYPSHFTS', str(hsp.hit.seq))
self.assertEqual('GS F TW +++ +L E E K D + KG++ L S TS', hsp.aln_annotation['similarity'])
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_tblastn_005(self):
xml_file = get_file('xml_2226_tblastn_005.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, '
'and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a '
'new generation of protein database search programs", '
'Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastn', qresult.program)
self.assertEqual('refseq_rna', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(32, qresult.seq_len)
self.assertEqual(2933984, qresult.stat_db_num)
self.assertEqual(4726730735, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|16080617|ref|NP_391444.1|', qresult.id)
self.assertEqual('membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]', qresult.description)
self.assertEqual(102, qresult.seq_len)
self.assertEqual(2933984, qresult.stat_db_num)
self.assertEqual(4726730735, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(3, len(qresult))
hit = qresult[0]
self.assertEqual('gi|145479850|ref|XM_001425911.1|', hit.id)
self.assertEqual('Paramecium tetraurelia hypothetical protein (GSPATT00004923001) partial mRNA', hit.description)
self.assertEqual(4632, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(34.6538, hsp.bitscore)
self.assertEqual(78, hsp.bitscore_raw)
self.assertEqual(0.755176, hsp.evalue)
self.assertEqual(30, hsp.query_start)
self.assertEqual(73, hsp.query_end)
self.assertEqual(1743, hsp.hit_start)
self.assertEqual(1872, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(15, hsp.ident_num)
self.assertEqual(26, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(43, hsp.aln_span)
self.assertEqual('PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD', str(hsp.query.seq))
self.assertEqual('PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID', str(hsp.hit.seq))
self.assertEqual('P + TK+GT +GL HTI + + +SL++ E++ D+D', hsp.aln_annotation['similarity'])
self.assertRaises(IndexError, hit.__getitem__, 1)
# test parsed values of the third qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|11464971:4-101', qresult.id)
self.assertEqual('pleckstrin [Mus musculus]', qresult.description)
self.assertEqual(98, qresult.seq_len)
self.assertEqual(2933984, qresult.stat_db_num)
self.assertEqual(4726730735, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.041, qresult.stat_kappa)
self.assertEqual(0.267, qresult.stat_lambda)
self.assertEqual(0.14, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|354480463|ref|XM_003502378.1|', hit.id)
self.assertEqual('PREDICTED: Cricetulus griseus pleckstrin-like (LOC100773128), mRNA', hit.description)
self.assertEqual(1119, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(205.297, hsp.bitscore)
self.assertEqual(521, hsp.bitscore_raw)
self.assertEqual(1.46172e-63, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(75, hsp.hit_start)
self.assertEqual(369, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(98, hsp.ident_num)
self.assertEqual(98, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(43.8986, hsp.bitscore)
self.assertEqual(102, hsp.bitscore_raw)
self.assertEqual(0.00054161, hsp.evalue)
self.assertEqual(2, hsp.query_start)
self.assertEqual(96, hsp.query_end)
self.assertEqual(801, hsp.hit_start)
self.assertEqual(1101, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(30, hsp.ident_num)
self.assertEqual(50, hsp.pos_num)
self.assertEqual(6, hsp.gap_num)
self.assertEqual(100, hsp.aln_span)
self.assertEqual('IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTSPCQDF-GKRM---FVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA', str(hsp.query.seq))
self.assertEqual('IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAIHLRGCVVTSVESNHDGKKSDDENLFEIITADEVHYYLQAAAPKERTEWIKAIQVA', str(hsp.hit.seq))
