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Added support for cmsearch hits with non-consecutive hits

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This commit is contained in:
Samuel Prince
2024-09-17 12:26:07 -04:00
committed by Wibowo Arindrarto
parent 6c753c0945
commit 2f2fef1b1d
8 changed files with 504 additions and 72 deletions
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16
Tests/Infernal/U2_Yeast-noali.txt
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@ -1,13 +1,12 @@
# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# INFERNAL 1.1.5 (Sep 2023)
# Copyright (C) 2023 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file: RF00004.cm
# target sequence database: GCA_000146045.2.fasta
# show alignments in output: no
# sequence reporting threshold: score >= 46
# number of worker threads: 56
# number of worker threads: 4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: U2 [CLEN=193]
@ -17,6 +16,11 @@ Hit scores:
rank E-value score bias sequence start end mdl trunc gc description
---- --------- ------ ----- ----------------------- ------ ------ --- ----- ---- -----------
(1) ! 5.9e-20 98.7 0.1 ENA|BK006936|BK006936.2 681858 681747 - cm no 0.33 TPA_inf: Saccharomyces cerevisiae S288C chromosome II,
------ inclusion threshold ------
(2) ? 0.49 19.8 0.0 ENA|BK006948|BK006948.2 737498 737324 - cm no 0.39 TPA_inf: Saccharomyces cerevisiae S288C chromosome XV,
(3) ? 5.7 15.3 0.0 ENA|BK006947|BK006947.3 266059 266208 + cm no 0.39 TPA_inf: Saccharomyces cerevisiae S288C chromosome XIV
(4) ? 6.6 15.1 0.4 ENA|BK006949|BK006949.2 443393 443253 - cm no 0.32 TPA_inf: Saccharomyces cerevisiae S288C chromosome XVI
(5) ? 7.1 14.9 0.0 ENA|BK006939|BK006939.2 190882 191043 + cm no 0.41 TPA_inf: Saccharomyces cerevisiae S288C chromosome V,
Internal CM pipeline statistics summary:
@ -33,8 +37,8 @@ Windows passing glocal HMM Forward filter: 596 (0.01251); e
Windows passing glocal HMM Forward bias filter: 438 (0.009175); expected (0.003)
Envelopes passing glocal HMM envelope defn filter: 460 (0.00429); expected (0.003)
Envelopes passing local CM CYK filter: 38 (0.000201); expected (0.0001)
Total CM hits reported: 1 (4.636e-06); includes 0 truncated hit(s)
Total CM hits reported: 5 (3.063e-05); includes 0 truncated hit(s)
# CPU time: 65.01u 2.28s 00:01:07.29 Elapsed: 00:00:03.20
# CPU time: 40.93u 0.55s 00:00:41.48 Elapsed: 00:00:10.59
//
[ok]

18
Tests/Infernal/U2_Yeast-shuf.tbl Normal file
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@ -0,0 +1,18 @@
#target name accession query name accession mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc description of target
#---------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
ENA|BK006936|BK006936.2 - U2 RF00004 cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.3e-20 ! -
ENA|BK006948|BK006948.2 - U2 RF00004 cm 1 193 737498 737324 - no 1 0.39 0.0 19.8 0.11 ? -
ENA|BK006936|BK006936.2 - U2 RF00004 cm 1 193 1370418 1370563 + no 1 0.34 0.1 15.6 1.1 ? -
ENA|BK006936|BK006936.2 - U2 RF00004 cm 1 193 1079243 1079392 + no 1 0.39 0.0 15.3 1.3 ? -
ENA|BK006948|BK006948.2 - U2 RF00004 cm 1 193 425490 425693 + no 1 0.34 0.9 13.7 3.1 ? -
ENA|BK006948|BK006948.2 - U2 RF00004 cm 1 193 1073786 1073950 + no 1 0.33 0.5 11.9 8.3 ? -
