# 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 hmmer2-text indexing.""" import os import unittest from search_tests_common import CheckRaw, CheckIndex class Hmmer2TextRawCases(CheckRaw): fmt = 'hmmer2-text' def test_hmmer2text_22_single_hmmsearch(self): """Test hmmer2-text raw string retrieval, single query, hmmsearch""" filename = os.path.join('Hmmer', 'text_22_hmmsearch_001.out') raw = """hmmsearch - search a sequence database with a profile HMM HMMER 2.2g (August 2001) Copyright (C) 1992-2001 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: Peptidase_C1.hmm [Peptidase_C1] Sequence database: cysprot1b.fa per-sequence score cutoff: [none] per-domain score cutoff: [none] per-sequence Eval cutoff: <= 10 per-domain Eval cutoff: [none] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query HMM: Peptidase_C1 Accession: PF00112 Description: Papain family cysteine protease [HMM has been calibrated; E-values are empirical estimates] Scores for complete sequences (score includes all domains): Sequence Description Score E-value N -------- ----------- ----- ------- --- CATL_RAT 449.4 2e-135 1 CATL_HUMAN 444.5 6.1e-134 1 CATH_RAT 381.8 4.8e-115 1 PAPA_CARPA 337.7 9e-102 1 Parsed for domains: Sequence Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- CATL_RAT 1/1 114 332 .. 1 337 [] 449.4 2e-135 CATL_HUMAN 1/1 114 332 .. 1 337 [] 444.5 6.1e-134 CATH_RAT 1/1 114 330 .. 1 337 [] 381.8 4.8e-115 PAPA_CARPA 1/1 134 343 .. 1 337 [] 337.7 9e-102 Alignments of top-scoring domains: CATL_RAT: domain 1 of 1, from 114 to 332: score 449.4, E = 2e-135 *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt +P+++DWRe kg VtpVK+QG qCGSCWAFSa g lEg+ ++kt CATL_RAT 114 IPKTVDWRE-KG-CVTPVKNQG-QCGSCWAFSASGCLEGQMFLKT-- 155 kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke gkl+sLSEQ+LvDC++ d gn+ GCnG Glmd Af+Yik+ CATL_RAT 156 ----GKLISLSEQNLVDCSH-DQGNQ------GCNG-GLMDFAFQYIKE- 192 qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt NgGl++E++Y PY+ +kd g+ CATL_RAT 193 ----NGGLDSEESY-----PYE----AKD-------------------GS 210 CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai Cky+ + ++ a+++g++d+p++ E+al+ka+a++GP+sVa+ CATL_RAT 211 CKYR-AEYAV-----ANDTGFVDIPQQ-----EKALMKAVATVGPISVAM 249 dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY das+ s q+Y+sG +Y+++ C+++ +LdH+Vl+VGY CATL_RAT 250 DASHPS---LQFYSSG-------IYYEP---NCSSK---DLDHGVLVVGY 283 GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW G e+ ++++ +YW CATL_RAT 284 GYEG-T------------------------------------DSNKDKYW 296 IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-* +VKNSWG++WG++GY++ia+++n n+CG+a+ asypi CATL_RAT 297 LVKNSWGKEWGMDGYIKIAKDRN----NHCGLATAASYPI 332 CATL_HUMAN: domain 1 of 1, from 114 to 332: score 444.5, E = 6.1e-134 *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt +P s+DWRe kg +VtpVK+QG qCGSCWAFSa+galEg+ ++kt CATL_HUMAN 114 APRSVDWRE-KG-YVTPVKNQG-QCGSCWAFSATGALEGQMFRKT-- 155 kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke g l+sLSEQ+LvDC+g + gn+ GCnG Glmd+Af+Y+++ CATL_HUMAN 156 ----GRLISLSEQNLVDCSG-PQGNE------GCNG-GLMDYAFQYVQD- 192 qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt NgGl++E++Y PY+ +++ + CATL_HUMAN 193 ----NGGLDSEESY-----PYE----ATE-------------------ES 210 CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai Ckyn +k s+ a+++g++d+p + E+al+ka+a++GP+sVai CATL_HUMAN 211 CKYN-PKYSV-----ANDTGFVDIPKQ-----EKALMKAVATVGPISVAI 249 dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY da++ s F +Yk G +Y ++ +C+++ + dH+Vl+VGY CATL_HUMAN 250 DAGHES---FLFYKEG-------IYFEP---DCSSE---DMDHGVLVVGY 283 GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW G e+ e+++ +YW CATL_HUMAN 284 GFES-T------------------------------------ESDNNKYW 296 IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-* +VKNSWG++WG+ GY+++a+++ n+CGIas asyp+ CATL_HUMAN 297 LVKNSWGEEWGMGGYVKMAKDRR----NHCGIASAASYPT 332 CATH_RAT: domain 1 of 1, from 114 to 330: score 381.8, E = 4.8e-115 *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt P s+DWR+ kg V+pVK+QG CGSCW FS++galE++ +i++ CATH_RAT 114 YPSSMDWRK-KGNVVSPVKNQG-ACGSCWTFSTTGALESAVAIAS-- 156 kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke gk L EQqLvDC +++n+ GC+G Gl+++AfeYi++ CATH_RAT 157 ----GKMMTLAEQQLVDCAQ-NFNNH------GCQG-GLPSQAFEYILY- 193 qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt N+G++ E++Y PY gk+ g+ CATH_RAT 194 ----NKGIMGEDSY-----PYI----GKN-------------------GQ 211 CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai Ck+n +++++ a++k+ ++++ n dE+a+ +a+a + Pvs a+ CATH_RAT 212 CKFN-PEKAV-----AFVKNVVNITLN----DEAAMVEAVALYNPVSFAF 251 dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY +++e DF++YksG vY++ +C +tp + ++HAVl+VGY CATH_RAT 252 EVTE----DFMMYKSG-------VYSSN---SCHKTP-DKVNHAVLAVGY 286 GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW G +n g YW CATH_RAT 287 GEQN-GLL----------------------------------------YW 295 IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-* IVKNSWG++WG nGYf i+Rgkn +CG+a +asypi CATH_RAT 296 IVKNSWGSNWGNNGYFLIERGKN-----MCGLAACASYPI 330 PAPA_CARPA: domain 1 of 1, from 134 to 343: score 337.7, E = 9e-102 *->lPesfDWReWkggaVtpVKdQGiqCGSCWAFSavgalEgryciktgt +Pe +DWR+ kg aVtpVK+QG +CGSCWAFSav ++Eg+++i+t PAPA_CARPA 134 IPEYVDWRQ-KG-AVTPVKNQG-SCGSCWAFSAVVTIEGIIKIRT-- 175 kawggklvsLSEQqLvDCdgedygnngesCGyGCnGGGlmdnAfeYikke g+l +SEQ+L+DCd+ ++ GCnG G+++ A++ + + PAPA_CARPA 176 ----GNLNEYSEQELLDCDR---RSY------GCNG-GYPWSALQLVAQ- 210 qIsnNgGlvtEsdYekgCkPYtdfPCgkdggndtyypCpgkaydpndTgt G++ Y PY+ g++ PAPA_CARPA 211 -----YGIHYRNTY-----PYE----GVQ-------------------RY 227 CkynckknskypktyakikgygdvpynvsTydEealqkalaknGPvsVai C+++ +k+ + +ak +g ++v+++ +E al + +a+ +PvsV PAPA_CARPA 228 CRSR-EKGPY----AAKTDGVRQVQPY----NEGALLYSIAN-QPVSVVL 267 dasedskgDFqlYksGendvgyGvYkhtsageCggtpfteLdHAVliVGY +a + DFqlY++G ++++ +Cg+ +dHAV++VGY PAPA_CARPA 268 EAAGK---DFQLYRGG-------IFVG----PCGN----KVDHAVAAVGY 299 GteneggtfdetssskksesgiqvssgsngssgSSgssgapiedkgkdYW G +Y PAPA_CARPA 300 G---------------------------------------------PNYI 304 IVKNSWGtdWGEnGYfriaRgknksgkneCGIaseasypi<-* ++KNSWGt WGEnGY+ri+Rg+++s ++ CG+ ++ yp+ PAPA_CARPA 305 LIKNSWGTGWGENGYIRIKRGTGNS-YGVCGLYTSSFYPV 343 Histogram of all scores: score obs exp (one = represents 1 sequences) ----- --- --- > 337 4 -|==== % Statistical details of theoretical EVD fit: mu = -195.8384 lambda = 0.1423 chi-sq statistic = 0.0000 P(chi-square) = 0 Total sequences searched: 4 Whole sequence top hits: tophits_s report: Total hits: 4 Satisfying E cutoff: 4 Total memory: 16K Domain top hits: tophits_s report: Total hits: 4 Satisfying E cutoff: 4 Total memory: 20K """ # noqa for pep8 W291 trailing whitespace