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# Copyright 2012 by Kai Blin.
# Revisions copyright 2012 by Wibowo Arindrarto
# 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.
import unittest
from os import path
from Bio import BiopythonExperimentalWarning
import warnings
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonExperimentalWarning)
from Bio.SearchIO import parse, read
class HmmpfamTests(unittest.TestCase):
fmt = 'hmmer2-text'
def test_hmmpfam_21(self):
"""Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out)"""
results = parse(path.join("Hmmer", "text_21_hmmpfam_001.out"), self.fmt)
res = next(results)
self.assertEqual('roa1_drome', res.id)
self.assertEqual('<unknown description>', res.description)
self.assertEqual('hmmpfam', res.program)
self.assertEqual('2.1.1', res.version)
self.assertEqual('pfam', res.target)
self.assertEqual(1, len(res))
hit = res[0]
self.assertEqual('SEED', hit.id)
self.assertEqual('<unknown description>', hit.description)
self.assertAlmostEqual(146.1, hit.bitscore)
self.assertAlmostEqual(6.3e-40, hit.evalue)
self.assertEqual(2, hit.domain_obs_num)
self.assertEqual(2, len(hit))
hsp = hit[0]
self.assertEqual(1, hsp.domain_index)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(77, hsp.hit_end)
self.assertEqual('[]', hsp.hit_endtype)
self.assertEqual(32, hsp.query_start)
self.assertEqual(103, hsp.query_end)
self.assertEqual('..', hsp.query_endtype)
self.assertAlmostEqual(71.2, hsp.bitscore)
self.assertAlmostEqual(2.2e-17, hsp.evalue)
self.assertEqual('lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnG.kelggrklrv',
str(hsp.hit.seq))
self.assertEqual('lf+g+L + +t+e Lk++F+k G iv++ +++D + t++s+Gf+F+++ ++ + A + +++++gr+++ ',
str(hsp.aln_annotation['similarity']))
self.assertEqual('LFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKD-----PRTKRSRGFGFITYSHSSMIDEAQK--SRpHKIDGRVVEP',
str(hsp.query.seq))
hsp = hit[1]
self.assertEqual(2, hsp.domain_index)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(77, hsp.hit_end)
self.assertEqual('[]', hsp.hit_endtype)
self.assertEqual(123, hsp.query_start)
self.assertEqual(194, hsp.query_end)
self.assertEqual('..', hsp.query_endtype)
self.assertAlmostEqual(75.5, hsp.bitscore)
self.assertAlmostEqual(1.1e-18, hsp.evalue)
self.assertEqual('lfVgNLppdvteedLkdlFskfGpivsikivrDiiekpketgkskGfaFVeFeseedAekAlealnGkelggrklrv',
str(hsp.hit.seq))
self.assertEqual('lfVg L d +e+ ++d+F++fG iv+i+iv+D ketgk +GfaFVeF++++ ++k + ++l+g+ + v',
str(hsp.aln_annotation['similarity']))
self.assertEqual('LFVGALKDDHDEQSIRDYFQHFGNIVDINIVID-----KETGKKRGFAFVEFDDYDPVDKVVL-QKQHQLNGKMVDV',
str(hsp.query.seq))
def test_hmmpfam_22(self):
"""Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out)"""
results = parse(path.join("Hmmer", "text_22_hmmpfam_001.out"), self.fmt)
res = next(results)
self.assertEqual('gi|1522636|gb|AAC37060.1|', res.id)
self.assertEqual('M. jannaschii predicted coding region MJECS02 [Methanococcus jannaschii]', res.description)
self.assertEqual('[none]', res.accession)
self.assertEqual('hmmpfam', res.program)
