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Changed tests files names

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This commit is contained in:
Samuel Prince
2024-09-18 12:53:16 -04:00
committed by Wibowo Arindrarto
parent 361870aa9d
commit 343b33473b
21 changed files with 58 additions and 1526 deletions
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45
Tests/Infernal/5S_Yeast-noali.txt
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# 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: RF00001.cm
# target sequence database: GCA_000146045.2.fasta
# show alignments in output: no
# sequence reporting threshold: score >= 46
# number of worker threads: 4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: 5S_rRNA [CLEN=119]
Accession: RF00001
Description: 5S ribosomal RNA
Hit scores:
rank E-value score bias sequence start end mdl trunc gc description
---- --------- ------ ----- ----------------------- ------ ------ --- ----- ---- -----------
(1) ! 1.6e-18 88.8 0.0 ENA|BK006945|BK006945.2 459676 459796 + cm no 0.52 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(2) ! 1.6e-18 88.8 0.0 ENA|BK006945|BK006945.2 489349 489469 + cm no 0.52 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(3) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 468813 468933 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(4) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 472465 472585 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(5) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 482045 482165 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(6) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 485697 485817 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (119 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (12416 residues re-searched)
Windows passing local HMM SSV filter: 24991 (0.2423); expected (0.35)
Windows passing local HMM Viterbi filter: 8464 (0.08504); expected (0.15)
Windows passing local HMM Viterbi bias filter: 8432 (0.08473); expected (0.15)
Windows passing local HMM Forward filter: 135 (0.001502); expected (0.003)
Windows passing local HMM Forward bias filter: 134 (0.001493); expected (0.003)
Windows passing glocal HMM Forward filter: 65 (0.0007404); expected (0.003)
Windows passing glocal HMM Forward bias filter: 65 (0.0007404); expected (0.003)
Envelopes passing glocal HMM envelope defn filter: 61 (0.0003446); expected (0.003)
Envelopes passing local CM CYK filter: 15 (6.52e-05); expected (0.0001)
Total CM hits reported: 6 (3.006e-05); includes 0 truncated hit(s)
# CPU time: 2.88u 0.05s 00:00:02.93 Elapsed: 00:00:00.71
//
[ok]

18
Tests/Infernal/5S_Yeast.tbl
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#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|BK006945|BK006945.2 - 5S_rRNA RF00001 cm 1 119 459676 459796 + no 1 0.52 0.0 88.8 1.6e-18 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
ENA|BK006945|BK006945.2 - 5S_rRNA RF00001 cm 1 119 489349 489469 + no 1 0.52 0.0 88.8 1.6e-18 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
ENA|BK006945|BK006945.2 - 5S_rRNA RF00001 cm 1 119 468813 468933 + no 1 0.53 0.0 83.2 4.4e-17 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
ENA|BK006945|BK006945.2 - 5S_rRNA RF00001 cm 1 119 472465 472585 + no 1 0.53 0.0 83.2 4.4e-17 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
ENA|BK006945|BK006945.2 - 5S_rRNA RF00001 cm 1 119 482045 482165 + no 1 0.53 0.0 83.2 4.4e-17 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
ENA|BK006945|BK006945.2 - 5S_rRNA RF00001 cm 1 119 485697 485817 + no 1 0.53 0.0 83.2 4.4e-17 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
#
# Program: cmsearch
# Version: 1.1.4 (Dec 2020)
# Pipeline mode: SEARCH
# Query file: RF00001.cm
# Target file: GCA_000146045.2.fasta
# Option settings: cmsearch --tblout 5S_Yeast.tbl -T 38.0 RF00001.cm GCA_000146045.2.fasta
# Current dir: /analysis/BioPython/Testing
# Date: Tue Sep 10 11:02:58 2024
# [ok]

162
Tests/Infernal/5S_Yeast.txt
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# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file: RF00001.cm
# target sequence database: GCA_000146045.2.fasta
# tabular output of hits: 5S_Yeast.tbl
# sequence reporting threshold: score >= 38
# number of worker threads: 56
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: 5S_rRNA [CLEN=119]
Accession: RF00001
Description: 5S ribosomal RNA
Hit scores:
rank E-value score bias sequence start end mdl trunc gc description
---- --------- ------ ----- ----------------------- ------ ------ --- ----- ---- -----------
(1) ! 1.6e-18 88.8 0.0 ENA|BK006945|BK006945.2 459676 459796 + cm no 0.52 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(2) ! 1.6e-18 88.8 0.0 ENA|BK006945|BK006945.2 489349 489469 + cm no 0.52 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(3) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 468813 468933 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(4) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 472465 472585 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(5) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 482045 482165 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(6) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 485697 485817 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
Hit alignments:
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 1.6e-18 88.8 0.0 cm 1 119 [] 459676 459796 + .. 0.99 no 0.52
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
G::UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 459676 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 459755
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA::C+
ENA|BK006945|BK006945.2 459756 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU 459796
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ! 1.6e-18 88.8 0.0 cm 1 119 [] 489349 489469 + .. 0.99 no 0.52
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
G::UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 489349 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 489428
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA::C+
ENA|BK006945|BK006945.2 489429 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU 489469
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(3) ! 4.4e-17 83.2 0.0 cm 1 119 [] 468813 468933 + .. 0.99 no 0.53
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
: UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 468813 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 468892
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA :
ENA|BK006945|BK006945.2 468893 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 468933
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(4) ! 4.4e-17 83.2 0.0 cm 1 119 [] 472465 472585 + .. 0.99 no 0.53
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
: UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 472465 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 472544
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA :
ENA|BK006945|BK006945.2 472545 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 472585
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(5) ! 4.4e-17 83.2 0.0 cm 1 119 [] 482045 482165 + .. 0.99 no 0.53
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
: UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 482045 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 482124
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA :
ENA|BK006945|BK006945.2 482125 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 482165
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(6) ! 4.4e-17 83.2 0.0 cm 1 119 [] 485697 485817 + .. 0.99 no 0.53
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
: UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 485697 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 485776
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA :
ENA|BK006945|BK006945.2 485777 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 485817
***********************9***************** PP
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (119 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (12416 residues re-searched)
Windows passing local HMM SSV filter: 24991 (0.2423); expected (0.35)
Windows passing local HMM Viterbi filter: 8464 (0.08504); expected (0.15)
Windows passing local HMM Viterbi bias filter: 8432 (0.08473); expected (0.15)
Windows passing local HMM Forward filter: 135 (0.001502); expected (0.003)
Windows passing local HMM Forward bias filter: 134 (0.001493); expected (0.003)
Windows passing glocal HMM Forward filter: 65 (0.0007404); expected (0.003)
Windows passing glocal HMM Forward bias filter: 65 (0.0007404); expected (0.003)
Envelopes passing glocal HMM envelope defn filter: 61 (0.0003446); expected (0.003)
Envelopes passing local CM CYK filter: 15 (6.52e-05); expected (0.0001)
Total CM hits reported: 6 (3.006e-05); includes 0 truncated hit(s)
# CPU time: 3.96u 0.20s 00:00:04.16 Elapsed: 00:00:00.36
//
[ok]

13
Tests/Infernal/IRES_5S_U2_Yeast-cmscan-fmt_2.tbl
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#idx target name accession query name accession clan name mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc olp anyidx afrct1 afrct2 winidx wfrct1 wfrct2 mdl len seq len description of target
#--- -------------------- --------- ----------------------- --------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- --- ------ ------ ------ ------ ------ ------ ------- ------- ---------------------
1 U2 RF00004 ENA|BK006936|BK006936.2 - - cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.2e-20 ! * - - - - - - 193 813184 U2 spliceosomal RNA
#
# Program: cmscan
# Version: 1.1.5 (Sep 2023)
# Pipeline mode: SCAN
# Query file: BK006936.fasta
# Target file: IRES_5S_U2.cm
# Option settings: cmscan --tblout IRES_5S_U2_Yeast-cmscan-fmt_2.tbl --fmt 2 IRES_5S_U2.cm BK006936.fasta
# Current dir: /analysis/BioPython/Testing
# Date: Thu Sep 12 05:17:28 2024
# [ok]