self.check_raw(filename, 'Peptidase_C1', raw) def test_hmmer2text_22_single_hmmpfam(self): """Test hmmer2-text raw string retrieval, single query, hmmpfam""" filename = os.path.join('Hmmer', 'text_22_hmmpfam_001.out') raw = """hmmpfam - search one or more sequences against HMM database HMMER 2.2g (August 2001) Copyright (C) 1992-2001 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: Pfam Sequence file: L77119.faa - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query sequence: gi|1522636|gb|AAC37060.1| Accession: [none] Description: M. jannaschii predicted coding region MJECS02 [Methanococcus jannaschii] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Methylase_M Type I restriction modification system, M -105.2 0.0022 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Methylase_M 1/1 280 481 .. 1 279 [] -105.2 0.0022 Alignments of top-scoring domains: Methylase_M: domain 1 of 1, from 280 to 481: score -105.2, E = 0.0022 *->lrnELentLWavADkLRGsmDaseYKdyVLGLlFlKYiSdkFlerri ++EL+++ av+ R L+F K++ dk gi|1522636 280 NTSELDKKKFAVLLMNR--------------LIFIKFLEDK------ 306 eieerktdtesepsldyakledqyeqlededlekedfyqkkGvFilPsql +i+ p + + +++y ++ ++ ++y ++ + l gi|1522636 307 GIV---------PRDLLRRTYEDY---KKSNVLI-NYYDAY-L----KPL 338 FwdfikeaeknkldedigtdldkifseledqialgypaSeedfkGlfpdl F++++ e ++ ++++ + + ++ + + Glf ++ gi|1522636 339 FYEVLNTPEDER--KENIRT-NPYYKDIPYL---N-G-------GLFRSN 374 dfnsnkLgskaqarnetLtelidlfselelgtPmHNG.dfeelgikDlfG ++ ++ +s+ +ne ++e+i+ +++ +++ G++ +el D++G gi|1522636 375 NV--PNELSFTIKDNEIIGEVINFLERYKFTLSTSEGsEEVELNP-DILG 421 DaYEYLLgkFAeneGKsGGeFYTPqeVSkLiaeiLtigqpsegdfsIYDP +YE L+ Ae K+ G +YTP e++ ia+ + i+ ++ gi|1522636 422 YVYEKLINILAEKGQKGLGAYYTPDEITSYIAKNT-IEPIVVE------- 463 AcGSGSLllqaskflgehdgkrnaisyYGQEsn<-* +++ ++ k+n+i + s+ gi|1522636 464 ---------RFKEIIK--NWKINDINF----ST 481 // """ # noqa for pep8 W291 trailing whitespace self.check_raw(filename, 'gi|1522636|gb|AAC37060.1|', raw) def test_hmmer2text_22_multiple_first_hmmpfam(self): """Test hmmer2-text raw string retrieval, multiple queries, hmmpfam""" filename = os.path.join('Hmmer', 'text_24_hmmpfam_001.out') raw = """hmmpfam - search one or more sequences against HMM database HMMER 2.4i (December 2006) Copyright (C) 1992-2006 HHMI Janelia Farm Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /home/bow/db/hmmer/Pfam_fs Sequence file: mult.fasta - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query sequence: random_s00 Accession: [none] Description: [none] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- [no hits above thresholds] Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- [no hits above thresholds] Alignments of top-scoring domains: [no hits above thresholds] // """ # noqa for pep8 W291 trailing whitespace self.check_raw(filename, 'random_s00', raw) def test_hmmer2text_22_multiple_middle_hmmpfam(self): """Test hmmer2-text raw string retrieval, multiple queries, hmmpfam""" filename = os.path.join('Hmmer', 'text_24_hmmpfam_001.out') raw = """hmmpfam - search one or more sequences against HMM database HMMER 2.4i (December 2006) Copyright (C) 1992-2006 HHMI Janelia Farm Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /home/bow/db/hmmer/Pfam_fs Sequence file: mult.fasta - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query sequence: gi|4885477|ref|NP_005359.1| Accession: [none] Description: myoglobin [Homo sapiens] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Globin Globin 129.8 5.8e-37 1 tRNA-synt_1b tRNA synthetases class I (W and Y) 1.8 2.2 1 Rotavirus_VP3 Rotavirus VP3 protein -1.2 7.9 1 DTHCT DTHCT (NUC029) region 1.5 9.8 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Globin 1/1 7 143 .. 