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# Copyright 2009-2012 by Peter Cock. 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.
"""Unit tests for Bio.SeqIO.index(...) and index_db() functions."""
try:
import sqlite3
except ImportError:
#Try and run what tests we can on Python 2.4 or Jython
#where we don't expect this to be installed.
sqlite3 = None
import sys
import os
import unittest
import gzip
from StringIO import StringIO
try:
#This is in Python 2.6+, but we need it on Python 3
from io import BytesIO
except ImportError:
BytesIO = StringIO
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from Bio.SeqIO._index import _FormatToRandomAccess
from Bio.Alphabet import generic_protein, generic_nucleotide, generic_dna
from seq_tests_common import compare_record
def add_prefix(key):
"""Dummy key_function for testing index code."""
return "id_" + key
def gzip_open(filename, format):
#At time of writing, under Python 3.2.2 seems gzip.open(filename, mode)
#insists on giving byte strings (i.e. binary mode)
#See http://bugs.python.org/issue13989
if sys.version_info[0] < 3 or format in SeqIO._BinaryFormats:
return gzip.open(filename)
handle = gzip.open(filename)
data = handle.read() #bytes!
handle.close()
return StringIO(_bytes_to_string(data))
if sqlite3:
class OldIndexTest(unittest.TestCase):
"""Testing a pre-built index (make sure cross platform etc).
>>> from Bio import SeqIO
>>> d = SeqIO.index_db("triple_sff.idx", ["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"], "sff")
>>> len(d)
54
"""
def test_old(self):
"""Load existing index with no options."""
d = SeqIO.index_db("Roche/triple_sff.idx")
self.assertEqual(54, len(d))
def test_old_format(self):
"""Load existing index with correct format."""
d = SeqIO.index_db("Roche/triple_sff.idx", format="sff")
self.assertEqual(54, len(d))
def test_old_format_wrong(self):
"""Load existing index with wrong format."""
self.assertRaises(ValueError, SeqIO.index_db,
"Roche/triple_sff.idx", format="fasta")
def test_old_files(self):
"""Load existing index with correct files."""
d = SeqIO.index_db("Roche/triple_sff.idx",
["E3MFGYR02_no_manifest.sff", "greek.sff", "paired.sff"])
self.assertEqual(54, len(d))
def test_old_files_wrong(self):
"""Load existing index with wrong files."""
self.assertRaises(ValueError, SeqIO.index_db,
"Roche/triple_sff.idx", ["a.sff", "b.sff", "c.sff"])
def test_old_files_wrong2(self):
"""Load existing index with wrong number of files."""
self.assertRaises(ValueError, SeqIO.index_db,
"Roche/triple_sff.idx",
["E3MFGYR02_no_manifest.sff", "greek.sff"])
class IndexDictTests(unittest.TestCase):
"""Cunning unit test where methods are added at run time."""
def simple_check(self, filename, format, alphabet, comp):
"""Check indexing (without a key function)."""
if comp:
h = gzip_open(filename, format)
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
h.close()
else:
id_list = [rec.id for rec in SeqIO.parse(filename, format, alphabet)]
rec_dict = SeqIO.index(filename, format, alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict._proxy._handle.close() #TODO - Better solution
del rec_dict
if not sqlite3:
return
#In memory,
#note here give filenames as list of strings
rec_dict = SeqIO.index_db(":memory:", [filename], format,
alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
del rec_dict
#check error conditions
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", format="dummy")
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", filenames=["dummy"])
#Saving to file...
index_tmp = filename + ".idx"
if os.path.isfile(index_tmp):
os.remove(index_tmp)
#To disk,
#note here we give the filename as a single string
#to confirm that works too (convience feature).