17
Tests/Infernal/IRES_5S_U2_Yeast-cmscan.tbl
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#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
#------------------- --------- ----------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
U2 RF00004 ENA|BK006935|BK006935.2 - cm 1 193 52929 53083 + no 1 0.44 0.0 13.5 0.91 ? U2 spliceosomal RNA
U2 RF00004 ENA|BK006935|BK006935.2 - cm 1 193 196571 196389 - no 1 0.33 5.3 12.8 1.3 ? U2 spliceosomal RNA
U2 RF00004 ENA|BK006936|BK006936.2 - cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.2e-20 ! U2 spliceosomal RNA
5S_rRNA RF00001 ENA|BK006937|BK006937.2 - cm 1 119 761 644 - no 1 0.41 0.3 14.1 2.4 ? 5S ribosomal RNA
U2 RF00004 ENA|BK006937|BK006937.2 - cm 1 193 229986 229885 - no 1 0.32 0.1 11.1 4.7 ? U2 spliceosomal RNA
#
# Program: cmscan
# Version: 1.1.5 (Sep 2023)
# Pipeline mode: SCAN
# Query file: BK006935_6_7.fasta
# Target file: IRES_5S_U2.cm
# Option settings: cmscan --tblout IRES_5S_U2_Yeast-cmscan.tbl IRES_5S_U2.cm BK006935_6_7.fasta
# Current dir: /analysis/BioPython/Testing
# Date: Thu Sep 12 05:06:09 2024
# [ok]

209
Tests/Infernal/IRES_5S_U2_Yeast-cmscan.txt
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@ -1,209 +0,0 @@
# cmscan :: search sequence(s) against a CM database
# INFERNAL 1.1.5 (Sep 2023)
# Copyright (C) 2023 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file: BK006935_6_7.fasta
# target CM database: IRES_5S_U2.cm
# tabular output of hits: IRES_5S_U2_Yeast-cmscan.tbl
# number of worker threads: 4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: ENA|BK006935|BK006935.2 [L=230218]
Hit scores:
rank E-value score bias modelname start end mdl trunc gc description
---- --------- ------ ----- --------- ------ ------ --- ----- ---- -----------
------ inclusion threshold ------
(1) ? 0.91 13.5 0.0 U2 52929 53083 + cm no 0.44 U2 spliceosomal RNA
(2) ? 1.3 12.8 5.3 U2 196571 196389 - cm no 0.33 U2 spliceosomal RNA
Hit alignments:
>> U2 U2 spliceosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ? 0.91 13.5 0.0 cm 1 193 [] 52929 53083 + .. 0.80 no 0.44
v v NC
::::::.<<<-<<<<..____>>>>->>>,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,,, CS
U2 1 AUacCU.UCucgGCc..UUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCU*[20]**[18]*aauuauaUUAaauuaAUUUUU 105
U +C UC:C:G UUUU C:A:GAUCAAG G AG UCUGU ++U+AUA AAUU AUU
ENA|BK006935|BK006935.2 52929 CUGGCAaUCCCGGAGugUUUUUGCCAGGAUCAAGAGCAGCUUCUGU---*[ 2]**[ 1]*UUUAAUAAACAAUUCAUUAAG 52998
**********8875544888999*************9999999987......7.....4..333555555566788888888 PP
vv v v vv v v v v NC
,,,,,,,<<<<<<<<----<<<<<__>>>>>-->>>>>>>>,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>: CS
U2 106 ggaacuaGugggggcauuuuggGCUUGCccauugcccccaCacggguugaccuggcaUUGCAcUaccgccagguucagcccA 187
GGAACU+: ::: : U++: U : U : ::: : ::::U C G: U CA U+C :C G U A::::A
ENA|BK006935|BK006935.2 52999 GGAACUUAGCCAUCUGGAUGAUAUGUGCA--GUGGGUGGUUCACAAAUA-GCUCGUCUGCCAGUUCAUCUGGUUGGAUUUGA 53077
88888888888888877664333333322..358999999999999999.8888999*********99999999******** PP
NC
:::::: CS
U2 188 cccuuu 193
C C+UU
ENA|BK006935|BK006935.2 53078 CACCUU 53083
****** PP
>> U2 U2 spliceosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ? 1.3 12.8 5.3 cm 1 193 [] 196571 196389 - .. 0.77 no 0.33
vvvv vvvv v v v NC
::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<~~~~~~>> CS
U2 1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggccc*[ 7]*gg 81
AU C UUC:C U UU+++ +:GAU A U U G A UUCU: CAG +UAAUAUCUG : GG :: ::
ENA|BK006935|BK006935.2 196571 AUUCUUUCCCA---UCUUUAUAUGGAUAAUAUUUUGAA----UUCUAUGCAGAGUAAUAUCUGUUU-GGUAU*[19]*AU 196487
**********5...44444555*******999999999....6********************999.65444...7..33 PP
v vvvv vvvv v v NC
>>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<----<<<<<_~~~~~~>>>>>-->>>>>>>>,,<<<<<<- CS
U2 82 gccaau.uauaUUAaauuaAUUUUUggaacuaGugggggcauuuuggGCU*[ 1]*GCccauugcccccaCacggguuga 155
CC++ UA A UA +UU+ UUUUU G +++ :: ++ +::A+G:: : A
ENA|BK006935|BK006935.2 196486 CCCUUGuUAGAGUAGUUUUUUUUUUUGGUUAGUG---------------G*[10]*---------AAGUCAAUGAAAGCA 196427
3444445666666666666666666666665544...............2...3...........34467899******* PP
v v v v NC
<<<<<<___________>>>>>>-->>>>>>::::::: CS
U2 156 ccuggcaUUGCAcUaccgccagguucagcccAcccuuu 193
:: :: U GCA +++:: ::UU : ::CA CC+
ENA|BK006935|BK006935.2 196426 UAAGUUUUAGCAUCUUUAAUAUAUUUCGUUCAGCCCGG 196389
************************************** PP
Internal CM pipeline statistics summary:
----------------------------------------
Query sequence(s): 1 (460436 residues searched)
Query sequences re-searched for truncated hits: 1 (1166.7 residues re-searched, avg per model)
Target model(s): 3 (664 consensus positions)
Windows passing local HMM SSV filter: 1951 (0.3874); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
Windows passing local HMM Forward filter: 932 (0.1928); expected (0.02)
Windows passing local HMM Forward bias filter: 386 (0.09111); expected (0.02)
Windows passing glocal HMM Forward filter: 129 (0.06346); expected (0.02)
Windows passing glocal HMM Forward bias filter: 75 (0.03339); expected (0.02)
Envelopes passing glocal HMM envelope defn filter: 84 (0.01354); expected (0.02)
Envelopes passing local CM CYK filter: 3 (0.0002665); expected (0.0001)
Total CM hits reported: 2 (0.0002441); includes 0 truncated hit(s)
# CPU time: 8.73u 0.20s 00:00:08.93 Elapsed: 00:00:08.28
//
Query: ENA|BK006936|BK006936.2 [L=813184]
Hit scores:
rank E-value score bias modelname start end mdl trunc gc description
---- --------- ------ ----- --------- ------ ------ --- ----- ---- -----------
(1) ! 1.2e-20 98.7 0.1 U2 681858 681747 - cm no 0.33 U2 spliceosomal RNA
Hit alignments:
>> U2 U2 spliceosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 1.2e-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
Internal CM pipeline statistics summary:
----------------------------------------
Query sequence(s): 1 (1626368 residues searched)
Query sequences re-searched for truncated hits: 1 (1166.7 residues re-searched, avg per model)
Target model(s): 3 (664 consensus positions)
Windows passing local HMM SSV filter: 6996 (0.3917); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
Windows passing local HMM Forward filter: 1952 (0.1271); expected (0.005)
Windows passing local HMM Forward bias filter: 311 (0.02308); expected (0.005)
Windows passing glocal HMM Forward filter: 162 (0.01766); expected (0.005)
Windows passing glocal HMM Forward bias filter: 104 (0.01062); expected (0.005)
Envelopes passing glocal HMM envelope defn filter: 109 (0.004945); expected (0.005)
Envelopes passing local CM CYK filter: 7 (0.0001391); expected (0.0001)
Total CM hits reported: 1 (2.294e-05); includes 0 truncated hit(s)
# CPU time: 10.01u 0.30s 00:00:10.31 Elapsed: 00:00:09.27
//
Query: ENA|BK006937|BK006937.2 [L=316620]
Hit scores:
rank E-value score bias modelname start end mdl trunc gc description
---- --------- ------ ----- --------- ------ ------ --- ----- ---- -----------
------ inclusion threshold ------
(1) ? 2.4 14.1 0.3 5S_rRNA 761 644 - cm no 0.41 5S ribosomal RNA
(2) ? 4.7 11.1 0.1 U2 229986 229885 - cm no 0.32 U2 spliceosomal RNA
Hit alignments:
>> 5S_rRNA 5S ribosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ? 2.4 14.1 0.3 cm 1 119 [] 761 644 - .. 0.90 no 0.41
v v v v v v v NC
(((((((((,,,,<<-<<.<<<.---<<--<<<<.<<______>>-->>>>-->>---->>>>>-->><<<-<<----<-<<---- CS
5S_rRNA 1 gccuGcggcCAUAccagc.gcg.aAagcACcgGa.uCCCAUCcGaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagGa 83
: :: ::: AUAC + :: G: C:::: CC AUC+G ::::AA:U AAG :: U+ GGC: :G GUA :+GGA
ENA|BK006937|BK006937.2 761 GAGAUGGUAUAUACUGUAgCAUcCGUGUGCGUAUgACCGAUCAGA--AUACAAGUGAAGGUGAGUAUGGCAUGUG--GUAGUGGGA 680
**************9753244314478889999889999999999..89**********9999999*********..********* PP
v NC
-<<____>>----->>->-->>->>>.))))))))): CS
5S_rRNA 84 UGgGuGAcCuCcUGggAAgaccagGu.gccgCaggcc 119
U :G G : G: AAG+: A:GU ::: :: : C
ENA|BK006937|BK006937.2 679 UUAGAG-UGGUAGGAUAAGUAUAUGUgUAUUAUUUAC 644
*99988.689999************************ PP
>> U2 U2 spliceosomal RNA
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ? 4.7 11.1 0.1 cm 1 193 [] 229986 229885 - .. 0.83 no 0.32
v v v v v v NC
::::::<<<-~~~~~~->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>>>>>>,, CS
U2 1 AUacCUUCuc*[12]*aaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAuugggggccaa 86
A CUU + + AUCAAGUGUAG AUCU UU :A : : UU +A+: : U: G: ::::A U::::+:CAA
ENA|BK006937|BK006937.2 229986 UCAACUUGUU*[ 4]*UUCAUCAAGUGUAGAAUCUAUUUCAAAAUACUUCCCAAUGUCUU-GU-AAGGAGUCCUUUACAA 229911
*******876...4..589****************9999888888888888888888888.88.5566666888888899 PP
NC
,,,,,,,,,,,,,,,,,,~~~~~~::::::: CS
U2 87 uuauaUUAaauuaAUUUU*[82]*Acccuuu 193
+U+ AU A AUUUU ACC+UU
ENA|BK006937|BK006937.2 229910 AUUCAUAACCACGAUUUU*[ 1]*ACCUUUG 229885
888888888888888876...8..******* PP
Internal CM pipeline statistics summary:
----------------------------------------
Query sequence(s): 1 (633240 residues searched)
Query sequences re-searched for truncated hits: 1 (1166.7 residues re-searched, avg per model)
Target model(s): 3 (664 consensus positions)
Windows passing local HMM SSV filter: 2708 (0.3858); expected (0.35)
Windows passing local HMM Viterbi filter: (off)
Windows passing local HMM Viterbi bias filter: (off)
Windows passing local HMM Forward filter: 1345 (0.2002); expected (0.02)
Windows passing local HMM Forward bias filter: 470 (0.08163); expected (0.02)
Windows passing glocal HMM Forward filter: 181 (0.05878); expected (0.02)
Windows passing glocal HMM Forward bias filter: 99 (0.03068); expected (0.02)
Envelopes passing glocal HMM envelope defn filter: 111 (0.01272); expected (0.02)
Envelopes passing local CM CYK filter: 6 (0.0003184); expected (0.0001)
Total CM hits reported: 2 (0.0001156); includes 0 truncated hit(s)
# CPU time: 10.51u 0.39s 00:00:10.90 Elapsed: 00:00:09.15
//
[ok]