self.assertEqual('2.2g', res.version)
self.assertEqual('Pfam', res.target)
self.assertEqual(1, len(res))
hit = res[0]
self.assertEqual('Methylase_M', hit.id)
self.assertEqual('Type I restriction modification system, M', hit.description)
self.assertAlmostEqual(-105.2, hit.bitscore)
self.assertAlmostEqual(0.0022, hit.evalue)
self.assertEqual(1, hit.domain_obs_num)
self.assertEqual(1, len(hit))
hsp = hit[0]
self.assertEqual(1, hsp.domain_index)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(279, hsp.hit_end)
self.assertEqual('[]', hsp.hit_endtype)
self.assertEqual(279, hsp.query_start)
self.assertEqual(481, hsp.query_end)
self.assertEqual('..', hsp.query_endtype)
self.assertAlmostEqual(-105.2, hsp.bitscore)
self.assertAlmostEqual(0.0022, hsp.evalue)
self.assertEqual('lrnELentLWavADkLRGsmDaseYKdyVLGLlFlKYiSdkFlerrieieerktdtesepsldyakledqyeqlededlekedfyqkkGvFilPsqlFwdfikeaeknkldedigtdldkifseledqialgypaSeedfkGlfpdldfnsnkLgskaqarnetLtelidlfselelgtPmHNG.dfeelgikDlfGDaYEYLLgkFAeneGKsGGeFYTPqeVSkLiaeiLtigqpsegdfsIYDPAcGSGSLllqaskflgehdgkrnaisyYGQEsn',
str(hsp.hit.seq))
self.assertEqual(' ++EL+++ av+ R L+F K++ dk +i+ p + + +++y ++ ++ ++y ++ + lF++++ e ++ ++++ + + ++ + + Glf ++++ ++ +s+ +ne ++e+i+ +++ +++ G++ +el D++G +YE L+ Ae K+ G +YTP e++ ia+ + i+ ++ +++ ++ k+n+i + s+',
str(hsp.aln_annotation['similarity']))
self.assertEqual('NTSELDKKKFAVLLMNR--------------LIFIKFLEDK------GIV---------PRDLLRRTYEDY---KKSNVLI-NYYDAY-L----KPLFYEVLNTPEDER--KENIRT-NPYYKDIPYL---N-G-------GLFRSNNV--PNELSFTIKDNEIIGEVINFLERYKFTLSTSEGsEEVELNP-DILGYVYEKLINILAEKGQKGLGAYYTPDEITSYIAKNT-IEPIVVE----------------RFKEIIK--NWKINDINF----ST',
str(hsp.query.seq))
def test_hmmpfam_23(self):
"""Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out)"""
results = parse(path.join("Hmmer", "text_23_hmmpfam_001.out"), self.fmt)
res = next(results)
self.assertEqual('gi|90819130|dbj|BAE92499.1|', res.id)
self.assertEqual('glutamate synthase [Porphyra yezoensis]', res.description)
self.assertEqual('[none]', res.accession)
self.assertEqual('hmmpfam', res.program)
self.assertEqual('2.3.2', res.version)
self.assertEqual('../Shared/Pfam_fs', res.target)
self.assertEqual(54, len(res))
hit = res[0]
self.assertEqual('Glu_synthase', hit.id)
self.assertEqual('Conserved region in glutamate synthas', hit.description)
self.assertAlmostEqual(858.6, hit.bitscore)
self.assertAlmostEqual(3.6e-255, hit.evalue)
self.assertEqual(2, hit.domain_obs_num)
self.assertEqual(2, len(hit))
hsp = hit[0]
self.assertEqual(1, hsp.domain_index)
self.assertEqual(296, hsp.hit_start)
self.assertEqual(323, hsp.hit_end)
self.assertEqual('..', hsp.hit_endtype)
self.assertEqual(649, hsp.query_start)
self.assertEqual(676, hsp.query_end)
self.assertEqual('..', hsp.query_endtype)
self.assertAlmostEqual(1.3, hsp.bitscore)
self.assertAlmostEqual(3, hsp.evalue)
self.assertEqual('lPwelgLaevhqtLvengLRdrVsLia',
str(hsp.hit.seq))
self.assertEqual('+P l++ +vh L++ gLR + s+ +',
str(hsp.aln_annotation['similarity']))
self.assertEqual('IPPLLAVGAVHHHLINKGLRQEASILV',
str(hsp.query.seq))
hsp = hit[1]