self.assertEqual('I++G L+K+G WK +L ED + +Y P G I L+G +TS + GK+ + +I T + ++ QAA +ER W++ I+ A', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|390474391|ref|XM_002757683.2|', hit.id)
self.assertEqual('PREDICTED: Callithrix jacchus pleckstrin (PLEK), mRNA', hit.description)
self.assertEqual(1402, hit.seq_len)
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(202.986, hsp.bitscore)
self.assertEqual(515, hsp.bitscore_raw)
self.assertEqual(1.27031e-61, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(98, hsp.query_end)
self.assertEqual(160, hsp.hit_start)
self.assertEqual(454, hsp.hit_end)
self.assertEqual(0, hsp.query_frame)
self.assertEqual(2, hsp.hit_frame)
self.assertEqual(96, hsp.ident_num)
self.assertEqual(97, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(98, hsp.aln_span)
self.assertEqual('KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.query.seq))
self.assertEqual('KRIREGYLVKKGSMFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', str(hsp.hit.seq))
self.assertEqual('KRIREGYLVKKGS+FNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFV KITTTKQQDHFFQAAFLEERDAWVRDIKKAIK', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(3, counter)
class TblastxXmlCases(unittest.TestCase):
def test_xml_2212L_tblastx_001(self):
xml_file = get_file('xml_2212L_tblastx_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test the first qresult
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.12', qresult.version)
self.assertEqual(REFERENCE, qresult.reference)
self.assertEqual('BLOSUM80', qresult.param_matrix)
self.assertEqual(1, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(10, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastx', qresult.program)
self.assertEqual('nr', qresult.target)
# test parsed values of the first qresult
self.assertEqual('gi|1348853|gb|G26621.1|G26621', qresult.id)
self.assertEqual('human STS STS_D12006, sequence tagged site', qresult.description)
self.assertEqual(615, qresult.seq_len)
self.assertEqual(3533718, qresult.stat_db_num)
# why is the value negative? is this a blast bug?
self.assertEqual(-1496331888, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0.177051, qresult.stat_kappa)
self.assertEqual(0.342969, qresult.stat_lambda)
self.assertEqual(0.656794, qresult.stat_entropy)
self.assertEqual(10, len(qresult))
hit = qresult[0]
self.assertEqual('gi|18072170|gb|AC010333.7|', hit.id)
self.assertEqual('Homo sapiens chromosome 16 clone CTD-3037G24, complete sequence', hit.description)
self.assertEqual(159870, hit.seq_len)
self.assertEqual(13, len(hit))
hsp = hit.hsps[0]
self.assertEqual(329.561, hsp.bitscore)
self.assertEqual(661.0, hsp.bitscore_raw)
self.assertEqual(5.29552e-90, hsp.evalue)
self.assertEqual(1, hsp.query_start)
self.assertEqual(355, hsp.query_end)
self.assertEqual(44323, hsp.hit_start)
self.assertEqual(44677, hsp.hit_end)
self.assertEqual(-3, hsp.query_frame)
self.assertEqual(-3, hsp.hit_frame)
self.assertEqual(117, hsp.ident_num)
self.assertEqual(117, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(118, hsp.aln_span)
self.assertEqual('ECXFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD', str(hsp.query.seq))
self.assertEqual('ECCFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD', str(hsp.hit.seq))
self.assertEqual('EC FIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|4309961|gb|AC005993.2|AC005993', hit.id)
self.assertEqual('Homo sapiens PAC clone RP6-114E22 from 14, complete sequence', hit.description)
self.assertEqual(143943, hit.seq_len)
self.assertEqual(1, len(hit))
hsp = hit.hsps[0]
self.assertEqual(41.0922, hsp.bitscore)
self.assertEqual(78, hsp.bitscore_raw)
self.assertEqual(0.716571, hsp.evalue)
self.assertEqual(166, hsp.query_start)
self.assertEqual(250, hsp.query_end)
self.assertEqual(43679, hsp.hit_start)
self.assertEqual(43763, hsp.hit_end)
self.assertEqual(2, hsp.query_frame)
self.assertEqual(3, hsp.hit_frame)
self.assertEqual(13, hsp.ident_num)