379
Tests/Infernal/IRES_5S_U2_Yeast.txt
View File

@ -1,379 +0,0 @@
# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file: IRES_5S_U2.cm
# target sequence database: GCA_000146045.2.fasta
# tabular output of hits: IRES_5S_U2_Yeast.tbl
# number of worker threads: 56
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: IRES_HCV [CLEN=352]
Accession: RF00061
Description: Hepatitis C virus internal ribosome entry site
Hit scores:
rank E-value score bias sequence start end mdl trunc gc description
---- --------- ------ ----- -------- ------ ------ --- ----- ---- -----------
[No hits detected that satisfy reporting thresholds]
Hit alignments:
[No hits detected that satisfy reporting thresholds]
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (352 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (28160 residues re-searched)
Windows passing local HMM SSV filter: 6432 (0.1374); expected (0.35)
Windows passing local HMM Viterbi filter: 1631 (0.03555); expected (0.15)
Windows passing local HMM Viterbi bias filter: 1607 (0.03502); expected (0.15)
Windows passing local HMM Forward filter: 9 (0.0001992); expected (0.003)
Windows passing local HMM Forward bias filter: 9 (0.0001992); expected (0.003)
Windows passing glocal HMM Forward filter: 1 (2.16e-05); expected (0.003)
Windows passing glocal HMM Forward bias filter: 1 (2.16e-05); expected (0.003)
Envelopes passing glocal HMM envelope defn filter: 1 (1.705e-05); expected (0.003)
Envelopes passing local CM CYK filter: 0 (0); expected (0.0001)
Total CM hits reported: 0 (0); includes 0 truncated hit(s)
# CPU time: 3.98u 0.19s 00:00:04.17 Elapsed: 00:00:00.87
//
Query: 5S_rRNA [CLEN=119]
Accession: RF00001
Description: 5S ribosomal RNA
Hit scores:
rank E-value score bias sequence start end mdl trunc gc description
---- --------- ------ ----- ----------------------- ------ ------ --- ----- ---- -----------
(1) ! 1.6e-18 88.8 0.0 ENA|BK006945|BK006945.2 459676 459796 + cm no 0.52 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(2) ! 1.6e-18 88.8 0.0 ENA|BK006945|BK006945.2 489349 489469 + cm no 0.52 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(3) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 468813 468933 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(4) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 472465 472585 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(5) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 482045 482165 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
(6) ! 4.4e-17 83.2 0.0 ENA|BK006945|BK006945.2 485697 485817 + cm no 0.53 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII
------ inclusion threshold ------
(7) ? 0.56 20.9 0.0 ENA|BK006943|BK006943.2 357031 357144 + cm no 0.46 TPA_inf: Saccharomyces cerevisiae S288C chromosome X,
(8) ? 6.6 16.7 0.3 ENA|BK006947|BK006947.3 7085 6968 - cm no 0.41 TPA_inf: Saccharomyces cerevisiae S288C chromosome XIV
Hit alignments:
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 1.6e-18 88.8 0.0 cm 1 119 [] 459676 459796 + .. 0.99 no 0.52
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
G::UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 459676 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 459755
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA::C+
ENA|BK006945|BK006945.2 459756 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU 459796
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ! 1.6e-18 88.8 0.0 cm 1 119 [] 489349 489469 + .. 0.99 no 0.52
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
G::UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 489349 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 489428
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA::C+
ENA|BK006945|BK006945.2 489429 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU 489469
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(3) ! 4.4e-17 83.2 0.0 cm 1 119 [] 468813 468933 + .. 0.99 no 0.53
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
: UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 468813 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 468892
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA :
ENA|BK006945|BK006945.2 468893 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 468933
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(4) ! 4.4e-17 83.2 0.0 cm 1 119 [] 472465 472585 + .. 0.99 no 0.53
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
: UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 472465 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 472544
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA :
ENA|BK006945|BK006945.2 472545 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 472585
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(5) ! 4.4e-17 83.2 0.0 cm 1 119 [] 482045 482165 + .. 0.99 no 0.53
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
: UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 482045 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 482124
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA :
ENA|BK006945|BK006945.2 482125 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 482165
***********************9***************** PP
>> ENA|BK006945|BK006945.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(6) ! 4.4e-17 83.2 0.0 cm 1 119 [] 485697 485817 + .. 0.99 no 0.53
v NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc.gAAguUAAGcgcgcUugggCcagggUA.GUAc 78
: UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA
ENA|BK006945|BK006945.2 485697 GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAG 485776
***********************************************99***********************8756**** PP
v vv NC
<-----<<____>>----->>->-->>->>>))))))))): CS
5S_rRNA 79 uagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc 119
+ +UGGGUGACC+ G AA :CAGGUGC:GCA :
ENA|BK006945|BK006945.2 485777 UGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAGUUG 485817
***********************9***************** PP
>> ENA|BK006943|BK006943.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome X, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(7) ? 0.56 20.9 0.0 cm 1 119 [] 357031 357144 + .. 0.86 no 0.46
v vv v vv vv v vv vv NC
(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>>-.->>---->>>>>-->><<<-<<----<-<< CS
5S_rRNA 1 gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCcgA.AguUAAGcgcgcUugggCcagggUAGUAcu 79
::: GC:G CA A:: G :G+AA: AC:: ++ CAU C ::A A :UAAGC: CU+:: C G:G GUACU
ENA|BK006943|BK006943.2 357031 CAGGGCUGGCAGAGGUGUCGGGAAAAACAAGGAU-CAUAU--CCUUUUAcAAUUAAGCCAUCUACCACCUGAG--GUACU 357105
****************************888743.44433..555555579**********************..***** PP
v v vvv NC
-----<<____>>----->>->-->>->>>)))))).))): CS
5S_rRNA 80 agGaUGgGuGAcCuCcUGggAAgaccagGugccgCa.ggcc 119
A + G CU C GGGAA+A:C+G C:GC :::+
