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biopython/Tests/test_SearchIO_hmmer2_text_index.py
Peter Cock 0938871295 black v23.9.1 
Had to tweak four conflicts with D202
2023-10-05 08:47:54 +01:00

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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
""" # noqa : W291
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 : W291
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 : W291
self.check_raw(filename, "random_s00", raw) # noqa : E101
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 : W291
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 : W291
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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