self.assertEqual(2, hsp.domain_index)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(412, hsp.hit_end)
self.assertEqual('[]', hsp.hit_endtype)
self.assertEqual(829, hsp.query_start)
self.assertEqual(1216, hsp.query_end)
self.assertEqual('..', hsp.query_endtype)
self.assertAlmostEqual(857.3, hsp.bitscore)
self.assertAlmostEqual(9e-255, hsp.evalue)
def test_hmmpfam_23_no_match(self):
"""Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out)"""
results = parse(path.join("Hmmer", "text_23_hmmpfam_002.out"), self.fmt)
res = next(results)
self.assertEqual('SEQ0001', res.id)
self.assertEqual(0, len(res.hits))
res = next(results)
self.assertEqual('SEQ0002', res.id)
self.assertEqual(0, len(res.hits))
def test_hmmpfam_23_missing_consensus(self):
"""Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out)"""
results = parse(path.join("Hmmer", "text_23_hmmpfam_003.out"), self.fmt)
res = next(results)
self.assertEqual('small_input', res.id)
self.assertEqual('[none]', res.description)
self.assertEqual('[none]', res.accession)
self.assertEqual('hmmpfam', res.program)
self.assertEqual('2.3.2', res.version)
self.assertEqual('antismash/specific_modules/lantipeptides/ClassIVLanti.hmm', res.target)
self.assertEqual(1, len(res))
hit = res[0]
self.assertEqual('ClassIVLanti', hit.id)
self.assertEqual('Class-IV', hit.description)
self.assertAlmostEqual(-79.3, hit.bitscore)
self.assertAlmostEqual(1, hit.evalue)
self.assertEqual(1, hit.domain_obs_num)
self.assertEqual(1, len(hit))
hsp = hit[0]
self.assertEqual(1, hsp.domain_index)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(66, hsp.hit_end)
self.assertEqual('[]', hsp.hit_endtype)
self.assertEqual(5, hsp.query_start)
self.assertEqual(20, hsp.query_end)
self.assertEqual('..', hsp.query_endtype)
self.assertAlmostEqual(-79.3, hsp.bitscore)
self.assertAlmostEqual(1, hsp.evalue)
self.assertEqual(len(hsp.query.seq), len(hsp.hit.seq))
self.assertEqual(len(hsp.query.seq), len(hsp.aln_annotation['similarity']))
self.assertEqual('msEEqLKAFiAKvqaDtsLqEqLKaEGADvvaiAKAaGFtitteDLnahiqakeLsdeeLEgvaGg',
str(hsp.hit.seq))
self.assertEqual(' F+ G +t Ln ',
str(hsp.aln_annotation['similarity']))
self.assertEqual('-------CFL---------------------------GCLVTNWVLNRS-----------------',
str(hsp.query.seq))
def test_hmmpfam_24(self):
"""Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out)"""
results = list(parse(path.join("Hmmer", "text_24_hmmpfam_001.out"), self.fmt))
self.assertEqual(5, len(results))
# first qresult
res = results[0]
self.assertEqual('random_s00', res.id)
self.assertEqual('[none]', res.accession)
self.assertEqual('[none]', res.description)
self.assertEqual('hmmpfam', res.program)
self.assertEqual('2.4i', res.version)
self.assertEqual('/home/bow/db/hmmer/Pfam_fs', res.target)
self.assertEqual(0, len(res))
# fourth qresult
res = results[3]
self.assertEqual('gi|22748937|ref|NP_065801.1|', res.id)
self.assertEqual('[none]', res.accession)
self.assertEqual('exportin-5 [Homo sapiens]', res.description)
self.assertEqual('hmmpfam', res.program)
self.assertEqual('2.4i', res.version)