rec_dict = SeqIO.index_db(index_tmp, filename, format,
alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() #hack for PyPy
del rec_dict
#Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format,
alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() #hack for PyPy
del rec_dict
#Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet)
self.check_dict_methods(rec_dict, id_list, id_list)
rec_dict.close()
rec_dict._con.close() #hack for PyPy
del rec_dict
os.remove(index_tmp)
def key_check(self, filename, format, alphabet, comp):
"""Check indexing with a key function."""
if comp:
h = gzip_open(filename, format)
id_list = [rec.id for rec in SeqIO.parse(h, format, alphabet)]
h.close()
else:
id_list = [rec.id for rec in SeqIO.parse(filename, format, alphabet)]
key_list = [add_prefix(id) for id in id_list]
rec_dict = SeqIO.index(filename, format, alphabet, add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict._proxy._handle.close() #TODO - Better solution
del rec_dict
if not sqlite3:
return
#In memory,
rec_dict = SeqIO.index_db(":memory:", [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
#check error conditions
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", format="dummy",
key_function=add_prefix)
self.assertRaises(ValueError, SeqIO.index_db,
":memory:", filenames=["dummy"],
key_function=add_prefix)
rec_dict.close()
del rec_dict
#Saving to file...
index_tmp = filename + ".key.idx"
if os.path.isfile(index_tmp):
os.remove(index_tmp)
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() #hack for PyPy
del rec_dict
#Now reload it...
rec_dict = SeqIO.index_db(index_tmp, [filename], format, alphabet,
add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() #hack for PyPy
del rec_dict
#Now reload without passing filenames and format
rec_dict = SeqIO.index_db(index_tmp, alphabet=alphabet,
key_function=add_prefix)
self.check_dict_methods(rec_dict, key_list, id_list)
rec_dict.close()
rec_dict._con.close() #hack for PyPy
del rec_dict
os.remove(index_tmp)
#Done
def check_dict_methods(self, rec_dict, keys, ids):
self.assertEqual(set(keys), set(rec_dict.keys()))
#This is redundant, I just want to make sure len works:
self.assertEqual(len(keys), len(rec_dict))
#Make sure boolean evaluation works
self.assertEqual(bool(keys), bool(rec_dict))
for key,id in zip(keys, ids):
self.assertTrue(key in rec_dict)
self.assertEqual(id, rec_dict[key].id)
self.assertEqual(id, rec_dict.get(key).id)
#Check non-existant keys,
assert chr(0) not in keys, "Bad example in test"
try:
rec = rec_dict[chr(0)]
raise ValueError("Accessing a non-existent key should fail")
except KeyError:
pass
self.assertEqual(rec_dict.get(chr(0)), None)
self.assertEqual(rec_dict.get(chr(0), chr(1)), chr(1))
if hasattr(dict, "iteritems"):
#Python 2.x
for key, rec in rec_dict.iteritems():
self.assertTrue(key in keys)
self.assertTrue(isinstance(rec, SeqRecord))
self.assertTrue(rec.id in ids)
#Now check non-defined methods...