1 148 [] 129.8 5.8e-37 DTHCT 1/1 101 106 .. 101 106 .] 1.5 9.8 tRNA-synt_1b 1/1 120 137 .. 320 337 .] 1.8 2.2 Rotavirus_VP3 1/1 134 147 .. 1 15 [. -1.2 7.9 Alignments of top-scoring domains: Globin: domain 1 of 1, from 7 to 143: score 129.8, E = 5.8e-37 *->dkalvkasWgkvkgtdnreelGaealarlFkayPdtktyFpkfgdls +++lv+ Wgkv++ +++ +G+e+l rlFk +P+t ++F kf+ l+ gi|4885477 7 EWQLVLNVWGKVEA--DIPGHGQEVLIRLFKGHPETLEKFDKFKHLK 51 sadaikgspkfkaHgkkVlaalgeavkhLgnddddgnlkaalkkLaarHa s d++k s+++k+Hg++Vl alg ++k +g + a +k La +Ha gi|4885477 52 SEDEMKASEDLKKHGATVLTALGGILKK------KGHHEAEIKPLAQSHA 95 erghvdpanFkllgeallIvvLaahlggeveftpevkaAWdkaldvvada ++++++ ++ + ++e+++ +vL+++ +g +f +++++A++kal + + gi|4885477 96 TKHKIPVKYLEFISECII-QVLQSKHPG--DFGADAQGAMNKALELFRKD 142 l<-* + gi|4885477 143 M 143 DTHCT: domain 1 of 1, from 101 to 106: score 1.5, E = 9.8 *->pvKYLe<-* pvKYLe gi|4885477 101 PVKYLE 106 tRNA-synt_1b: domain 1 of 1, from 120 to 137: score 1.8, E = 2.2 *->hggelKkaaaeavnalls<-* h+g++ +a+ a+n++l+ gi|4885477 120 HPGDFGADAQGAMNKALE 137 Rotavirus_VP3: domain 1 of 1, from 134 to 147: score -1.2, E = 7.9 *->MkVLaLFrrgvalnY<-* k L LFr+++a+nY gi|4885477 134 -KALELFRKDMASNY 147 // """ # noqa for pep8 W291 trailing whitespace self.check_raw(filename, 'gi|4885477|ref|NP_005359.1|', raw) def test_hmmer2text_22_multiple_last_hmmpfam(self): """Test hmmer2-text raw string retrieval, multiple queries, hmmpfam""" filename = os.path.join('Hmmer', 'text_24_hmmpfam_001.out') raw = """hmmpfam - search one or more sequences against HMM database HMMER 2.4i (December 2006) Copyright (C) 1992-2006 HHMI Janelia Farm Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /home/bow/db/hmmer/Pfam_fs Sequence file: mult.fasta - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query sequence: gi|125490392|ref|NP_038661.2| Accession: [none] Description: POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus] Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- Pou Pou domain - N-terminal to homeobox d 171.2 2.4e-48 1 Homeobox Homeobox domain 86.7 6.5e-23 1 HTH_3 Helix-turn-helix 7.5 0.33 1 WSC WSC domain 2.1 1.5 1 ComC COMC family 3.4 2.3 1 CBM_1 Fungal cellulose binding domain 3.3 3.6 1 Peptidase_M29 Thermophilic metalloprotease (M29) -2.1 4.4 1 DUF1690 Protein of Unknown function (DUF1690) 1.1 4.5 1 DUF137 Protein of unknown function DUF137 1.0 4.7 1 DASH_Duo1 DASH complex subunit Duo1 2.3 5.7 1 TFIIB Transcription factor TFIIB repeat 2.6 6.1 1 DUF1392 Protein of unknown function (DUF1392) 0.8 6.7 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- WSC 1/1 59 67 .. 80 87 .] 2.1 1.5 CBM_1 1/1 61 73 .. 1 13 [. 3.3 3.6 Pou 1/1 131 205 .. 1 78 [] 171.2 2.4e-48 ComC 1/1 132 145 .. 1 20 [. 3.4 2.3 Peptidase_M29 1/1 132 145 .. 1 14 [. -2.1 4.4 DASH_Duo1 1/1 133 141 .. 1 9 [. 2.3 5.7 DUF1690 1/1 137 147 .. 151 161 .] 1.1 4.5 HTH_3 1/1 146 166 .. 1 25 [. 7.5 0.33 DUF137 1/1 197 213 .. 164 180 .. 1.0 4.7 Homeobox 1/1 224 280 .. 