self.assertEqual('/home/bow/db/hmmer/Pfam_fs', res.target)
self.assertEqual(33, len(res))
# fourth qresult, first hit
hit = res[0]
self.assertEqual('Xpo1', hit.id)
self.assertEqual('Exportin 1-like protein', hit.description)
self.assertAlmostEqual(170.1, hit.bitscore)
self.assertAlmostEqual(5.1e-48, hit.evalue)
self.assertEqual(1, hit.domain_obs_num)
self.assertEqual(1, len(hit))
# fourth qresult, first hit, first hsp
hsp = hit[0]
self.assertEqual(1, hsp.domain_index)
self.assertAlmostEqual(170.1, hsp.bitscore)
self.assertAlmostEqual(5.1e-148, hsp.evalue)
self.assertEqual(108, hsp.query_start)
self.assertEqual(271, hsp.query_end)
self.assertEqual('..', hsp.query_endtype)
self.assertEqual('ENHIKDALSRIVVEMIKREWPQHWPDMLIELDTLSKQG--',
str(hsp.query.seq)[:40])
self.assertEqual('+++++ L+++++e++k+ewP++Wp+ + +l l++++ ',
str(hsp.aln_annotation['similarity'])[:40])
self.assertEqual('WVSMSHITA-ENCkLLEILCLLL----NEQELQLGAAECL',
str(hsp.query.seq)[-40:])
self.assertEqual(0, hsp.hit_start)
self.assertEqual(178, hsp.hit_end)
self.assertEqual('[]', hsp.hit_endtype)
self.assertEqual('pkflrnKLalalaelakqewPsnWpsffpdlvsllsssss',
str(hsp.hit.seq)[:40])
self.assertEqual('W+++++i + ++++ll++l+ lL + +l++ A+eCL',
str(hsp.aln_annotation['similarity'])[-40:])
self.assertEqual('Wipiglianvnpi.llnllfslLsgpesdpdlreaAveCL',
str(hsp.hit.seq)[-40:])
# fourth qresult, second from last hit
hit = res[-2]
self.assertEqual('Rad50_zn_hook', hit.id)
self.assertEqual('Rad50 zinc hook motif', hit.description)
self.assertAlmostEqual(2.2, hit.bitscore)
self.assertAlmostEqual(9.2, hit.evalue)
self.assertEqual(2, hit.domain_obs_num)
self.assertEqual(2, len(hit))
# fourth qresult, second from last hit, first hsp
hsp = hit[0]
self.assertEqual(1, hsp.domain_index)
self.assertAlmostEqual(0.8, hsp.bitscore)
self.assertAlmostEqual(22, hsp.evalue)
self.assertEqual(20, hsp.query_start)
self.assertEqual(47, hsp.query_end)
self.assertEqual('..', hsp.query_endtype)
self.assertEqual('MDPNSTQRYRLEALKFCEEFKE-KCPIC', str(hsp.query.seq))
self.assertEqual(0, hsp.hit_start)
self.assertEqual(28, hsp.hit_end)
self.assertEqual('[.', hsp.hit_endtype)
self.assertEqual('galesekaelkkaieeleeeesscCPvC', str(hsp.hit.seq))
# fourth qresult, second from last hit, last hsp
hsp = hit[-1]
self.assertEqual(2, hsp.domain_index)
self.assertAlmostEqual(1.3, hsp.bitscore)
self.assertAlmostEqual(16, hsp.evalue)
self.assertEqual(789, hsp.query_start)
self.assertEqual(811, hsp.query_end)
self.assertEqual('..', hsp.query_endtype)
self.assertEqual('EMLAKMAEPFTKALDMLDAEKS', str(hsp.query.seq))
self.assertEqual(0, hsp.hit_start)
self.assertEqual(22, hsp.hit_end)
self.assertEqual('[.', hsp.hit_endtype)
self.assertEqual('galesekaelkkaieeleeees', str(hsp.hit.seq))
class HmmsearchTests(unittest.TestCase):
fmt = 'hmmer2-text'
def test_hmmsearch_20(self):
"""Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out)"""
res = read(path.join("Hmmer", "text_20_hmmsearch_001.out"), self.fmt)
# first query
self.assertEqual('SEED', res.id)
self.assertEqual('<unknown description>', res.description)
self.assertEqual('hmmsearch', res.program)
