# Copyright 2012 by Wibowo Arindrarto. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for SearchIO hmmer3-text indexing.""" import unittest from search_tests_common import CheckRaw, CheckIndex class Hmmer3TextRawCases(CheckRaw): fmt = 'hmmer3-text' def test_hmmer3text_30_multiple_first(self): """Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out)""" filename = 'Hmmer/text_30_hmmscan_001.out' raw = """# hmmscan :: search sequence(s) against a profile database # HMMER 3.0 (March 2010); http://hmmer.org/ # Copyright (C) 2010 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: mult.fasta # target HMM database: /home/bow/db/hmmer/Pfam-A.hmm # output directed to file: hmmer_cases/text_hmmscan_mult.out # per-seq hits tabular output: hmmer_cases/tab_hmmscan_mult.out # per-dom hits tabular output: hmmer_cases/domtab_hmmscan_mult.out # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: random_s00 [L=32] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- [No hits detected that satisfy reporting thresholds] Domain annotation for each model (and alignments): [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (32 residues) Target model(s): 13672 (2396357 nodes) Passed MSV filter: 338 (0.0247221); expected 273.4 (0.02) Passed bias filter: 87 (0.00636337); expected 273.4 (0.02) Passed Vit filter: 23 (0.00168227); expected 13.7 (0.001) Passed Fwd filter: 14 (0.00102399); expected 0.1 (1e-05) Initial search space (Z): 13672 [actual number of targets] Domain search space (domZ): 0 [number of targets reported over threshold] # CPU time: 0.20u 0.12s 00:00:00.32 Elapsed: 00:00:00.19 # Mc/sec: 403.60 // """ self.check_raw(filename, "random_s00", raw) def test_hmmer3text_30_multiple_middle(self): """Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out)""" filename = 'Hmmer/text_30_hmmscan_001.out' raw = """# hmmscan :: search sequence(s) against a profile database # HMMER 3.0 (March 2010); http://hmmer.org/ # Copyright (C) 2010 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: mult.fasta # target HMM database: /home/bow/db/hmmer/Pfam-A.hmm # output directed to file: hmmer_cases/text_hmmscan_mult.out # per-seq hits tabular output: hmmer_cases/tab_hmmscan_mult.out # per-dom hits tabular output: hmmer_cases/domtab_hmmscan_mult.out # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|4885477|ref|NP_005359.1| [L=154] Description: myoglobin [Homo sapiens] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-21 74.6 0.3 9.2e-21 74.0 0.2 1.3 1 Globin Globin Domain annotation for each model (and alignments): >> Globin Globin # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 74.0 0.2 6.7e-25 9.2e-21 1 107 [. 7 112 .. 7 113 .. 0.97 Alignments for each domain: == domain 1 score: 74.0 bits; conditional E-value: 6.7e-25 HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHSGGGGGGGCCCTTTT.HHHHHTSCHHHHHHHHHHHHHHHHHHCTTSHHHHHH CS Globin 1 qkalvkaswekvkanaeeigaeilkrlfkaypdtkklFkkfgdls.aedlksspkfkahakkvlaaldeavknldnddnlka 81 +++lv w+kv+a+++ +g+e+l rlfk +p+t ++F kf+ l+ +++k s+++k+h+++vl al+ ++k+ ++ ++a gi|4885477|ref|NP_005359.1| 7 EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKsEDEMKASEDLKKHGATVLTALGGILKK---KGHHEA 85 5789*********************************************************************...6899** PP HHHHHHHHHHTT-.--HHHHCCHHHHH CS Globin 82 alkklgarHakrg.vdpanfklfgeal 107 ++k l+++Ha+++ ++ ++ + ++e++ gi|4885477|ref|NP_005359.1| 86 EIKPLAQSHATKHkIPVKYLEFISECI 112 *********************999998 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (154 residues) Target model(s): 13672 (2396357 nodes) Passed MSV filter: 458 (0.0334991); expected 273.4 (0.02) Passed bias filter: 404 (0.0295494); expected 273.4 (0.02) Passed Vit filter: 31 (0.00226741); expected 13.7 (0.001) Passed Fwd filter: 1 (7.31422e-05); expected 0.1 (1e-05) Initial search space (Z): 13672 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.33u 0.16s 00:00:00.49 Elapsed: 00:00:00.21 # Mc/sec: 1757.33 // """ # noqa for pep8 W291 trailing whitespace self.check_raw(filename, "gi|4885477|ref|NP_005359.1|", raw) def test_hmmer3text_30_multiple_last(self): """Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out)""" filename = 'Hmmer/text_30_hmmscan_001.out' raw = """# hmmscan :: search sequence(s) against a profile database # HMMER 3.0 (March 2010); http://hmmer.org/ # Copyright (C) 2010 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: mult.fasta # target HMM database: /home/bow/db/hmmer/Pfam-A.hmm # output directed to file: hmmer_cases/text_hmmscan_mult.out # per-seq hits tabular output: hmmer_cases/tab_hmmscan_mult.out # per-dom hits tabular output: hmmer_cases/domtab_hmmscan_mult.out # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|125490392|ref|NP_038661.2| [L=352] Description: POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-37 124.8 0.5 1.4e-36 123.9 0.3 1.5 1 Pou Pou domain - N-terminal to homeobox domain 2.1e-18 65.5 1.1 4.1e-18 64.6 0.7 1.5 1 Homeobox Homeobox domain ------ inclusion threshold ------ 0.012 15.6 0.0 0.16 12.0 0.0 2.2 2 HTH_31 Helix-turn-helix domain 0.039 13.5 0.0 0.095 12.3 0.0 1.6 1 Homeobox_KN Homeobox KN domain 0.14 10.5 0.1 0.26 9.6 0.1 1.4 1 DUF521 Protein of unknown function (DUF521) Domain annotation for each model (and alignments): >> Pou Pou domain - N-terminal to homeobox domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 123.9 0.3 5e-40 1.4e-36 3 75 .] 133 205 .. 131 205 .. 0.97 Alignments for each domain: == domain 1 score: 123.9 bits; conditional E-value: 5e-40 Pou 3 eldleeleefakefkqrrikLgltqadvgsalgalyGkefsqttIcrFEalqLslknmckLkpllekWLeeae 75 ++ ++ele+fak +kq+ri+Lg+tqadvg +lg+l+Gk+fsqttIcrFEalqLslknmckL+pllekW+eea+ gi|125490392|ref|NP_038661.2| 133 KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSLKNMCKLRPLLEKWVEEAD 205 67899******************************************************************96 PP >> Homeobox Homeobox domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 64.6 0.7 1.5e-21 4.1e-18 1 57 [] 224 280 .. 224 280 .. 0.98 Alignments for each domain: == domain 1 score: 64.6 bits; conditional E-value: 1.5e-21 SS--SS--HHHHHHHHHHCCTSSS--HHHHHHHHHH----HHHHHHHHHHHHHHHHH CS Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57 +rkRt++++ Le +F k+++ps ++++++A++lgL++++V+vWF+NrR+k k+ gi|125490392|ref|NP_038661.2| 224 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 280 79****************************************************997 PP >> HTH_31 Helix-turn-helix domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.0 0.0 5.7e-05 0.16 1 35 [. 141 181 .. 141 184 .. 0.96 2 ? 0.8 0.0 0.19 5.2e+02 39 62 .. 245 268 .. 243 270 .. 0.86 Alignments for each domain: == domain 1 score: 12.0 bits; conditional E-value: 5.7e-05 HTH_31 1 aLGarLralReraGLtqeevAerlg......vSastlsrlE 35 +++ +L++ R + G tq++v+ lg +S++t++r E gi|125490392|ref|NP_038661.2| 141 QFAKLLKQKRITLGYTQADVGLTLGvlfgkvFSQTTICRFE 181 6999***********************************99 PP == domain 2 score: 0.8 bits; conditional E-value: 0.19 HTH_31 39 rgrpsaavlaalaralgldpaera 62 ++ ps+++++ +a+ lgl+ + ++ gi|125490392|ref|NP_038661.2| 245 CPKPSLQQITHIANQLGLEKDVVR 268 678**************9988765 PP >> Homeobox_KN Homeobox KN domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 12.3 0.0 3.5e-05 0.095 7 39 .. 244 276 .. 241 277 .. 0.91 Alignments for each domain: == domain 1 score: 12.3 bits; conditional E-value: 3.5e-05 Homeobox_KN 7 hnPYPskevkeelakqTglsrkqidnWFiNaRr 39 + P Ps +++ +a+q gl + + WF N R gi|125490392|ref|NP_038661.2| 244 KCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 276 56779*************************996 PP >> DUF521 Protein of unknown function (DUF521) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 9.6 0.1 9.4e-05 0.26 273 334 .. 221 280 .. 197 294 .. 