1 57 [] 86.7 6.5e-23 DUF1392 1/1 248 269 .. 127 164 .] 0.8 6.7 TFIIB 1/1 253 268 .. 1 19 [. 2.6 6.1 Alignments of top-scoring domains: WSC: domain 1 of 1, from 59 to 67: score 2.1, E = 1.5 *->p.pseiCGG<-* p+++e CGG gi|1254903 59 PpAYEFCGG 67 CBM_1: domain 1 of 1, from 61 to 73: score 3.3, E = 3.6 *->vygQCGGigysGp<-* +y+ CGG+ y Gp gi|1254903 61 AYEFCGGMAYCGP 73 Pou: domain 1 of 1, from 131 to 205: score 171.2, E = 2.4e-48 *->deatdleeLEkFAkeFKqRRIkLGyTQadVGlALgalygPGvnafSQ d+++ ++eLE+FAk +Kq+RI+LGyTQadVGl+Lg l+g ++fSQ gi|1254903 131 DMKALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFG---KVFSQ 174 tTICRFEaLqLSfKNmcKLKPlLekWLeeAE<-* tTICRFEaLqLS KNmcKL+PlLekW+eeA+ gi|1254903 175 TTICRFEALQLSLKNMCKLRPLLEKWVEEAD 205 ComC: domain 1 of 1, from 132 to 145: score 3.4, E = 2.3 *->MKntvkkkllkkeLeqFkeL<-* MK ++k eLeqF L gi|1254903 132 MKALQK------ELEQFAKL 145 Peptidase_M29: domain 1 of 1, from 132 to 145: score -2.1, E = 4.4 *->MdaFkkeLekyAeL<-* M a +keLe +A L gi|1254903 132 MKALQKELEQFAKL 145 DASH_Duo1: domain 1 of 1, from 133 to 141: score 2.3, E = 5.7 *->aaLqkELeq<-* +aLqkELeq gi|1254903 133 KALQKELEQ 141 DUF1690: domain 1 of 1, from 137 to 147: score 1.1, E = 4.5 *->eEvEqFKklvr<-* +E EqF+kl++ gi|1254903 137 KELEQFAKLLK 147 HTH_3: domain 1 of 1, from 146 to 166: score 7.5, E = 0.33 *->lkelRkkkelglsqeeLAeklGskv<-* lk++R lg++q+++ lG v gi|1254903 146 LKQKRI--TLGYTQADVGLTLG--V 166 DUF137: domain 1 of 1, from 197 to 213: score 1.0, E = 4.7 *->LeeIVEnyDNkKnLkEv<-* Le+ VE+ DN++nL+E+ gi|1254903 197 LEKWVEEADNNENLQEI 213 Homeobox: domain 1 of 1, from 224 to 280: score 86.7, E = 6.5e-23 *->rrkRTtftpeQleeLEkeFqknrYPsreeReeLAkkLgLterqVkvW +rkRT++ + + LE +F k+++Ps +++ ++A++LgL++++V+vW gi|1254903 224 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVW 270 FQNRRaKwKk<-* F+NRR+K K+ gi|1254903 271 FCNRRQKGKR 280 DUF1392: domain 1 of 1, from 248 to 269: score 0.8, E = 6.7 *->PtLsqtttEGlCIFPrssqGnkmpnRfsLvrerDLVrV<-* P+L q+t +n++ L e+D VrV gi|1254903 248 PSLQQITH--------------IANQLGL--EKDVVRV 269 TFIIB: domain 1 of 1, from 253 to 268: score 2.6, E = 6.1 *->ikrfadaLeLpeKkikVad<-* i+++a +L+L + V++ gi|1254903 253 ITHIANQLGLEK---DVVR 268 // """ # noqa for pep8 W291 trailing whitespace self.check_raw(filename, 'gi|125490392|ref|NP_038661.2|', raw) class Hmmer2TextIndexCases(CheckIndex): fmt = 'hmmer2-text' def test_hmmertext_text_21_hmmpfam_001(self): """Test hmmer2-text indexing, HMMER 2.1""" filename = os.path.join('Hmmer', 'text_21_hmmpfam_001.out') self.check_index(filename, self.fmt) def test_hmmertext_text_22_hmmpfam_001(self): """Test hmmer2-text indexing, HMMER 2.2""" filename = os.path.join('Hmmer', 'text_22_hmmpfam_001.out') self.check_index(filename, self.fmt) def test_hmmertext_text_23_hmmpfam_001(self): """Test hmmer2-text indexing, HMMER 2.3""" filename = os.path.join('Hmmer', 'text_23_hmmpfam_001.out') self.check_index(filename, self.fmt) def test_hmmertext_text_24_hmmpfam_001(self): """Test hmmer2-text indexing, HMMER 2.4""" filename = os.path.join('Hmmer', 'text_24_hmmpfam_001.out') self.check_index(filename, self.fmt) def test_hmmertext_text_22_hmmsearch_001(self): """Test hmmer2-text indexing, HMMER 2.2""" filename = os.path.join('Hmmer', 'text_22_hmmsearch_001.out') self.check_index(filename, self.fmt) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)