self.assertRaises(NotImplementedError, rec_dict.items)
self.assertRaises(NotImplementedError, rec_dict.values)
else:
#Python 3
assert not hasattr(rec_dict, "iteritems")
for key, rec in rec_dict.iteritems():
self.assertTrue(key in keys)
self.assertTrue(isinstance(rec, SeqRecord))
self.assertTrue(rec.id in ids)
for rec in rec_dict.itervalues():
self.assertTrue(key in keys)
self.assertTrue(isinstance(rec, SeqRecord))
self.assertTrue(rec.id in ids)
#Check the following fail
self.assertRaises(NotImplementedError, rec_dict.popitem)
self.assertRaises(NotImplementedError, rec_dict.pop, chr(0))
self.assertRaises(NotImplementedError, rec_dict.pop, chr(0), chr(1))
self.assertRaises(NotImplementedError, rec_dict.clear)
self.assertRaises(NotImplementedError, rec_dict.__setitem__, "X", None)
self.assertRaises(NotImplementedError, rec_dict.copy)
self.assertRaises(NotImplementedError, rec_dict.fromkeys, [])
def get_raw_check(self, filename, format, alphabet, comp):
#Also checking the key_function here
if comp:
h = gzip.open(filename, "rb")
raw_file = h.read()
h.close()
h = gzip_open(filename, format)
id_list = [rec.id.lower() for rec in \
SeqIO.parse(h, format, alphabet)]
h.close()
else:
h = open(filename, "rb")
raw_file = h.read()
h.close()
id_list = [rec.id.lower() for rec in \
SeqIO.parse(filename, format, alphabet)]
rec_dict = SeqIO.index(filename, format, alphabet,
key_function = lambda x : x.lower())
self.assertEqual(set(id_list), set(rec_dict.keys()))
self.assertEqual(len(id_list), len(rec_dict))
for key in id_list:
self.assertTrue(key in rec_dict)
self.assertEqual(key, rec_dict[key].id.lower())
self.assertEqual(key, rec_dict.get(key).id.lower())
raw = rec_dict.get_raw(key)
self.assertTrue(raw.strip())
self.assertTrue(raw in raw_file)
rec1 = rec_dict[key]
#Following isn't very elegant, but it lets me test the
#__getitem__ SFF code is working.
if format in SeqIO._BinaryFormats:
handle = BytesIO(raw)
else:
handle = StringIO(_bytes_to_string(raw))
if format == "sff":
rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=False)
elif format == "sff-trim":
rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=True)
elif format == "uniprot-xml":
self.assertTrue(raw.startswith(_as_bytes("<entry ")))
self.assertTrue(raw.endswith(_as_bytes("</entry>")))
#Currently the __getitem__ method uses this
#trick too, but we hope to fix that later
raw = """<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://uniprot.org/uniprot
http://www.uniprot.org/support/docs/uniprot.xsd">
%s
</uniprot>
""" % _bytes_to_string(raw)
handle = StringIO(raw)
rec2 = SeqIO.read(handle, format, alphabet)
else:
rec2 = SeqIO.read(handle, format, alphabet)
self.assertEqual(True, compare_record(rec1, rec2))
rec_dict._proxy._handle.close() #TODO - Better solution
del rec_dict
if sqlite3:
def test_duplicates_index_db(self):
"""Index file with duplicate identifers with Bio.SeqIO.index_db()"""
self.assertRaises(ValueError, SeqIO.index_db, ":memory:",
["Fasta/dups.fasta"], "fasta")
def test_duplicates_index(self):
"""Index file with duplicate identifers with Bio.SeqIO.index()"""
self.assertRaises(ValueError, SeqIO.index, "Fasta/dups.fasta", "fasta")
def test_duplicates_to_dict(self):
"""Index file with duplicate identifers with Bio.SeqIO.to_dict()"""
handle = open("Fasta/dups.fasta", "rU")
iterator = SeqIO.parse(handle, "fasta")
self.assertRaises(ValueError, SeqIO.to_dict, iterator)
handle.close()
tests = [
("Ace/contig1.ace", "ace", generic_dna),
("Ace/consed_sample.ace", "ace", None),
("Ace/seq.cap.ace", "ace", generic_dna),