ENA|BK006943|BK006943.2 357106 AAAG-G-AAAGGCUACCGGGAAUAUCUGAAACAGCUgCUGU 357144
9994.3.33334778889****************9879*** PP
>> ENA|BK006947|BK006947.3 TPA_inf: Saccharomyces cerevisiae S288C chromosome XIV, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(8) ? 6.6 16.7 0.3 cm 1 119 [] 7085 6968 - .. 0.91 no 0.41
v v v v v v v NC
(((((((((,,,,<<-<<.<<<.---<<--<<<<.<<______>>-->>>>-->>---->>>>>-->><<<-<<----<-<<-- CS
5S_rRNA 1 gccuGcggcCAUAccagc.gcg.aAagcACcgGa.uCCCAUCcGaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuag 81
: :: ::: AUAC + :: G:AC:::: CC AUC+G ::::AA:U AAG :: U+ GGC: :G GUA U+G
ENA|BK006947|BK006947.3 7085 GAGAUGGUAUAUACUGUAgCAUcCGUGUACGUAUgACCGAUCAGA--AUACAAGUGAAGGUGAGUAUGGCAUGUG--GUAGUGG 7006
**************976325541459999****989999999999..89**********9999999*********..******* PP
v NC
---<<____>>----->>->-->>->>>.))))))))): CS
5S_rRNA 82 GaUGgGuGAcCuCcUGggAAgaccagGu.gccgCaggcc 119
GAU :G G : GG AAG+: A:GU ::: :: : C
ENA|BK006947|BK006947.3 7005 GAUUAGAG-UGGUAGGGUAAGUAUAUGUgUAUUAUUUAC 6968
***99988.689999************************ PP
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (119 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (12416 residues re-searched)
Windows passing local HMM SSV filter: 24991 (0.2423); expected (0.35)
Windows passing local HMM Viterbi filter: 8464 (0.08504); expected (0.15)
Windows passing local HMM Viterbi bias filter: 8432 (0.08473); expected (0.15)
Windows passing local HMM Forward filter: 135 (0.001502); expected (0.003)
Windows passing local HMM Forward bias filter: 134 (0.001493); expected (0.003)
Windows passing glocal HMM Forward filter: 65 (0.0007404); expected (0.003)
Windows passing glocal HMM Forward bias filter: 65 (0.0007404); expected (0.003)
Envelopes passing glocal HMM envelope defn filter: 61 (0.0003446); expected (0.003)
Envelopes passing local CM CYK filter: 15 (6.52e-05); expected (0.0001)
Total CM hits reported: 8 (3.966e-05); includes 0 truncated hit(s)
# CPU time: 4.17u 0.21s 00:00:04.38 Elapsed: 00:00:00.40
//
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) ! 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,
Hit alignments:
>> ENA|BK006936|BK006936.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 5.9e-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 TPA_inf: Saccharomyces cerevisiae S288C chromosome XV, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ? 0.49 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|BK006947|BK006947.3 TPA_inf: Saccharomyces cerevisiae S288C chromosome XIV, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(3) ? 5.7 15.3 0.0 cm 1 193 [] 266059 266208 + .. 0.91 no 0.39
v v v NC
::::::.<<<.-<<<<____>>>>->>>,,,,.,,,,,,~~~~~~,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<< CS
U2 1 AUacCU.UCu.cgGCcUUUUgGCuaaGAUCAA.GUGUAG*[48]*aauuauaUUAaauuaAUUUUUggaacuaGuggggg 119
AU UCU + G C UUG C AGAU A GUGUAG UUAUAU +UU AU UUU G +A:: : G:
ENA|BK006947|BK006947.3 266059 AUGUUGaUCUaUCGUCAAUUGACCCAGAUGAUaGUGUAG*[ 1]*-GUUAUAUAGUUUUGAUAUUUUGGCGAAAAGUUGA 266132
*****9****999****************9988999987...5...3377778888888888888888888888888888 PP
v v v v v v v v v NC
<----.<<<<<__>>>>>-..->>>>>>>>,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>::::::: CS
U2 120 cauuu.uggGCUUGCccau..ugcccccaCacggguugaccuggcaUUGCAcUaccgccagguucagcccAcccuuu 193
:A+U+ U :GCUUGC: AU +::C : :: G: :AC: G U GCA UA+ C :GU+: :C +U +
ENA|BK006947|BK006947.3 266133 GAAUAuUGCGCUUGCGUAUauAUUCCAUUUGAGGUGGCACUAGAGCUCGCAUUAU-UACCAGUAGUGGCAGGAUUGC 266208
888888**************99999******************************.99******************* PP
>> ENA|BK006949|BK006949.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XVI, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(4) ? 6.6 15.1 0.4 cm 1 193 [] 443393 443253 - .. 0.71 no 0.32
v v v v NC
::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,~~~~~~,<<<<<<<___>>>>>>>,,,..,,,,, CS
U2 1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCU*[20]*uggcccccAuugggggccaau..uauaU 92
A U C:+G C G UA:G UCAAG UAGUAU UGUUCU ::: C A+ G :::++U
ENA|BK006949|BK006949.2 443393 CCAUUUACAUGAACCCCAGUUUAUGUUCAAG--UAGUAUAUGUUCU*[ 4]*-UCAACGCAAACUGCUGAUUUcaCC--- 443322
***************999************6..7**********98...4...222222222222222222222222... PP
v v v v v v v NC
,,,,,,,,,,,,,,,,,,,,<<<<<<<<----<<<<<__>>>>>-->>>>>>>>,,<<<<<<-<<<<<<___________ CS
U2 93 UAaauuaAUUUUUggaacuaGugggggcauuuuggGCUUGCccauugcccccaCacggguugaccuggcaUUGCAcUacc 172
:U : :::+U U UU+ ::: : A:A+ ::: G+C: : :A U CAC AC
ENA|BK006949|BK006949.2 443321 --------------------AUUGAAUAUUGU-----UUA------UAUAUGAUAUAUACCGUCAAAUUACUUCACGAC- 443274
....................222222222222.....221......3333345599***********************. PP
v v v NC
>>>>>>-->>>>>>::::::: CS
U2 173 gccagguucagcccAcccuuu 193
: : :G++C ::: + U+
ENA|BK006949|BK006949.2 443273 AGUGUGAACUGUGAUAAAUCA 443253
********************* PP
>> ENA|BK006939|BK006939.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome V, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(5) ? 7.1 14.9 0.0 cm 1 193 [] 190882 191043 + .. 0.92 no 0.41
v v NC
::::::<<<.-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,,, CS
U2 1 AUacCUUCu.cgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCU*[20]**[18]*aauuauaUUAaauuaAUUUUU 105
AU CC U : +: C: UUU:G : : AUCA AA ++U+UUAAAU AA UUUU
ENA|BK006939|BK006939.2 190882 AUUCCAUGAuUUCCUGUUUAGCU-UCAUCA-----------------*[ 4]**[ 4]*AACAUUUUUAAAUGAAAUUUU 190939
*******9955678899999976.799997....................9.....9..77699**************** PP
vv v v vv v NC
,,,,,,,<<<<<<<<----.<<<<<_._>>>>>-.........->>>>>>>>,,<<<<<<-<<<<<<__________... CS
U2 106 ggaacuaGugggggcauuu.uggGCU.UGCccau.........ugcccccaCacggguugaccuggcaUUGCAcUac... 171
+ + +GU:: : AUU :G:GCU UGC:C: + : ::ACA+ :: :: : :::: U CAC AC
ENA|BK006939|BK006939.2 190940 AAUGUCUGUUUCCUUAUUGaAGAGCUuUGCUCUGgauuuuccaACAUUAAACAUGCCGCCGAGGCCUCCUCCACCACcac 191019
***********9999998899999964799999999999999999999**************************999888 PP
v NC
.._>>>>>>-->>>>>>::::::: CS
U2 172 ..cgccagguucagcccAcccuuu 193
+:::: :UU:: :: + CU+U
ENA|BK006939|BK006939.2 191020 caUUGGCAUUUGGUGGUGAACUAU 191043
988********************* PP
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (193 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (15424 residues re-searched)
Windows passing local HMM SSV filter: 72732 (0.7978); expected (0.35)
Windows passing local HMM Viterbi filter: 24175 (0.3233); expected (0.15)
Windows passing local HMM Viterbi bias filter: 6671 (0.09669); expected (0.15)
Windows passing local HMM Forward filter: 2037 (0.03161); expected (0.003)
Windows passing local HMM Forward bias filter: 1133 (0.01757); expected (0.003)
Windows passing glocal HMM Forward filter: 596 (0.01251); expected (0.003)
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: 5 (3.063e-05); includes 0 truncated hit(s)
# CPU time: 67.17u 2.23s 00:01:09.40 Elapsed: 00:00:03.24
//
[ok]