#
# Program: cmsearch
# Version: 1.1.5 (Sep 2023)
# Pipeline mode: SEARCH
# Query file: RF00004.cm
# Target file: BK006936_7-8.fasta
# Option settings: cmsearch --tblout U2_Yeast-shuf.tbl RF00004.cm BK006936_7-8.fasta
# Current dir: /analysis/BioPython/Testing
# Date: Tue Sep 17 08:23:50 2024
# [ok]

182
Tests/Infernal/U2_Yeast-shuf.txt Normal file
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@ -0,0 +1,182 @@
# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.5 (Sep 2023)
# Copyright (C) 2023 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file: RF00004.cm
# target sequence database: BK006936_7-8.fasta
# number of worker threads: 4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: U2 [CLEN=193]
Accession: RF00004
Description: U2 spliceosomal RNA
Hit scores:
rank E-value score bias sequence start end mdl trunc gc description
---- --------- ------ ----- ----------------------- ------- ------- --- ----- ---- -----------
(1) ! 1.3e-20 98.7 0.1 ENA|BK006936|BK006936.2 681858 681747 - cm no 0.33 -
------ inclusion threshold ------
(2) ? 0.11 19.8 0.0 ENA|BK006948|BK006948.2 737498 737324 - cm no 0.39 -
(3) ? 1.1 15.6 0.1 ENA|BK006936|BK006936.2 1370418 1370563 + cm no 0.34 -
(4) ? 1.3 15.3 0.0 ENA|BK006936|BK006936.2 1079243 1079392 + cm no 0.39 -
(5) ? 3.1 13.7 0.9 ENA|BK006948|BK006948.2 425490 425693 + cm no 0.34 -
(6) ? 8.3 11.9 0.5 ENA|BK006948|BK006948.2 1073786 1073950 + cm no 0.33 -
Hit alignments:
>> ENA|BK006936|BK006936.2
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 1.3e-20 98.7 0.1 cm 1 193 [] 681858 681747 - .. 0.91 no 0.33
v NC
::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>> CS
U2 1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAuuggg 80
AU+ UCU+:GCCUUUUGGC:+AGAUCAAGUGUAGUAUCUGUUCUU:UCAGU+UAA+A+CUGA:AUG: CC:CA+UG:G
ENA|BK006936|BK006936.2 681858 AUC---UCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAAUGA-CCUCAAUGAG 681783
***...************************************************************999.********** PP
v NC
>>>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~::::::: CS
U2 81 ggccaau.uauaUUAaauuaAUUUUUggaacua*[34]**[40]*Acccuuu 193
G+:CA+U U+UUAA+UU AC +UUU
ENA|BK006936|BK006936.2 681782 GCUCAUUaCCUUUUAAUUUG-------------*[ 6]**[ 3]*ACAUUUU 681747
******86555555555443................7.....9..******* PP
>> ENA|BK006948|BK006948.2
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ? 0.11 19.8 0.0 cm 1 193 [] 737498 737324 - .. 0.96 no 0.39
NC
::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<~~~~~~>>>>>>,<<<<<<<___>>>>> CS
U2 1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAG*[ 8]*CUGauAuggcccccAuuggggg 82
AU+CC U U+ GCC U GGC +A AU AAGU UA UA C GUUCU:A::A U::U: ::::::A U:::::
ENA|BK006948|BK006948.2 737498 AUCCCAUAUUUGCCAUC-GGCAUAUAUUAAGUAUAUUAGCAGUUCUAAUUAC*[88]*GUAGUUGGAAGGAUACUAUCCU 737338
**************999.*******************************996...*..6999999999999999999999 PP
NC
>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~::::::: CS
U2 83 ccaauuauaUUAaauuaAUUUUUggaacua*[34]**[40]*Acccuuu 193
: A+ A CC++U
ENA|BK006948|BK006948.2 737337 UUAU--------------------------*[ 2]**[ 1]*AUCCCCU 737324
9987.............................6.....9..******* PP
>> ENA|BK006936|BK006936.2