("Quality/wrapping_original_sanger.fastq", "fastq", None),
("Quality/example.fastq", "fastq", None),
("Quality/example.fastq", "fastq-sanger", generic_dna),
("Quality/tricky.fastq", "fastq", generic_nucleotide),
("Quality/sanger_faked.fastq", "fastq-sanger", generic_dna),
("Quality/solexa_faked.fastq", "fastq-solexa", generic_dna),
("Quality/illumina_faked.fastq", "fastq-illumina", generic_dna),
("EMBL/epo_prt_selection.embl", "embl", None),
("EMBL/U87107.embl", "embl", None),
("EMBL/TRBG361.embl", "embl", None),
("EMBL/A04195.imgt", "embl", None), #Not a proper EMBL file, an IMGT file
("EMBL/A04195.imgt", "imgt", None),
("GenBank/NC_000932.faa", "fasta", generic_protein),
("GenBank/NC_005816.faa", "fasta", generic_protein),
("GenBank/NC_005816.tsv", "tab", generic_protein),
("GenBank/NC_005816.ffn", "fasta", generic_dna),
("GenBank/NC_005816.fna", "fasta", generic_dna),
("GenBank/NC_005816.gb", "gb", None),
("GenBank/cor6_6.gb", "genbank", None),
("IntelliGenetics/vpu_nucaligned.txt", "ig", generic_nucleotide),
("IntelliGenetics/TAT_mase_nuc.txt", "ig", None),
("IntelliGenetics/VIF_mase-pro.txt", "ig", generic_protein),
("Phd/phd1", "phd", generic_dna),
("Phd/phd2", "phd", None),
("Phd/phd_solexa", "phd", generic_dna),
("Phd/phd_454", "phd", generic_dna),
("NBRF/B_nuc.pir", "pir", generic_nucleotide),
("NBRF/Cw_prot.pir", "pir", generic_protein),
("NBRF/clustalw.pir", "pir", None),
("SwissProt/sp001", "swiss", None),
("SwissProt/sp010", "swiss", None),
("SwissProt/sp016", "swiss", None),
("SwissProt/multi_ex.txt", "swiss", None),
("SwissProt/multi_ex.xml", "uniprot-xml", None),
("SwissProt/multi_ex.fasta", "fasta", None),
("Roche/E3MFGYR02_random_10_reads.sff", "sff", generic_dna),
("Roche/E3MFGYR02_random_10_reads.sff", "sff-trim", generic_dna),
("Roche/E3MFGYR02_index_at_start.sff", "sff", generic_dna),
("Roche/E3MFGYR02_index_in_middle.sff", "sff", generic_dna),
("Roche/E3MFGYR02_alt_index_at_start.sff", "sff", generic_dna),
("Roche/E3MFGYR02_alt_index_in_middle.sff", "sff", generic_dna),
("Roche/E3MFGYR02_alt_index_at_end.sff", "sff", generic_dna),
("Roche/E3MFGYR02_no_manifest.sff", "sff", generic_dna),
("Roche/greek.sff", "sff", generic_nucleotide),
("Roche/greek.sff", "sff-trim", generic_nucleotide),
("Roche/paired.sff", "sff", None),
("Roche/paired.sff", "sff-trim", None),
]
for filename, format, alphabet in tests:
assert format in _FormatToRandomAccess
tasks = [(filename, None)]
if os.path.isfile(filename + ".bgz"):
tasks.append((filename + ".bgz","bgzf"))
for filename, comp in tasks:
def funct(fn,fmt,alpha,c):
f = lambda x : x.simple_check(fn, fmt, alpha, c)
f.__doc__ = "Index %s file %s defaults" % (fmt, fn)
return f
setattr(IndexDictTests, "test_%s_%s_simple" \
% (format, filename.replace("/","_").replace(".","_")),
funct(filename, format, alphabet, comp))
del funct
def funct(fn,fmt,alpha,c):
f = lambda x : x.key_check(fn, fmt, alpha, c)
f.__doc__ = "Index %s file %s with key function" % (fmt, fn)
return f
setattr(IndexDictTests, "test_%s_%s_keyf" \
% (format, filename.replace("/","_").replace(".","_")),
funct(filename, format, alphabet, comp))
del funct
def funct(fn,fmt,alpha,c):
f = lambda x : x.get_raw_check(fn, fmt, alpha, c)
f.__doc__ = "Index %s file %s get_raw" % (fmt, fn)
return f
setattr(IndexDictTests, "test_%s_%s_get_raw" \
% (format, filename.replace("/","_").replace(".","_")),
funct(filename, format, alphabet, comp))
del funct
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
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