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Add tests for hmmer2-text indexing

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commit 73e7ce3b8ca1113020eb9c26adc4cc72712d14e7 1 parent 5592932
@bow bow authored
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  1. +512 −0 Tests/test_SearchIO_hmmer2_text_index.py
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512 Tests/test_SearchIO_hmmer2_text_index.py
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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 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
+"""
+ 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
+
+//
+"""
+ 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]
+//
+"""
+ 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
+
+//
+"""
+ 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
+
+//
+"""
+ 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)
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