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(3) ? 1.1 15.6 0.1 cm 1 193 [] 1370418 1370563 + .. 0.77 no 0.34
vv vv v NC
::::::<<<-<<<<____>>>>->>>,,,,,~~~~~~,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<----. CS
U2 1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAG*[53]*aauuauaUUAaauuaAUUUUUggaacuaGugggggcauuu. 124
U UUCU :G UUU C:AAGAUCAAG AA AUAUUAA+ AA UUUUG+A ++A::::: :: +
ENA|BK006936|BK006936.2 1370418 UUUUGUUCUAUGUAAUUUGCCUAAGAUCAAG*[ 8]*AA-CAUAUUAAUAGAACUUUUGAAGUGACAAUCGCGCGAAg 1370496
******************99*********98...7..44.99**********************99999988877666 PP
v v v v vvvvv vvvvv v NC
.....<<~~~~~>>-.->>>>>>>>,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>::::::: CS
U2 125 .....ug*[8]*cau.ugcccccaCacggguugaccuggcaUUGCAcUaccgccagguucagcccAcccuuu 193
U +:: ::::: +: ::U A U+ :AUU UAC+: U A:: :ACC+ U
ENA|BK006936|BK006936.2 1370497 uuuccAG*[8]*UAUaAUGGGAUUGUUUGCCUUAGGUACAAUUA---UACUU-----GUGAGGGGACCUAGU 1370563
6644433..4..44467899999999988888754444444433...22222.....46888899******* PP
>> ENA|BK006936|BK006936.2
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(4) ? 1.3 15.3 0.0 cm 1 193 [] 1079243 1079392 + .. 0.91 no 0.39
v v v NC
::::::.<<<.-<<<<____>>>>->>>,,,,.,,,,,,~~~~~~,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<< CS
U2 1 AUacCU.UCu.cgGCcUUUUgGCuaaGAUCAA.GUGUAG*[48]*aauuauaUUAaauuaAUUUUUggaacuaGuggg 117
AU UCU + G C UUG C AGAU A GUGUAG UUAUAU +UU AU UUU G +A:: :
ENA|BK006936|BK006936.2 1079243 AUGUUGaUCUaUCGUCAAUUGACCCAGAUGAUaGUGUAG*[ 1]*-GUUAUAUAGUUUUGAUAUUUUGGCGAAAAGUU 1079314
*****9****999****************9988999987...5...33777788888888888888888888888888 PP
v v v v v v v v v NC
<<<----.<<<<<__>>>>>-..->>>>>>>>,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>:::::: CS
U2 118 ggcauuu.uggGCUUGCccau..ugcccccaCacggguugaccuggcaUUGCAcUaccgccagguucagcccAcccuu 192
G::A+U+ U :GCUUGC: AU +::C : :: G: :AC: G U GCA UA+ C :GU+: :C +U
ENA|BK006936|BK006936.2 1079315 GAGAAUAuUGCGCUUGCGUAUauAUUCCAUUUGAGGUGGCACUAGAGCUCGCAUUAU-UACCAGUAGUGGCAGGAUUG 1079391
88888888**************99999******************************.99****************** PP
NC
: CS
U2 193 u 193
+
ENA|BK006936|BK006936.2 1079392 C 1079392
* PP
>> ENA|BK006948|BK006948.2
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(5) ? 3.1 13.7 0.9 cm 1 193 [] 425490 425693 + .. 0.72 no 0.34
v v v NC
::::::<<<-~~~~~~->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<__~~~~~~>>>> CS
U2 1 AUacCUUCuc*[12]*aaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAu*[ 1]*gggg 81
A +CUUCU+ AAGAUCAAGU U UAUC U U:UC : U A AU: GA:AU:: ::CCA+ GG::
ENA|BK006948|BK006948.2 425490 AAUGCUUCUU*[21]*AAGAUCAAGUUUUUUAUCCUUCGAUUUCAAAUGGAGAUUGGAAAUAUAUUCCAA*[11]*GGAA 425589
*********7...*..5*****************877778888888888899989999999999999986...5..4444 PP
v vvvvvvv vvvvvvv v vvvvv NC
>>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,,..<<<<<<<<----~~~~~~->>>>>>>>,,<<<<<<-<<<<<<____ CS
U2 82 gccaau.uauaUUAaauuaAUUUUUggaacua..Gugggggcauuu*[13]*ugcccccaCacggguugaccuggcaUUG 165
::+AU U+U UAAA +A UUUU GAA+U+ G + C+++++C ::UU :AU G
ENA|BK006948|BK006948.2 425590 AAUUAUcUUUGCUAAAACUAGUUUUAGAAAUUggG-----------*[19]*ACCUAAUUCGACUCUUUC-----GAUAG 425666
44444474444444444444444444444444233..............5..344555555555555555.....89*** PP