self.assertEqual(19, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(28, hsp.aln_span)
self.assertEqual('PLTKAHRLFQTSIVFYVTCFTASSQQLL', str(hsp.query.seq))
self.assertEqual('PLNKYHTIFQISLCFYLFCYNMAQKQLL', str(hsp.hit.seq))
self.assertEqual('PL K H +FQ S+ FY+ C+ + +QLL', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_tblastx_001(self):
xml_file = get_file('xml_2226_tblastx_001.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, '
'and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a '
'new generation of protein database search programs", '
'Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastx', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(128, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(-1, qresult.stat_kappa)
self.assertEqual(-1, qresult.stat_lambda)
self.assertEqual(-1, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|296147483:1-350', qresult.id)
self.assertEqual('Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds', qresult.description)
self.assertEqual(350, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(1954618.0, qresult.stat_eff_space)
self.assertEqual(0.133956144488482, qresult.stat_kappa)
self.assertEqual(0.317605957635731, qresult.stat_lambda)
self.assertEqual(0.401214524497119, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|296147483|ref|NM_001183135.1|', hit.id)
self.assertEqual('Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds', hit.description)
self.assertEqual(4911, hit.seq_len)
self.assertEqual(8, len(hit))
hsp = hit.hsps[0]
self.assertEqual(289.739, hsp.bitscore)
self.assertEqual(626, hsp.bitscore_raw)
self.assertEqual(2.35531e-81, hsp.evalue)
self.assertEqual(1, hsp.query_start)
self.assertEqual(349, hsp.query_end)
self.assertEqual(1, hsp.hit_start)
self.assertEqual(349, hsp.hit_end)
self.assertEqual(2, hsp.query_frame)
self.assertEqual(2, hsp.hit_frame)
self.assertEqual(116, hsp.ident_num)
self.assertEqual(116, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(116, hsp.aln_span)
self.assertEqual('WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K', str(hsp.hit.seq))
self.assertEqual('WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K', str(hsp.query.seq))
self.assertEqual('WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(18.9375, hsp.bitscore)
self.assertEqual(35, hsp.bitscore_raw)
self.assertEqual(7.78658, hsp.evalue)
self.assertEqual(292, hsp.query_start)
self.assertEqual(325, hsp.query_end)
self.assertEqual(340, hsp.hit_start)
self.assertEqual(373, hsp.hit_end)
self.assertEqual(2, hsp.query_frame)
self.assertEqual(-3, hsp.hit_frame)
self.assertEqual(6, hsp.ident_num)
self.assertEqual(9, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(11, hsp.aln_span)
self.assertEqual('KFWMPSLRLLI', str(hsp.query.seq))
self.assertEqual('KKWVPPVKLLI', str(hsp.hit.seq))
self.assertEqual('K W+P ++LLI', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|254579534|ref|XM_002495708.1|', hit.id)
self.assertEqual('Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds', hit.description)
self.assertEqual(4866, hit.seq_len)
self.assertEqual(6, len(hit))
hsp = hit.hsps[0]
self.assertEqual(141.279, hsp.bitscore)
self.assertEqual(302, hsp.bitscore_raw)
self.assertEqual(1.15566e-36, hsp.evalue)
self.assertEqual(96, hsp.query_start)
self.assertEqual(348, hsp.query_end)
self.assertEqual(96, hsp.hit_start)
self.assertEqual(348, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(57, hsp.ident_num)
self.assertEqual(72, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(84, hsp.aln_span)
self.assertEqual('IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK', str(hsp.query.seq))
self.assertEqual('IRNASDKSIEILKVVHSYEELSRHPDFIVPLVMSCASKNAKLTTISMQCFQKLATVPCIPVDKLSDVLDAFIEANQLAMDIKLK', str(hsp.hit.seq))
self.assertEqual('IR+ASDKSIEILK VHS+EEL RHPDF +P V++C S+NAK+TT++MQC Q L+TVP IP +LS++LDAFIEA LAM+I+LK', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(2, counter)