self.assertEqual('2.0', res.version)
self.assertEqual('HMM.dbtemp.29591', res.target)
self.assertEqual(751, len(res))
# first hit
hit = res[0]
self.assertEqual('PAB2_ARATH', hit.id)
self.assertEqual('P42731 POLYADENYLATE-BINDING PROTEIN 2 (PO', hit.description)
self.assertAlmostEqual(393.8, hit.bitscore)
self.assertAlmostEqual(6.1e-114, hit.evalue)
self.assertEqual(4, hit.domain_obs_num)
self.assertEqual(4, len(hit))
# first hit, first hsp
hsp = hit[0]
self.assertEqual('SEED', hsp.query_id)
self.assertEqual('<unknown description>', hsp.query_description)
self.assertEqual('PAB2_ARATH', hsp.hit_id)
self.assertEqual('P42731 POLYADENYLATE-BINDING PROTEIN 2 (PO', hsp.hit_description)
self.assertEqual(3, hsp.domain_index)
self.assertAlmostEqual(109.1, hsp.bitscore)
self.assertAlmostEqual(3e-28, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(77, hsp.query_end)
self.assertEqual('[]', hsp.query_endtype)
self.assertEqual(216, hsp.hit_start)
self.assertEqual(287, hsp.hit_end)
self.assertEqual('..', hsp.hit_endtype)
# first hit, last hsp
hsp = hit[-1]
self.assertEqual('SEED', hsp.query_id)
self.assertEqual('<unknown description>', hsp.query_description)
self.assertEqual('PAB2_ARATH', hsp.hit_id)
self.assertEqual('P42731 POLYADENYLATE-BINDING PROTEIN 2 (PO', hsp.hit_description)
self.assertEqual(1, hsp.domain_index)
self.assertAlmostEqual(92.1, hsp.bitscore)
self.assertAlmostEqual(3.9e-23, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(77, hsp.query_end)
self.assertEqual('[]', hsp.query_endtype)
self.assertEqual(37, hsp.hit_start)
self.assertEqual(109, hsp.hit_end)
self.assertEqual('..', hsp.hit_endtype)
# last hit
hit = res[-1]
self.assertEqual('O00369', hit.id)
self.assertEqual('O00369 L1 ELEMENT L1.20 P40 AND PUTATIVE P', hit.description)
self.assertAlmostEqual(-23.8, hit.bitscore)
self.assertAlmostEqual(9.9e+02, hit.evalue)
self.assertEqual(1, hit.domain_obs_num)
self.assertEqual(1, len(hit))
# last hit, first hsp
hsp = hit[0]
self.assertEqual('SEED', hsp.query_id)
self.assertEqual('<unknown description>', hsp.query_description)
self.assertEqual('O00369', hsp.hit_id)
self.assertEqual('O00369 L1 ELEMENT L1.20 P40 AND PUTATIVE P', hsp.hit_description)
self.assertEqual(1, hsp.domain_index)
self.assertAlmostEqual(-23.8, hsp.bitscore)
self.assertAlmostEqual(9.9e+02, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(77, hsp.query_end)
self.assertEqual('[]', hsp.query_endtype)
self.assertEqual(180, hsp.hit_start)
self.assertEqual(249, hsp.hit_end)
self.assertEqual('..', hsp.hit_endtype)
def test_hmmsearch_22(self):
"""Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out)"""
res = read(path.join("Hmmer", "text_22_hmmsearch_001.out"), self.fmt)
# first query
self.assertEqual('Peptidase_C1', res.id)
self.assertEqual('Papain family cysteine protease', res.description)
self.assertEqual('hmmsearch', res.program)
self.assertEqual('2.2g', res.version)
self.assertEqual('cysprot1b.fa', res.target)
self.assertEqual(4, len(res))
# first hit
hit = res[0]
self.assertEqual('CATL_RAT', hit.id)