vvvvv v NC
_______>>>>>>-->>>>>>::::::: CS
U2 166 CAcUaccgccagguucagcccAcccuuu 193
CACU++ :++A+++U AG:: AC ++UU
ENA|BK006948|BK006948.2 425667 CACUUU-CAAAAAAUGAGGAUACAUCUU 425693
******.56666679************* PP
>> ENA|BK006948|BK006948.2
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(6) ? 8.3 11.9 0.5 cm 1 193 [] 1073786 1073950 + .. 0.87 no 0.33
v NC
::::::~~~~~~,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~,,,.,,,,,,,,,,,,,,,,,,,,,,,,,<<<<< CS
U2 1 AUacCU*[20]*UCAAGUGUAGUAUCUGUUCU*[20]**[18]*aau.uauaUUAaauuaAUUUUUggaacuaGuggg 117
AUA CU AU AUAUUA AAUUUUU GA ++A : :
ENA|BK006948|BK006948.2 1073786 AUAUCU*[25]*--------------------*[10]**[10]*-AUgCAUAUUAUCGAAAUUUUUAGAGAAAGGUUC 1073869
***777...9.........................8.....8...336*************************99999 PP
vv v v vv v v v vv v v vv v v NC
<<<----....<<<<<__>>>>>-.->>>>>>>>,,<<<<<<-<<<<<<__________.._>>>>>>-->>>>>>:: CS
U2 118 ggcauuu....uggGCUUGCccau.ugcccccaCacggguugaccuggcaUUGCAcUac..cgccagguucagcccAc 188
: AUU U: G:UU:C :AU U :: : AC G::U ++: :: UUGCA U +:: : UU A::C AC
ENA|BK006948|BK006948.2 1073870 ACGAUUCaagcUUUGUUUACCAAUgUGAUGUAUUACAGUGUUCAUGUCACUUGCAUUGAcaUUGUC--UUUACACCAC 1073945
988888899***************888899999*********988888889****98774334433..4699****** PP
NC
::::: CS
U2 189 ccuuu 193
+U+
ENA|BK006948|BK006948.2 1073946 AUUAA 1073950
***** PP
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (193 consensus positions)
Target sequences: 2 (5377616 residues searched)
Target sequences re-searched for truncated hits: 2 (1928 residues re-searched)
Windows passing local HMM SSV filter: 16114 (0.7946); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
Windows passing local HMM Forward filter: 6428 (0.38); expected (0.005)
Windows passing local HMM Forward bias filter: 943 (0.06533); expected (0.005)
Windows passing glocal HMM Forward filter: 489 (0.04832); expected (0.005)
Windows passing glocal HMM Forward bias filter: 276 (0.02619); expected (0.005)
Envelopes passing glocal HMM envelope defn filter: 298 (0.01273); expected (0.005)
Envelopes passing local CM CYK filter: 19 (0.0004309); expected (0.0001)
Total CM hits reported: 6 (0.000177); includes 0 truncated hit(s)
# CPU time: 30.84u 0.50s 00:00:31.34 Elapsed: 00:00:08.41
//
[ok]

70
Tests/test_SearchIO_infernal_tab.py
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@ -269,15 +269,17 @@ class CmsearchCases(unittest.TestCase):
self.assertEqual("ENA|BK006936|BK006936.2", hit.id)
self.assertEqual("-", hit.accession)
self.assertEqual("TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.", hit.description)
hsp = hit[0]
self.assertEqual(1, len(hsp))
self.assertEqual(5.9e-20, hsp.evalue)
self.assertEqual(98.7, hsp.bitscore)
self.assertEqual(0.1, hsp.bias)
self.assertEqual(True, hsp.is_included)
self.assertEqual(0.33, hsp.gc)
self.assertEqual("no", hsp.truncated)
self.assertEqual(1, hsp.pipeline_pass)
self.assertEqual(True, hsp.is_included)
frag = hsp[0]
self.assertEqual(1, frag.query_start)
self.assertEqual(193, frag.query_end)
@ -345,6 +347,72 @@ class CmsearchCases(unittest.TestCase):
self.assertEqual(1, counter)
def test_cmsearch_1q_mm(self):
"""Test parsing infernal-tab, cmsearch, one queries, multiple non-consecutive hits, one hsp"""