def test_xml_2226_tblastx_002(self):
xml_file = get_file('xml_2226_tblastx_002.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, '
'and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a '
'new generation of protein database search programs", '
'Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastx', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(128, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(-1, qresult.stat_kappa)
self.assertEqual(-1, qresult.stat_lambda)
self.assertEqual(-1, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_tblastx_003(self):
xml_file = get_file('xml_2226_tblastx_003.xml')
qresults = parse(xml_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, '
'and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a '
'new generation of protein database search programs", '
'Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastx', qresult.program)
self.assertEqual('db/minirefseq_mrna', qresult.target)
self.assertEqual('gi|296147483:1-350', qresult.id)
self.assertEqual('Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds', qresult.description)
self.assertEqual(350, qresult.seq_len)
self.assertEqual(23, qresult.stat_db_num)
self.assertEqual(67750, qresult.stat_db_len)
self.assertEqual(1954618.0, qresult.stat_eff_space)
self.assertEqual(0.133956144488482, qresult.stat_kappa)
self.assertEqual(0.317605957635731, qresult.stat_lambda)
self.assertEqual(0.401214524497119, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
hit = qresult[0]
self.assertEqual('gi|296147483|ref|NM_001183135.1|', hit.id)
self.assertEqual('Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds', hit.description)
self.assertEqual(4911, hit.seq_len)
self.assertEqual(8, len(hit))
hsp = hit.hsps[0]
self.assertEqual(289.739, hsp.bitscore)
self.assertEqual(626, hsp.bitscore_raw)
self.assertEqual(2.35531e-81, hsp.evalue)
self.assertEqual(1, hsp.query_start)
self.assertEqual(349, hsp.query_end)
self.assertEqual(1, hsp.hit_start)
self.assertEqual(349, hsp.hit_end)
self.assertEqual(2, hsp.query_frame)
self.assertEqual(2, hsp.hit_frame)
self.assertEqual(116, hsp.ident_num)
self.assertEqual(116, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(116, hsp.aln_span)
self.assertEqual('WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K', str(hsp.hit.seq))
self.assertEqual('WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K', str(hsp.query.seq))
self.assertEqual('WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(18.9375, hsp.bitscore)
self.assertEqual(35, hsp.bitscore_raw)
self.assertEqual(7.78658, hsp.evalue)
self.assertEqual(292, hsp.query_start)
self.assertEqual(325, hsp.query_end)
self.assertEqual(340, hsp.hit_start)
self.assertEqual(373, hsp.hit_end)
self.assertEqual(2, hsp.query_frame)
self.assertEqual(-3, hsp.hit_frame)
self.assertEqual(6, hsp.ident_num)
self.assertEqual(9, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(11, hsp.aln_span)
self.assertEqual('KFWMPSLRLLI', str(hsp.query.seq))
self.assertEqual('KKWVPPVKLLI', str(hsp.hit.seq))
self.assertEqual('K W+P ++LLI', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|254579534|ref|XM_002495708.1|', hit.id)
self.assertEqual('Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds', hit.description)
self.assertEqual(4866, hit.seq_len)
self.assertEqual(6, len(hit))
hsp = hit.hsps[0]
self.assertEqual(141.279, hsp.bitscore)
self.assertEqual(302, hsp.bitscore_raw)
self.assertEqual(1.15566e-36, hsp.evalue)
self.assertEqual(96, hsp.query_start)
self.assertEqual(348, hsp.query_end)
self.assertEqual(96, hsp.hit_start)
self.assertEqual(348, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(57, hsp.ident_num)
self.assertEqual(72, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(84, hsp.aln_span)
self.assertEqual('IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK', str(hsp.query.seq))