12
Tests/Infernal/IRES_Yeast.tbl
View File

@ -1,12 +0,0 @@
#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
#------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
#
# Program: cmsearch
# Version: 1.1.4 (Dec 2020)
# Pipeline mode: SEARCH
# Query file: RF00061.cm
# Target file: GCA_000146045.2.fasta
# Option settings: cmsearch --tblout IRES_Yeast.tbl -T 298.2 RF00061.cm GCA_000146045.2.fasta
# Current dir: /analysis/BioPython/Testing
# Date: Tue Sep 10 11:02:58 2024
# [ok]

46
Tests/Infernal/IRES_Yeast.txt
View File

@ -1,46 +0,0 @@
# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file: RF00061.cm
# target sequence database: GCA_000146045.2.fasta
# tabular output of hits: IRES_Yeast.tbl
# sequence reporting threshold: score >= 298.2
# number of worker threads: 56
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: IRES_HCV [CLEN=352]
Accession: RF00061
Description: Hepatitis C virus internal ribosome entry site
Hit scores:
rank E-value score bias sequence start end mdl trunc gc description
---- --------- ------ ----- -------- ------ ------ --- ----- ---- -----------
[No hits detected that satisfy reporting thresholds]
Hit alignments:
[No hits detected that satisfy reporting thresholds]
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (352 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (28160 residues re-searched)
Windows passing local HMM SSV filter: 6432 (0.1374); expected (0.35)
Windows passing local HMM Viterbi filter: 1631 (0.03555); expected (0.15)
Windows passing local HMM Viterbi bias filter: 1607 (0.03502); expected (0.15)
Windows passing local HMM Forward filter: 9 (0.0001992); expected (0.003)
Windows passing local HMM Forward bias filter: 9 (0.0001992); expected (0.003)
Windows passing glocal HMM Forward filter: 1 (2.16e-05); expected (0.003)
Windows passing glocal HMM Forward bias filter: 1 (2.16e-05); expected (0.003)
Envelopes passing glocal HMM envelope defn filter: 1 (1.705e-05); expected (0.003)
Envelopes passing local CM CYK filter: 0 (0); expected (0.0001)
Total CM hits reported: 0 (0); includes 0 truncated hit(s)
# CPU time: 3.93u 0.19s 00:00:04.12 Elapsed: 00:00:00.86
//
[ok]

54
Tests/Infernal/U2_Yeast-hmmonly.txt
View File

@ -1,54 +0,0 @@
# 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: GCA_000146045.2.fasta
# sequence reporting threshold: score >= 46
# HMM-only mode (for all models): on [CM will not be used]
# 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) ! 1.5e-19 73.1 2.7 ENA|BK006936|BK006936.2 681855 681762 - hmm - 0.35 TPA_inf: Saccharomyces cerevisiae S288C chromosome II,
Hit alignments:
>> ENA|BK006936|BK006936.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 1.5e-19 73.1 2.7 hmm 7 100 .. 681855 681762 - .. 0.74 - 0.35
<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>>>>>>,, CS
U2 7 UCucgGCcUUUUGGCUaaGAUCAAGUGUAGUAUCUGUUCUUuuCAGUuUAAuAuCUGauAuugucucuAuugggggccaa 86
UCu+ GCcUUUUGGCU+aGAUCAAGUGUAGUAUCUGUUCUUuuCAGU+UAA+A+CUGa+Au+ +cuc Au g+gg ca+
ENA|BK006936|BK006936.2 681855 UCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAAUGACCUCAAU-GAGGCUCAU 681777
999*********************************************************7777666666.777776666 PP
,.,,,,,,,,,,,,, CS
U2 87 u.uauaUUAaauuaA 100
u u+UUAa+uu
ENA|BK006936|BK006936.2 681776 UaCCUUUUAAUUUGU 681762
544444444433221 PP
Internal HMM-only pipeline statistics summary: (--hmmonly used)
---------------------------------------------------------------
Query model(s): 1 (193 consensus positions)
Target sequences: 16 (24142652 residues searched)
Windows passing local HMM SSV filter: 14742 (0.1733); expected (0.02)
Windows passing local HMM MSV bias filter: 3067 (0.03652); expected (0.02)
Windows passing local HMM Viterbi filter: 143 (0.001824); expected (0.001)
Windows passing local HMM Forward filter: 29 (0.000422); expected (1e-05)
Total HMM hits reported: 1 (3.894e-06)
# CPU time: 1.28u 0.02s 00:00:01.30 Elapsed: 00:00:00.32
//
[ok]

44
Tests/Infernal/U2_Yeast-noali.txt
View File

@ -1,44 +0,0 @@
# 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: GCA_000146045.2.fasta
# show alignments in output: no
# 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) ! 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:
----------------------------------------
Query model(s): 1 (193 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (15424 residues re-searched)
Windows passing local HMM SSV filter: 72732 (0.7978); expected (0.35)
Windows passing local HMM Viterbi filter: 24175 (0.3233); expected (0.15)
Windows passing local HMM Viterbi bias filter: 6671 (0.09669); expected (0.15)
Windows passing local HMM Forward filter: 2037 (0.03161); expected (0.003)
Windows passing local HMM Forward bias filter: 1133 (0.01757); expected (0.003)
Windows passing glocal HMM Forward filter: 596 (0.01251); expected (0.003)
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: 5 (3.063e-05); includes 0 truncated hit(s)
# CPU time: 40.93u 0.55s 00:00:41.48 Elapsed: 00:00:10.59
//
[ok]