tab_file = get_file("U2_Yeast-shuf.tbl")
qresults = parse(tab_file, FMT)
counter = 0
qresult = next(qresults)
counter += 1
self.assertEqual(2, len(qresult))
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.accession, "RF00004")
# first hit
# first hit (3 hsps at rank 1,3 and 4)
hit = qresult[0]
self.assertEqual(3, len(hit))
self.assertEqual(hit.id, "ENA|BK006936|BK006936.2")
self.assertEqual(hit.description, "-")
self.assertEqual(hit.query_id, "U2")
# first hsp (rank 1)
hsp = hit[0]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 681747)
self.assertEqual(hsp.hit_end, 681858)
# second hsp (rank 3)
hsp = hit[1]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 1370418)
self.assertEqual(hsp.hit_end, 1370563)
# last hsp (rank 4)
hsp = hit[2]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 1079243)
self.assertEqual(hsp.hit_end, 1079392)
# second hit
hit = qresult[1]
self.assertEqual(3, len(hit))
self.assertEqual(hit.id, "ENA|BK006948|BK006948.2")
self.assertEqual(hit.description, "-")
self.assertEqual(hit.query_id, "U2")
# first hsp (rank 2)
hsp = hit[0]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 737324)
self.assertEqual(hsp.hit_end, 737498)
# second hsp (rank 5)
hsp = hit[1]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 425490)
self.assertEqual(hsp.hit_end, 425693)
# last hsp (rank 6)
hsp = hit[2]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 1073786)
self.assertEqual(hsp.hit_end, 1073950)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, counter)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)

153
Tests/test_SearchIO_infernal_text.py
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@ -264,6 +264,75 @@ class CmsearchCases(unittest.TestCase):
self.assertEqual(1, count)
def test_cmsearch_1q_mm_1h_mf_shuf(self):
"""Test parsing infernal-text, cmsearch, one queries, multiple non-consecutive hits, one hsp, multiple fragments"""
tab_file = get_file("U2_Yeast-shuf.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(2, len(qresult))
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.seq_len, 193)
self.assertEqual(qresult.accession, "RF00004")
self.assertEqual(qresult.description, "U2 spliceosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.5")
self.assertEqual(qresult.target, "BK006936_7-8.fasta")
# first hit (3 hsps at rank 1,3 and 4)
hit = qresult[0]
self.assertEqual(3, len(hit))
self.assertEqual(hit.id, "ENA|BK006936|BK006936.2")
self.assertEqual(hit.description, "")
self.assertEqual(hit.query_id, "U2")
# first hsp (rank 1)
hsp = hit[0]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 681747)
self.assertEqual(hsp.hit_end, 681858)
# second hsp (rank 3)
hsp = hit[1]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 1370418)
self.assertEqual(hsp.hit_end, 1370563)
# last hsp (rank 4)
hsp = hit[2]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 1079243)
self.assertEqual(hsp.hit_end, 1079392)
# second hit
hit = qresult[1]
self.assertEqual(3, len(hit))
self.assertEqual(hit.id, "ENA|BK006948|BK006948.2")
self.assertEqual(hit.description, "")
self.assertEqual(hit.query_id, "U2")
# first hsp (rank 2)
hsp = hit[0]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 737324)
self.assertEqual(hsp.hit_end, 737498)
