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Add consensus sequence tests for hmmer2-text

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commit 829ee60353e0d7fe6201c4f78064b5be9ce94f56 1 parent 2d86cd8
@bow bow authored
Showing with 20 additions and 0 deletions.
  1. +20 −0 Tests/test_SearchIO_hmmer2_text.py
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20 Tests/test_SearchIO_hmmer2_text.py
@@ -45,6 +45,8 @@ def test_hmmpfam_21(self):
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['homology']))
self.assertEqual('LFIGGLDYRTTDENLKAHFEKWGNIVDVVVMKD-----PRTKRSRGFGFITYSHSSMIDEAQK--SRpHKIDGRVVEP',
str(hsp.query.seq))
@@ -60,6 +62,8 @@ def test_hmmpfam_21(self):
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['homology']))
self.assertEqual('LFVGALKDDHDEQSIRDYFQHFGNIVDINIVID-----KETGKKRGFAFVEFDDYDPVDKVVL-QKQHQLNGKMVDV',
str(hsp.query.seq))
@@ -95,6 +99,8 @@ def test_hmmpfam_22(self):
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['homology']))
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))
@@ -131,6 +137,8 @@ def test_hmmpfam_23(self):
self.assertAlmostEqual(3, hsp.evalue)
self.assertEqual('lPwelgLaevhqtLvengLRdrVsLia',
str(hsp.hit.seq))
+ self.assertEqual('+P l++ +vh L++ gLR + s+ +',
+ str(hsp.aln_annotation['homology']))
self.assertEqual('IPPLLAVGAVHHHLINKGLRQEASILV',
str(hsp.query.seq))
@@ -202,6 +210,8 @@ def test_hmmpfam_24(self):
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['homology'])[:40])
self.assertEqual('WVSMSHITA-ENCkLLEILCLLL----NEQELQLGAAECL',
str(hsp.query.seq)[-40:])
self.assertEqual(0, hsp.hit_start)
@@ -209,6 +219,8 @@ def test_hmmpfam_24(self):
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['homology'])[-40:])
self.assertEqual('Wipiglianvnpi.llnllfslLsgpesdpdlreaAveCL',
str(hsp.hit.seq)[-40:])
@@ -368,6 +380,10 @@ def test_hmmsearch_22(self):
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['homology'])[:40])
+ self.assertEqual('+VKNSWG++WG++GY++ia+++n n+CG+a+ asypi',
+ str(hsp.aln_annotation['homology'])[-40:])
self.assertEqual(113, hsp.hit_start)
self.assertEqual(332, hsp.hit_end)
self.assertEqual('..', hsp.hit_endtype)
@@ -399,6 +415,10 @@ def test_hmmsearch_22(self):
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['homology'])[:40])
+ self.assertEqual('++KNSWGt WGEnGY+ri+Rg+++s ++ CG+ ++ yp+',
+ str(hsp.aln_annotation['homology'])[-40:])
self.assertEqual(133, hsp.hit_start)
self.assertEqual(343, hsp.hit_end)
self.assertEqual('..', hsp.hit_endtype)
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