18
Tests/Infernal/U2_Yeast-shuf.tbl
View File

@ -1,18 +0,0 @@
#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
View File

@ -1,182 +0,0 @@
# 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]

40
Tests/Infernal/U2_Yeast-threshold-noali.txt
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@ -1,40 +0,0 @@
# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 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
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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) ! 5.9e-20 98.7 0.1 ENA|BK006936|BK006936.2 681858 681747 - cm no 0.33 TPA_inf: Saccharomyces cerevisiae S288C chromosome II,
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (193 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (15424 residues re-searched)
Windows passing local HMM SSV filter: 72732 (0.7978); expected (0.35)
Windows passing local HMM Viterbi filter: 24175 (0.3233); expected (0.15)
Windows passing local HMM Viterbi bias filter: 6671 (0.09669); expected (0.15)
Windows passing local HMM Forward filter: 2037 (0.03161); expected (0.003)
Windows passing local HMM Forward bias filter: 1133 (0.01757); expected (0.003)
Windows passing glocal HMM Forward filter: 596 (0.01251); expected (0.003)
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)
# CPU time: 65.01u 2.28s 00:01:07.29 Elapsed: 00:00:03.20
//
[ok]

13
Tests/Infernal/U2_Yeast-threshold.tbl
View File

@ -1,13 +0,0 @@
#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 5.9e-20 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.
#
# Program: cmsearch
# Version: 1.1.4 (Dec 2020)
# Pipeline mode: SEARCH
# Query file: RF00004.cm
# Target file: GCA_000146045.2.fasta
# Option settings: cmsearch --tblout U2_Yeast-threshold.tbl -T 46.0 RF00004.cm GCA_000146045.2.fasta
# Current dir: /analysis/BioPython/Testing
# Date: Tue Sep 10 11:44:33 2024
# [ok]

62
Tests/Infernal/U2_Yeast-threshold.txt
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@ -1,62 +0,0 @@
# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file: RF00004.cm
# target sequence database: GCA_000146045.2.fasta
# tabular output of hits: U2_Yeast-threshold.tbl
# sequence reporting threshold: score >= 46
# number of worker threads: 56
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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) ! 5.9e-20 98.7 0.1 ENA|BK006936|BK006936.2 681858 681747 - cm no 0.33 TPA_inf: Saccharomyces cerevisiae S288C chromosome II,
Hit alignments:
>> ENA|BK006936|BK006936.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 5.9e-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
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (193 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (15424 residues re-searched)
Windows passing local HMM SSV filter: 72732 (0.7978); expected (0.35)
Windows passing local HMM Viterbi filter: 24175 (0.3233); expected (0.15)
Windows passing local HMM Viterbi bias filter: 6671 (0.09669); expected (0.15)
Windows passing local HMM Forward filter: 2037 (0.03161); expected (0.003)
Windows passing local HMM Forward bias filter: 1133 (0.01757); expected (0.003)
Windows passing glocal HMM Forward filter: 596 (0.01251); expected (0.003)
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)
# CPU time: 64.67u 2.16s 00:01:06.83 Elapsed: 00:00:03.09
//
[ok]

156
Tests/Infernal/U2_Yeast.txt
View File

@ -1,156 +0,0 @@
# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file: RF00004.cm
# target sequence database: GCA_000146045.2.fasta
# tabular output of hits: U2_Yeast.tbl
# number of worker threads: 56
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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) ! 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,
Hit alignments:
>> ENA|BK006936|BK006936.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(1) ! 5.9e-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 TPA_inf: Saccharomyces cerevisiae S288C chromosome XV, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(2) ? 0.49 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|BK006947|BK006947.3 TPA_inf: Saccharomyces cerevisiae S288C chromosome XIV, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(3) ? 5.7 15.3 0.0 cm 1 193 [] 266059 266208 + .. 0.91 no 0.39
v v v NC
::::::.<<<.-<<<<____>>>>->>>,,,,.,,,,,,~~~~~~,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<< CS
U2 1 AUacCU.UCu.cgGCcUUUUgGCuaaGAUCAA.GUGUAG*[48]*aauuauaUUAaauuaAUUUUUggaacuaGuggggg 119
AU UCU + G C UUG C AGAU A GUGUAG UUAUAU +UU AU UUU G +A:: : G:
ENA|BK006947|BK006947.3 266059 AUGUUGaUCUaUCGUCAAUUGACCCAGAUGAUaGUGUAG*[ 1]*-GUUAUAUAGUUUUGAUAUUUUGGCGAAAAGUUGA 266132
*****9****999****************9988999987...5...3377778888888888888888888888888888 PP
v v v v v v v v v NC
<----.<<<<<__>>>>>-..->>>>>>>>,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>::::::: CS
U2 120 cauuu.uggGCUUGCccau..ugcccccaCacggguugaccuggcaUUGCAcUaccgccagguucagcccAcccuuu 193
:A+U+ U :GCUUGC: AU +::C : :: G: :AC: G U GCA UA+ C :GU+: :C +U +
ENA|BK006947|BK006947.3 266133 GAAUAuUGCGCUUGCGUAUauAUUCCAUUUGAGGUGGCACUAGAGCUCGCAUUAU-UACCAGUAGUGGCAGGAUUGC 266208
888888**************99999******************************.99******************* PP
>> ENA|BK006949|BK006949.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome XVI, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(4) ? 6.6 15.1 0.4 cm 1 193 [] 443393 443253 - .. 0.71 no 0.32
v v v v NC
::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,~~~~~~,<<<<<<<___>>>>>>>,,,..,,,,, CS
U2 1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCU*[20]*uggcccccAuugggggccaau..uauaU 92
A U C:+G C G UA:G UCAAG UAGUAU UGUUCU ::: C A+ G :::++U
ENA|BK006949|BK006949.2 443393 CCAUUUACAUGAACCCCAGUUUAUGUUCAAG--UAGUAUAUGUUCU*[ 4]*-UCAACGCAAACUGCUGAUUUcaCC--- 443322
***************999************6..7**********98...4...222222222222222222222222... PP
v v v v v v v NC
,,,,,,,,,,,,,,,,,,,,<<<<<<<<----<<<<<__>>>>>-->>>>>>>>,,<<<<<<-<<<<<<___________ CS
U2 93 UAaauuaAUUUUUggaacuaGugggggcauuuuggGCUUGCccauugcccccaCacggguugaccuggcaUUGCAcUacc 172
:U : :::+U U UU+ ::: : A:A+ ::: G+C: : :A U CAC AC
ENA|BK006949|BK006949.2 443321 --------------------AUUGAAUAUUGU-----UUA------UAUAUGAUAUAUACCGUCAAAUUACUUCACGAC- 443274
....................222222222222.....221......3333345599***********************. PP
v v v NC
>>>>>>-->>>>>>::::::: CS
U2 173 gccagguucagcccAcccuuu 193
: : :G++C ::: + U+
ENA|BK006949|BK006949.2 443273 AGUGUGAACUGUGAUAAAUCA 443253
********************* PP
>> ENA|BK006939|BK006939.2 TPA_inf: Saccharomyces cerevisiae S288C chromosome V, complete sequence.
rank E-value score bias mdl mdl from mdl to seq from seq to acc trunc gc
---- --------- ------ ----- --- -------- -------- ----------- ----------- ---- ----- ----
(5) ? 7.1 14.9 0.0 cm 1 193 [] 190882 191043 + .. 0.92 no 0.41
v v NC
::::::<<<.-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,,, CS
U2 1 AUacCUUCu.cgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCU*[20]**[18]*aauuauaUUAaauuaAUUUUU 105
AU CC U : +: C: UUU:G : : AUCA AA ++U+UUAAAU AA UUUU
ENA|BK006939|BK006939.2 190882 AUUCCAUGAuUUCCUGUUUAGCU-UCAUCA-----------------*[ 4]**[ 4]*AACAUUUUUAAAUGAAAUUUU 190939
*******9955678899999976.799997....................9.....9..77699**************** PP
vv v v vv v NC
,,,,,,,<<<<<<<<----.<<<<<_._>>>>>-.........->>>>>>>>,,<<<<<<-<<<<<<__________... CS
U2 106 ggaacuaGugggggcauuu.uggGCU.UGCccau.........ugcccccaCacggguugaccuggcaUUGCAcUac... 171
+ + +GU:: : AUU :G:GCU UGC:C: + : ::ACA+ :: :: : :::: U CAC AC
ENA|BK006939|BK006939.2 190940 AAUGUCUGUUUCCUUAUUGaAGAGCUuUGCUCUGgauuuuccaACAUUAAACAUGCCGCCGAGGCCUCCUCCACCACcac 191019
***********9999998899999964799999999999999999999**************************999888 PP
v NC
.._>>>>>>-->>>>>>::::::: CS
U2 172 ..cgccagguucagcccAcccuuu 193
+:::: :UU:: :: + CU+U
ENA|BK006939|BK006939.2 191020 caUUGGCAUUUGGUGGUGAACUAU 191043
988********************* PP
Internal CM pipeline statistics summary:
----------------------------------------
Query model(s): 1 (193 consensus positions)
Target sequences: 16 (24142652 residues searched)
Target sequences re-searched for truncated hits: 16 (15424 residues re-searched)
Windows passing local HMM SSV filter: 72732 (0.7978); expected (0.35)
Windows passing local HMM Viterbi filter: 24175 (0.3233); expected (0.15)
Windows passing local HMM Viterbi bias filter: 6671 (0.09669); expected (0.15)
Windows passing local HMM Forward filter: 2037 (0.03161); expected (0.003)
Windows passing local HMM Forward bias filter: 1133 (0.01757); expected (0.003)
Windows passing glocal HMM Forward filter: 596 (0.01251); expected (0.003)
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: 5 (3.063e-05); includes 0 truncated hit(s)
# CPU time: 66.56u 2.31s 00:01:08.87 Elapsed: 00:00:03.41
//
[ok]