0.77 Alignments for each domain: == domain 1 score: 9.6 bits; conditional E-value: 9.4e-05 DUF521 273 adlaavleelnkakkeevdlvvlGcPhlsleeleelaellkgrkkkvsvelvvttsravlsk 334 + +++ + +++++ +++ ++l cP sl++++++a++l +k v+++ + r+ ++ gi|125490392|ref|NP_038661.2| 221 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEK--DVVRVWFCNRRQKGKR 280 345666667778888899************************99..9999999988876554 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (352 residues) Target model(s): 13672 (2396357 nodes) Passed MSV filter: 603 (0.0441047); expected 273.4 (0.02) Passed bias filter: 465 (0.0340111); expected 273.4 (0.02) Passed Vit filter: 44 (0.00321826); expected 13.7 (0.001) Passed Fwd filter: 5 (0.000365711); expected 0.1 (1e-05) Initial search space (Z): 13672 [actual number of targets] Domain search space (domZ): 5 [number of targets reported over threshold] # CPU time: 0.51u 0.15s 00:00:00.66 Elapsed: 00:00:00.23 # Mc/sec: 3667.47 // """ # noqa for pep8 W291 trailing whitespace self.check_raw(filename, "gi|125490392|ref|NP_038661.2|", raw) def test_hmmer3text_30_single(self): """Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out)""" filename = 'Hmmer/text_30_hmmscan_003.out' raw = """# hmmscan :: search sequence(s) against a profile database # HMMER 3.0 (March 2010); http://hmmer.org/ # Copyright (C) 2010 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: s01.fasta # target HMM database: /home/bow/db/hmmer/Pfam-A.hmm # output directed to file: hmmer_cases/text_hmmscan_s01.out # per-seq hits tabular output: hmmer_cases/tab_hmmscan_s01.out # per-dom hits tabular output: hmmer_cases/domtab_hmmscan_s01.out # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|4885477|ref|NP_005359.1| [L=154] Description: myoglobin [Homo sapiens] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-21 74.6 0.3 9.2e-21 74.0 0.2 1.3 1 Globin Globin Domain annotation for each model (and alignments): >> Globin Globin # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 74.0 0.2 6.7e-25 9.2e-21 1 107 [. 7 112 .. 7 113 .. 0.97 Alignments for each domain: == domain 1 score: 74.0 bits; conditional E-value: 6.7e-25 HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHSGGGGGGGCCCTTTT.HHHHHTSCHHHHHHHHHHHHHHHHHHCTTSHHHHHH CS Globin 1 qkalvkaswekvkanaeeigaeilkrlfkaypdtkklFkkfgdls.aedlksspkfkahakkvlaaldeavknldnddnlka 81 +++lv w+kv+a+++ +g+e+l rlfk +p+t ++F kf+ l+ +++k s+++k+h+++vl al+ ++k+ ++ ++a gi|4885477|ref|NP_005359.1| 7 EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKsEDEMKASEDLKKHGATVLTALGGILKK---KGHHEA 85 5789*********************************************************************...6899** PP HHHHHHHHHHTT-.--HHHHCCHHHHH CS Globin 82 alkklgarHakrg.vdpanfklfgeal 107 ++k l+++Ha+++ ++ ++ + ++e++ gi|4885477|ref|NP_005359.1| 86 EIKPLAQSHATKHkIPVKYLEFISECI 112 *********************999998 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (154 residues) Target model(s): 13672 (2396357 nodes) Passed MSV filter: 458 (0.0334991); expected 273.4 (0.02) Passed bias filter: 404 (0.0295494); expected 273.4 (0.02) Passed Vit filter: 31 (0.00226741); expected 13.7 (0.001) Passed Fwd filter: 1 (7.31422e-05); expected 0.1 (1e-05) Initial search space (Z): 13672 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.28u 0.17s 00:00:00.45 Elapsed: 00:00:00.21 # Mc/sec: 1757.33 // """ # noqa for pep8 W291 trailing whitespace self.check_raw(filename, "gi|4885477|ref|NP_005359.1|", raw) class Hmmer3TextIndexCases(CheckIndex): fmt = 'hmmer3-text' def test_hmmertext_text_30_hmmscan_001(self): """Test hmmer3-text indexing, HMMER 3.0, multiple queries""" filename = 'Hmmer/text_30_hmmscan_001.out' self.check_index(filename, self.fmt) def test_hmmertext_text_30_hmmscan_002(self): """Test hmmer3-text indexing, HMMER 3.0, single query, no hits""" filename = 'Hmmer/text_30_hmmscan_002.out' self.check_index(filename, self.fmt) def test_hmmertext_text_30_hmmscan_006(self): """Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits""" filename = 'Hmmer/text_30_hmmscan_006.out' self.check_index(filename, self.fmt) def test_hmmertext_text_30_hmmscan_007(self): """Test hmmer3-text indexing, HMMER 3.0, single query, no alignments""" filename = 'Hmmer/text_30_hmmscan_007.out' self.check_index(filename, self.fmt) def test_hmmertext_text_30_hmmscan_008(self): """Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width""" filename = 'Hmmer/text_30_hmmscan_008.out' self.check_index(filename, self.fmt) def test_hmmertext_text_30_hmmsearch_005(self): """Test hmmer3-text indexing, HMMER 3.0, multiple queries""" filename = 'Hmmer/text_30_hmmsearch_005.out' self.check_index(filename, self.fmt) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)