# second hsp (rank 5)
hsp = hit[1]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 425490)
self.assertEqual(hsp.hit_end, 425693)
# last hsp (rank 6)
hsp = hit[2]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 1073786)
self.assertEqual(hsp.hit_end, 1073950)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_mm_mh_1f(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, multiple hsp, one fragment"""
tab_file = get_file("5S_Yeast.txt")
@ -419,6 +488,90 @@ class CmsearchCases(unittest.TestCase):
self.assertEqual(1, count)
def test_cmsearch_1q_1m_mh_noali_inc(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, multiple hsp, noali, inclusion threshold"""
tab_file = get_file("U2_Yeast-noali.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(5, len(qresult))
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.seq_len, 193)
self.assertEqual(qresult.accession, "RF00004")
self.assertEqual(qresult.description, "U2 spliceosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.5")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
# first hit
hit = qresult[0]
self.assertEqual(1, len(hit))
self.assertEqual(hit.id, "ENA|BK006936|BK006936.2")
self.assertEqual(hit.description, "TPA_inf: Saccharomyces cerevisiae S288C chromosome II,")
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(1, len(hsp))
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.33)
self.assertEqual(hsp.evalue, 5.9e-20)
self.assertEqual(hsp.bitscore, 98.7)
self.assertEqual(hsp.bias, 0.1)
self.assertEqual(hsp.is_included, True)
self.assertEqual(hsp.hit_start, 681747)
self.assertEqual(hsp.hit_end, 681858)
frag = hsp[0]
self.assertEqual(frag.hit_start, 681747)
self.assertEqual(frag.hit_end, 681858)
self.assertEqual(frag.hit_strand, -1)
# second hit
hit = qresult[1]
self.assertEqual(1, len(hit))
self.assertEqual(hit.id, "ENA|BK006948|BK006948.2")
self.assertEqual(hit.description, "TPA_inf: Saccharomyces cerevisiae S288C chromosome XV,")
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(1, len(hsp))
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.39)
self.assertEqual(hsp.evalue, 0.49)
self.assertEqual(hsp.bitscore, 19.8)
self.assertEqual(hsp.bias, 0.0)
self.assertEqual(hsp.is_included, False)
self.assertEqual(hsp.hit_start, 737324)
self.assertEqual(hsp.hit_end, 737498)
frag = hsp[0]
self.assertEqual(frag.hit_start, 737324)
self.assertEqual(frag.hit_end, 737498)
self.assertEqual(frag.hit_strand, -1)
# last hit
hit = qresult[-1]
self.assertEqual(1, len(hit))
self.assertEqual(hit.id, "ENA|BK006939|BK006939.2")
self.assertEqual(hit.description, "TPA_inf: Saccharomyces cerevisiae S288C chromosome V,")
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(1, len(hsp))
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.41)
self.assertEqual(hsp.evalue, 7.1)
self.assertEqual(hsp.bitscore, 14.9)
self.assertEqual(hsp.bias, 0.0)
self.assertEqual(hsp.is_included, False)
self.assertEqual(hsp.hit_start, 190882)
self.assertEqual(hsp.hit_end, 191043)
frag = hsp[0]
self.assertEqual(frag.hit_start, 190882)
self.assertEqual(frag.hit_end, 191043)
self.assertEqual(frag.hit_strand, 0)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_1m_1h_1f_hmmonly(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, one fragments, hmmonly"""
tab_file = get_file("U2_Yeast-hmmonly.txt")