self.assertEqual('IRNASDKSIEILKVVHSYEELSRHPDFIVPLVMSCASKNAKLTTISMQCFQKLATVPCIPVDKLSDVLDAFIEANQLAMDIKLK', str(hsp.hit.seq))
self.assertEqual('IR+ASDKSIEILK VHS+EEL RHPDF +P V++C S+NAK+TT++MQC Q L+TVP IP +LS++LDAFIEA LAM+I+LK', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
def test_xml_2226_tblastx_004(self):
xml_file = get_file('xml_2226_tblastx_004.xml')
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
# test meta variables, only for the first one
self.assertEqual('2.2.26+', qresult.version)
self.assertEqual('Stephen F. Altschul, Thomas L. Madden, Alejandro '
'A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, '
'and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a '
'new generation of protein database search programs", '
'Nucleic Acids Res. 25:3389-3402.', qresult.reference)
self.assertEqual('BLOSUM62', qresult.param_matrix)
self.assertEqual(10.0, qresult.param_evalue_threshold)
self.assertEqual('L;', qresult.param_filter)
self.assertEqual(11, qresult.param_gap_open)
self.assertEqual(1, qresult.param_gap_extend)
self.assertEqual('tblastx', qresult.program)
self.assertEqual('refseq_rna', qresult.target)
# test parsed values of the first qresult
self.assertEqual('random_s00', qresult.id)
self.assertEqual('', qresult.description)
self.assertEqual(128, qresult.seq_len)
self.assertEqual(2933984, qresult.stat_db_num)
self.assertEqual(4726730735, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0, qresult.stat_kappa)
self.assertEqual(0, qresult.stat_lambda)
self.assertEqual(0, qresult.stat_entropy)
self.assertEqual(0, len(qresult))
# test parsed values of the second qresult
qresult = next(qresults)
counter += 1
self.assertEqual('gi|296147483:1-350', qresult.id)
self.assertEqual('Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds', qresult.description)
self.assertEqual(350, qresult.seq_len)
self.assertEqual(2933984, qresult.stat_db_num)
self.assertEqual(4726730735, qresult.stat_db_len)
self.assertEqual(0, qresult.stat_eff_space)
self.assertEqual(0, qresult.stat_kappa)
self.assertEqual(0, qresult.stat_lambda)
self.assertEqual(0, qresult.stat_entropy)
self.assertEqual(5, len(qresult))
# check for alternative ID results
self.assertEqual(qresult['gi|296147483|ref|NM_001183135.1|'],
qresult['gi|116616412|gb|EF059095.1|'])
hit = qresult[0]
self.assertEqual('gi|296147483|ref|NM_001183135.1|', hit.id)
self.assertEqual('Saccharomyces cerevisiae S288c Mon2p (MON2) '
'mRNA, complete cds', hit.description)
self.assertEqual('gi|116616412|gb|EF059095.1|', hit.id_all[1])
self.assertEqual('Synthetic construct Saccharomyces cerevisiae '
'clone FLH203015.01X MON2, complete sequence', hit.description_all[1])
self.assertEqual(4911, hit.seq_len)
self.assertEqual(7, len(hit))
hsp = hit.hsps[0]
self.assertEqual(289.739, hsp.bitscore)
self.assertEqual(626, hsp.bitscore_raw)
self.assertEqual(1.05874e-76, hsp.evalue)
self.assertEqual(1, hsp.query_start)
self.assertEqual(349, hsp.query_end)
self.assertEqual(1, hsp.hit_start)
self.assertEqual(349, hsp.hit_end)
self.assertEqual(2, hsp.query_frame)
self.assertEqual(2, hsp.hit_frame)
self.assertEqual(116, hsp.ident_num)
self.assertEqual(116, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(116, hsp.aln_span)
self.assertEqual('WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K', str(hsp.hit.seq))
self.assertEqual('WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K', str(hsp.query.seq))
self.assertEqual('WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K', hsp.aln_annotation['similarity'])
hsp = hit.hsps[-1]
self.assertEqual(36.3494, hsp.bitscore)
self.assertEqual(73, hsp.bitscore_raw)
self.assertEqual(9.12288e-54, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(42, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(42, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(14, hsp.ident_num)
self.assertEqual(14, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(14, hsp.aln_span)