0
Tests/Infernal/IRES_5S_U2_Yeast-cmscan-fmt_3.tbl → Tests/Infernal/cmscan_IRES_5S_U2_Yeast_fmt_3.tbl
View File

28
Tests/test_SearchIO_infernal_tab.py
View File

@ -36,8 +36,8 @@ class CmscanCases(unittest.TestCase):
def test_cmscan_mq_mm(self):
"""Test parsing infernal-tab, cmscan, multiple queries, multiple match, one hsp, default format"""
tab_file = get_file("IRES_5S_U2_Yeast-cmscan.tbl")
"""Test parsing infernal-tab, cmscan, multiple queries, multiple match, one hsp, default format (IRES_5S_U2_Yeast)"""
tab_file = get_file("cmscan_115_IRES_5S_U2_Yeast.tbl")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -163,8 +163,8 @@ class CmscanCases(unittest.TestCase):
def test_cmscan_mq_mm_fmt2(self):
"""Test parsing infernal-tab, cmscan, multiple queries, multiple match, one hsp, fmt 2"""
tab_file = get_file("IRES_5S_U2_Yeast-cmscan-fmt_2.tbl")
"""Test parsing infernal-tab, cmscan, multiple queries, multiple match, one hsp, fmt 2 (IRES_5S_U2_Yeast_fmt_2)"""
tab_file = get_file("cmscan_115_IRES_5S_U2_Yeast_fmt_2.tbl")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -209,8 +209,8 @@ class CmscanCases(unittest.TestCase):
@unittest.skip("Unsupported format")
def test_cmscan_mq_mm_fmt3(self):
"""Test parsing infernal-tab, cmscan, multiple queries, multiple match, one hsp, fmt 3"""
tab_file = get_file("IRES_5S_U2_Yeast-cmscan-fmt_3.tbl")
"""Test parsing infernal-tab, cmscan, multiple queries, multiple match, one hsp, fmt 3 (IRES_5S_U2_Yeast_fmt_3)"""
tab_file = get_file("cmscan_115_IRES_5S_U2_Yeast_fmt_3.tbl")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -250,16 +250,16 @@ class CmsearchCases(unittest.TestCase):
def test_1q_0m(self):
"""Test parsing infernal-tab, cmsearch, single query, no hits"""
tab_file = get_file("IRES_Yeast.tbl")
"""Test parsing infernal-tab, cmsearch, single query, no hits (IRES_Yeast)"""
tab_file = get_file("cmsearch_114_IRES_Yeast.tbl")
qresults = parse(tab_file, FMT)
self.assertRaises(StopIteration, next, qresults)
def test_cmsearch_1q_1m(self):
"""Test parsing infernal-tab, cmsearch, one queries, one match, one hsp"""
tab_file = get_file("U2_Yeast-threshold.tbl")
"""Test parsing infernal-tab, cmsearch, one queries, one match, one hsp (U2_Yeast)"""
tab_file = get_file("cmsearch_114_U2_Yeast.tbl")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -297,8 +297,8 @@ class CmsearchCases(unittest.TestCase):
def test_cmsearch_1q_mm(self):
"""Test parsing infernal-tab, cmsearch, one queries, multiple match, one hsp"""
tab_file = get_file("5S_Yeast.tbl")
"""Test parsing infernal-tab, cmsearch, one queries, multiple match, one hsp (5S_Yeast)"""
tab_file = get_file("cmsearch_114_5S_Yeast.tbl")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -351,8 +351,8 @@ class CmsearchCases(unittest.TestCase):
def test_cmsearch_1q_mm_shuf(self):
"""Test parsing infernal-tab, cmsearch, one queries, multiple non-consecutive hits, one hsp"""
tab_file = get_file("U2_Yeast-shuf.tbl")
"""Test parsing infernal-tab, cmsearch, one queries, multiple non-consecutive hits, one hsp (U2_Yeast_full_shuffled)"""
tab_file = get_file("cmsearch_114_U2_Yeast_full_shuffled.tbl")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)

