# Copyright 2024 by Samuel Prince. All rights reserved. # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Tests for SearchIO InfernalIO infernal-text indexing""" import os import unittest from search_tests_common import CheckIndex from search_tests_common import CheckRaw class InfernalTabRawCases(CheckRaw): fmt = "infernal-text" def test_infernal_text_1q(self): """Test infernal-text raw string retrieval, cmsearch, one query (U2_Yeast).""" filename = os.path.join("Infernal", "cmsearch_114_U2_Yeast.txt") raw = """# 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 // """ self.check_raw(filename, "U2", raw) def test_infernal_text_mq_first(self): """Test infernal-text raw string retrieval, cmsearch, multiple queries, first (IRES_5S_U2_Yeast).""" filename = os.path.join("Infernal", "cmsearch_114_IRES_5S_U2_Yeast.txt") raw = """# 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 // """ self.check_raw(filename, "IRES_HCV", raw) def test_infernal_text_mq_middle(self): """Test infernal-text raw string retrieval, cmsearch, multiple queries, middle (IRES_5S_U2_Yeast).""" filename = os.path.join("Infernal", "cmsearch_114_IRES_5S_U2_Yeast.txt") raw = """# 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: 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 // """ self.check_raw(filename, "5S_rRNA", raw) def test_infernal_text_mq_last(self): """Test infernal-text raw string retrieval, cmsearch, multiple queries, last (IRES_5S_U2_Yeast).""" filename = os.path.join("Infernal", "cmsearch_114_IRES_5S_U2_Yeast.txt") raw = """# 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: 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 // """ self.check_raw(filename, "U2", raw) class Hmmer3TextIndexCases(CheckIndex): fmt = "infernal-text" def test_infernal_text_1q_0m(self): """Test infernal-text indexing, cmsearch, one queries, no hits""" filename = os.path.join("Infernal", "cmsearch_114_IRES_Yeast.txt") self.check_index(filename, self.fmt) def test_infernal_text_1q_mm(self): """Test infernal-text indexing, cmsearch, one queries, multiple hits""" filename = os.path.join("Infernal", "cmsearch_114_5S_Yeast.txt") self.check_index(filename, self.fmt) def test_infernal_text_mq(self): """Test infernal-text indexing, cmsearch, multiple queries""" filename = os.path.join("Infernal", "cmsearch_114_IRES_5S_U2_Yeast.txt") self.check_index(filename, self.fmt) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)