self.assertEqual('MAMNTGGFDSMQRQ', str(hsp.query.seq))
self.assertEqual('MAMNTGGFDSMQRQ', str(hsp.hit.seq))
self.assertEqual('MAMNTGGFDSMQRQ', hsp.aln_annotation['similarity'])
hit = qresult[-1]
self.assertEqual('gi|254579534|ref|XM_002495708.1|', hit.id)
self.assertEqual('Zygosaccharomyces rouxii hypothetical protein '
'(ZYRO0C02266g) mRNA, complete cds', hit.description)
self.assertEqual(4866, hit.seq_len)
self.assertEqual(4, len(hit))
hsp = hit.hsps[0]
self.assertEqual(141.279, hsp.bitscore)
self.assertEqual(302, hsp.bitscore_raw)
self.assertEqual(5.19486e-32, hsp.evalue)
self.assertEqual(96, hsp.query_start)
self.assertEqual(348, hsp.query_end)
self.assertEqual(96, hsp.hit_start)
self.assertEqual(348, hsp.hit_end)
self.assertEqual(1, hsp.query_frame)
self.assertEqual(1, hsp.hit_frame)
self.assertEqual(57, hsp.ident_num)
self.assertEqual(72, hsp.pos_num)
self.assertEqual(0, hsp.gap_num)
self.assertEqual(84, hsp.aln_span)
self.assertEqual('IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK', str(hsp.query.seq))
self.assertEqual('IRNASDKSIEILKVVHSYEELSRHPDFIVPLVMSCASKNAKLTTISMQCFQKLATVPCIPVDKLSDVLDAFIEANQLAMDIKLK', str(hsp.hit.seq))
self.assertEqual('IR+ASDKSIEILK VHS+EEL RHPDF +P V++C S+NAK+TT++MQC Q L+TVP IP +LS++LDAFIEA LAM+I+LK', hsp.aln_annotation['similarity'])
# check if we've finished iteration over qresults
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(2, counter)
class BlastXmlSpecialCases(unittest.TestCase):
def test_xml_2226_blastn_006(self):
xml_file = get_file('xml_2226_blastn_006.xml')
qresults = parse(xml_file, FMT)
exp_warning = 1
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always', BiopythonParserWarning)
qresult = next(qresults)
self.assertEqual(exp_warning, len(w), "Expected {0} warning(s), got"
" {1}".format(exp_warning, len(w)))
self.assertEqual(qresult.blast_id, 'Query_1')
hit1 = qresult[0]
hit2 = qresult[1]
self.assertEqual('gnl|BL_ORD_ID|18', hit1.blast_id)
self.assertEqual('gi|347972582|ref|XM_309352.4|', hit1.id)
self.assertEqual('Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds', hit1.description)
self.assertEqual('gnl|BL_ORD_ID|17', hit2.blast_id)
self.assertEqual('gnl|BL_ORD_ID|17', hit2.id)
self.assertEqual('gi|347972582|ref|XM_309352.4| Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds', hit2.description)
def test_xml_2226_blastn_006_use_raw_hit_ids(self):
xml_file = get_file('xml_2226_blastn_006.xml')
qresults = parse(xml_file, FMT, use_raw_hit_ids=True)
exp_warning = 0
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always', BiopythonParserWarning)
qresult = next(qresults)
self.assertEqual(exp_warning, len(w), "Expected {0} warning(s), got"
" {1}".format(exp_warning, len(w)))
self.assertEqual(qresult.blast_id, 'Query_1')
hit1 = qresult[0]
hit2 = qresult[1]
self.assertEqual('gnl|BL_ORD_ID|18', hit1.blast_id)
self.assertEqual('gnl|BL_ORD_ID|18', hit1.id)
self.assertEqual('gi|347972582|ref|XM_309352.4| Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds', hit1.description)
self.assertEqual('gnl|BL_ORD_ID|17', hit2.blast_id)
self.assertEqual('gnl|BL_ORD_ID|17', hit2.id)
self.assertEqual('gi|347972582|ref|XM_309352.4| Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds', hit2.description)
def test_xml_2226_blastn_006_use_raw_query_ids(self):
xml_file = get_file('xml_2226_blastn_006.xml')
qresults = parse(xml_file, FMT, use_raw_query_ids=True)
exp_warning = 1
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always', BiopythonParserWarning)
qresult = next(qresults)
self.assertEqual(exp_warning, len(w), "Expected {0} warning(s), got"
" {1}".format(exp_warning, len(w)))
self.assertEqual(qresult.id, 'Query_1')
self.assertEqual(qresult.description, 'gi|347972582|ref|XM_309352.4| Anopheles gambiae str. PEST AGAP011294-PA (DEFI_ANOGA) mRNA, complete cds')
self.assertEqual(qresult.blast_id, 'Query_1')
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)