24
Tests/test_SearchIO_infernal_tab_index.py
View File

@ -20,16 +20,16 @@ class InfernalTabRawCases(CheckRaw):
def test_infernal_tab_single(self):
"""Test infernal-tab raw string retrieval, cmsearch, single query."""
filename = os.path.join("Infernal", "U2_Yeast-threshold.tbl")
"""Test infernal-tab raw string retrieval, cmsearch, single query (U2_Yeast)."""
filename = os.path.join("Infernal", "cmsearch_114_U2_Yeast.tbl")
raw = """ENA|BK006936|BK006936.2 - U2 RF00004 cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 5.9e-20 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.
"""
self.check_raw(filename, "U2", raw)
def test_infernal_tab_multiple(self):
"""Test infernal-tab raw string retrieval, cmsearch, single query, multiple non-consecutive hits."""
filename = os.path.join("Infernal", "U2_Yeast-shuf.tbl")
"""Test infernal-tab raw string retrieval, cmsearch, single query, multiple non-consecutive hits (U2_Yeast_full_shuffled)."""
filename = os.path.join("Infernal", "cmsearch_114_U2_Yeast_full_shuffled.tbl")
raw = """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 ? -
@ -42,7 +42,7 @@ ENA|BK006948|BK006948.2 - U2 RF00004 cm 1
def test_infernal_tab_single_first(self):
"""Test infernal-tab raw string retrieval, cmsearch, multiple queries, first."""
filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan.tbl")
filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast.tbl")
raw = """U2 RF00004 ENA|BK006935|BK006935.2 - cm 1 193 52929 53083 + no 1 0.44 0.0 13.5 0.91 ? U2 spliceosomal RNA
U2 RF00004 ENA|BK006935|BK006935.2 - cm 1 193 196571 196389 - no 1 0.33 5.3 12.8 1.3 ? U2 spliceosomal RNA
"""
@ -51,7 +51,7 @@ U2 RF00004 ENA|BK006935|BK006935.2 - cm 1
def test_infernal_tab_multiple_middle(self):
"""Test infernal-tab raw string retrieval, cmsearch, multiple queries, middle."""
filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan.tbl")
filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast.tbl")
raw = """U2 RF00004 ENA|BK006936|BK006936.2 - cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.2e-20 ! U2 spliceosomal RNA
"""
self.check_raw(filename, "ENA|BK006936|BK006936.2", raw)
@ -59,7 +59,7 @@ U2 RF00004 ENA|BK006935|BK006935.2 - cm 1
def test_infernal_tab_multiple_last(self):
"""Test infernal-tab raw string retrieval, cmsearch, multiple queries, last."""
filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan.tbl")
filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast.tbl")
raw = """5S_rRNA RF00001 ENA|BK006937|BK006937.2 - cm 1 119 761 644 - no 1 0.41 0.3 14.1 2.4 ? 5S ribosomal RNA
U2 RF00004 ENA|BK006937|BK006937.2 - cm 1 193 229986 229885 - no 1 0.32 0.1 11.1 4.7 ? U2 spliceosomal RNA
"""
@ -68,7 +68,7 @@ U2 RF00004 ENA|BK006937|BK006937.2 - cm 1
def test_infernal_tab_multiple_fmt_2(self):
"""Test infernal-tab raw string retrieval, cmsearch, multiple queries, fmt 2."""
filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan-fmt_2.tbl")
filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast_fmt_2.tbl")
raw = """1 U2 RF00004 ENA|BK006936|BK006936.2 - - cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.2e-20 ! * - - - - - - 193 813184 U2 spliceosomal RNA
"""
self.check_raw(filename, "ENA|BK006936|BK006936.2", raw)
@ -80,25 +80,25 @@ class InfernalTabIndexCases(CheckIndex):
def test_infernal_tab_single(self):
"""Test infernal-tab indexing, cmsearch, single query."""
filename = os.path.join("Infernal", "U2_Yeast-threshold.tbl")
filename = os.path.join("Infernal", "cmsearch_114_U2_Yeast.tbl")
self.check_index(filename, self.fmt)
def test_infernal_tab_single_no_hit(self):
"""Test infernal-tab indexing, cmsearch, single query."""
filename = os.path.join("Infernal", "IRES_Yeast.tbl")
filename = os.path.join("Infernal", "cmsearch_114_IRES_Yeast.tbl")
self.check_index(filename, self.fmt)
def test_infernal_tab_single_multiple_hit(self):
"""Test infernal-tab indexing, cmsearch, single query."""
filename = os.path.join("Infernal", "5S_Yeast.tbl")
filename = os.path.join("Infernal", "cmsearch_114_5S_Yeast.tbl")
self.check_index(filename, self.fmt)
def test_infernal_tab_multiple_multiple_hit(self):
"""Test infernal-tab indexing, cmscan, multiple query."""
filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan.tbl")
filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast.tbl")
self.check_index(filename, self.fmt)

62
Tests/test_SearchIO_infernal_text.py
View File

@ -7,12 +7,14 @@
"""Tests for SearchIO InfernalIO infernal-text parser."""
import os
import unittest
import itertools
from Bio.SearchIO import parse
# test case files are in the Blast directory
TEST_DIR = "Infernal"
FMT = "infernal-text"
@ -32,9 +34,9 @@ class CmscanCases(unittest.TestCase):
"""Test parsing cmsearch output."""
def test_cmscan_mq(self):
def test_cmscan(self):
"""Test parsing infernal-text, cmscan, multiple queries"""
tab_file = get_file("IRES_5S_U2_Yeast-cmscan.txt")
tab_file = get_file("cmscan_115_IRES_5S_U2_Yeast.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -117,8 +119,8 @@ class CmsearchCases(unittest.TestCase):
def test_cmsearch_1q_0m(self):
"""Test parsing infernal-text, cmsearch, single query, no hits"""
text_file = get_file("IRES_Yeast.txt")
"""Test parsing infernal-text, cmsearch, single query, no hits (IRES_Yeast)"""
text_file = get_file("cmsearch_114_IRES_Yeast.txt")
qresults = parse(text_file, FMT)
counter = itertools.count(start=1)
@ -137,9 +139,9 @@ class CmsearchCases(unittest.TestCase):
self.assertEqual(1, count)
def test_cmsearch_1q_1m_1h_1f(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, two fragments"""
tab_file = get_file("U2_Yeast-threshold.txt")
def test_cmsearch_1q_1m_1h(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, multiple fragments (U2_Yeast)"""
tab_file = get_file("cmsearch_114_U2_Yeast.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -217,9 +219,9 @@ class CmsearchCases(unittest.TestCase):
self.assertEqual(1, count)
def test_cmsearch_1q_mm_1h_mf(self):
"""Test parsing infernal-text, cmsearch, one queries, multiple hits, one hsp, multiple fragments"""
tab_file = get_file("U2_Yeast.txt")
def test_cmsearch_1q_mm_1h(self):
"""Test parsing infernal-text, cmsearch, one queries, multiple hits, one hsp, multiple fragments (U2_Yeast_full)"""
tab_file = get_file("cmsearch_114_U2_Yeast_full.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -348,9 +350,9 @@ 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")
def test_cmsearch_1q_mm_1h_shuffled(self):
"""Test parsing infernal-text, cmsearch, one queries, multiple non-consecutive hits, one hsp, multiple fragments (U2_Yeast_full_shuffled)"""
tab_file = get_file("cmsearch_114_U2_Yeast_full_shuffled.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -361,7 +363,7 @@ class CmsearchCases(unittest.TestCase):
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.version, "1.1.4")
self.assertEqual(qresult.target, "BK006936_7-8.fasta")
# first hit (3 hsps at rank 1,3 and 4)
hit = qresult[0]
@ -417,9 +419,9 @@ class CmsearchCases(unittest.TestCase):
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")
def test_cmsearch_1q_mm_mh(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, multiple hsp, one fragment (5S_Yeast)"""
tab_file = get_file("cmsearch_114_5S_Yeast.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -473,8 +475,8 @@ class CmsearchCases(unittest.TestCase):
def test_cmsearch_1q_1m_1h_noali(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, noali"""
tab_file = get_file("U2_Yeast-threshold-noali.txt")
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, noali (U2_Yeast_noali)"""
tab_file = get_file("cmsearch_114_U2_Yeast_noali.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -515,8 +517,8 @@ class CmsearchCases(unittest.TestCase):
def test_cmsearch_1q_1m_mh_noali(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, multiple hsp, noali"""
tab_file = get_file("5S_Yeast-noali.txt")
"""Test parsing infernal-text, cmsearch, one queries, one hit, multiple hsp, noali (5S_Yeast_noali)"""
tab_file = get_file("cmsearch_114_5S_Yeast_noali.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -527,7 +529,7 @@ class CmsearchCases(unittest.TestCase):
self.assertEqual(qresult.accession, "RF00001")
self.assertEqual(qresult.description, "5S ribosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.5")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
hit = qresult[0]
self.assertEqual(6, len(hit))
@ -573,8 +575,8 @@ class CmsearchCases(unittest.TestCase):
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")
"""Test parsing infernal-text, cmsearch, one queries, one hit, multiple hsp, noali, inclusion threshold (U2_Yeast_full_noali)"""
tab_file = get_file("cmsearch_114_U2_Yeast_full_noali.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -585,7 +587,7 @@ class CmsearchCases(unittest.TestCase):
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.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
# first hit
hit = qresult[0]
@ -656,9 +658,9 @@ class CmsearchCases(unittest.TestCase):
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")
def test_cmsearch_1q_1m_1h_hmmonly(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, one fragments, hmmonly (U2_Yeast_hmmonly)"""
tab_file = get_file("cmsearch_114_U2_Yeast_hmmonly.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
@ -669,7 +671,7 @@ class CmsearchCases(unittest.TestCase):
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.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
hit = qresult[0]
self.assertEqual(1, len(hit))
@ -712,7 +714,7 @@ class CmsearchCases(unittest.TestCase):
def test_cmsearch_mq(self):
"""Test parsing infernal-text, cmsearch, multiple queries"""
tab_file = get_file("IRES_5S_U2_Yeast.txt")
tab_file = get_file("cmsearch_114_IRES_5S_U2_Yeast.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)