self.assertEqual('<unknown description>', hit.description)
self.assertAlmostEqual(449.4, hit.bitscore)
self.assertAlmostEqual(2e-135, hit.evalue)
self.assertEqual(1, hit.domain_obs_num)
self.assertEqual(1, len(hit))
# first hit, first hsp
hsp = hit[0]
self.assertEqual('Peptidase_C1', hsp.query_id)
self.assertEqual('Papain family cysteine protease', hsp.query_description)
self.assertEqual('CATL_RAT', hit.id)
self.assertEqual('<unknown description>', hit.description)
self.assertEqual(1, hsp.domain_index)
self.assertAlmostEqual(449.4, hsp.bitscore)
self.assertAlmostEqual(2e-135, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(337, hsp.query_end)
self.assertEqual('[]', hsp.query_endtype)
self.assertEqual('lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgr', str(hsp.query.seq)[:40])
self.assertEqual('IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi', str(hsp.query.seq)[-40:])
self.assertEqual(337, len(hsp.query.seq))
self.assertEqual('+P+++DWRe kg VtpVK+QG qCGSCWAFSa g lEg+',
str(hsp.aln_annotation['similarity'])[:40])
self.assertEqual('+VKNSWG++WG++GY++ia+++n n+CG+a+ asypi',
str(hsp.aln_annotation['similarity'])[-40:])
self.assertEqual(113, hsp.hit_start)
self.assertEqual(332, hsp.hit_end)
self.assertEqual('..', hsp.hit_endtype)
self.assertEqual('IPKTVDWRE-KG-CVTPVKNQG-QCGSCWAFSASGCLEGQ', str(hsp.hit.seq)[:40])
self.assertEqual('LVKNSWGKEWGMDGYIKIAKDRN----NHCGLATAASYPI', str(hsp.hit.seq)[-40:])
self.assertEqual(337, len(hsp.hit.seq))
# last hit
hit = res[-1]
self.assertEqual('PAPA_CARPA', hit.id)
self.assertEqual('<unknown description>', hit.description)
self.assertAlmostEqual(337.7, hit.bitscore)
self.assertAlmostEqual(9e-102, hit.evalue)
self.assertEqual(1, hit.domain_obs_num)
self.assertEqual(1, len(hit))
# last hit, last hsp
hsp = hit[-1]
self.assertEqual('Peptidase_C1', hsp.query_id)
self.assertEqual('Papain family cysteine protease', hsp.query_description)
self.assertEqual('PAPA_CARPA', hit.id)
self.assertEqual('<unknown description>', hit.description)
self.assertEqual(1, hsp.domain_index)
self.assertAlmostEqual(337.7, hsp.bitscore)
self.assertAlmostEqual(9e-102, hsp.evalue)
self.assertEqual(0, hsp.query_start)
self.assertEqual(337, hsp.query_end)
self.assertEqual('[]', hsp.query_endtype)
self.assertEqual('lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgr', str(hsp.query.seq)[:40])
self.assertEqual('IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi', str(hsp.query.seq)[-40:])
self.assertEqual(337, len(hsp.query.seq))
self.assertEqual('+Pe +DWR+ kg aVtpVK+QG +CGSCWAFSav ++Eg+',
str(hsp.aln_annotation['similarity'])[:40])
self.assertEqual('++KNSWGt WGEnGY+ri+Rg+++s ++ CG+ ++ yp+',
str(hsp.aln_annotation['similarity'])[-40:])
self.assertEqual(133, hsp.hit_start)
self.assertEqual(343, hsp.hit_end)
self.assertEqual('..', hsp.hit_endtype)
self.assertEqual('IPEYVDWRQ-KG-AVTPVKNQG-SCGSCWAFSAVVTIEGI', str(hsp.hit.seq)[:40])
self.assertEqual('LIKNSWGTGWGENGYIRIKRGTGNS-YGVCGLYTSSFYPV', str(hsp.hit.seq)[-40:])
self.assertEqual(337, len(hsp.hit.seq))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)