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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
340 lines
18 KiB
Python
340 lines
18 KiB
Python
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Tests for SearchIO hmmer3-text indexing."""
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import unittest
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from search_tests_common import CheckIndex
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from search_tests_common import CheckRaw
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class Hmmer3TextRawCases(CheckRaw):
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fmt = "hmmer3-text"
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def test_hmmer3text_30_multiple_first(self):
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"""Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out)."""
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filename = "Hmmer/text_30_hmmscan_001.out"
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raw = """# hmmscan :: search sequence(s) against a profile database
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# HMMER 3.0 (March 2010); http://hmmer.org/
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# Copyright (C) 2010 Howard Hughes Medical Institute.
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# Freely distributed under the GNU General Public License (GPLv3).
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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# query sequence file: mult.fasta
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# target HMM database: /home/bow/db/hmmer/Pfam-A.hmm
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# output directed to file: hmmer_cases/text_hmmscan_mult.out
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# per-seq hits tabular output: hmmer_cases/tab_hmmscan_mult.out
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# per-dom hits tabular output: hmmer_cases/domtab_hmmscan_mult.out
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Query: random_s00 [L=32]
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Scores for complete sequence (score includes all domains):
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--- full sequence --- --- best 1 domain --- -#dom-
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E-value score bias E-value score bias exp N Model Description
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------- ------ ----- ------- ------ ----- ---- -- -------- -----------
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[No hits detected that satisfy reporting thresholds]
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Domain annotation for each model (and alignments):
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[No targets detected that satisfy reporting thresholds]
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Internal pipeline statistics summary:
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-------------------------------------
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Query sequence(s): 1 (32 residues)
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Target model(s): 13672 (2396357 nodes)
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Passed MSV filter: 338 (0.0247221); expected 273.4 (0.02)
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Passed bias filter: 87 (0.00636337); expected 273.4 (0.02)
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Passed Vit filter: 23 (0.00168227); expected 13.7 (0.001)
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Passed Fwd filter: 14 (0.00102399); expected 0.1 (1e-05)
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Initial search space (Z): 13672 [actual number of targets]
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Domain search space (domZ): 0 [number of targets reported over threshold]
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# CPU time: 0.20u 0.12s 00:00:00.32 Elapsed: 00:00:00.19
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# Mc/sec: 403.60
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//
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"""
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self.check_raw(filename, "random_s00", raw)
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def test_hmmer3text_30_multiple_middle(self):
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"""Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out)."""
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filename = "Hmmer/text_30_hmmscan_001.out"
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raw = """# hmmscan :: search sequence(s) against a profile database
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# HMMER 3.0 (March 2010); http://hmmer.org/
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# Copyright (C) 2010 Howard Hughes Medical Institute.
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# Freely distributed under the GNU General Public License (GPLv3).
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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# query sequence file: mult.fasta
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# target HMM database: /home/bow/db/hmmer/Pfam-A.hmm
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# output directed to file: hmmer_cases/text_hmmscan_mult.out
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# per-seq hits tabular output: hmmer_cases/tab_hmmscan_mult.out
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# per-dom hits tabular output: hmmer_cases/domtab_hmmscan_mult.out
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Query: gi|4885477|ref|NP_005359.1| [L=154]
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Description: myoglobin [Homo sapiens]
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Scores for complete sequence (score includes all domains):
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--- full sequence --- --- best 1 domain --- -#dom-
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E-value score bias E-value score bias exp N Model Description
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------- ------ ----- ------- ------ ----- ---- -- -------- -----------
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6e-21 74.6 0.3 9.2e-21 74.0 0.2 1.3 1 Globin Globin
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Domain annotation for each model (and alignments):
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>> Globin Globin
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ! 74.0 0.2 6.7e-25 9.2e-21 1 107 [. 7 112 .. 7 113 .. 0.97
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Alignments for each domain:
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== domain 1 score: 74.0 bits; conditional E-value: 6.7e-25
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HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHSGGGGGGGCCCTTTT.HHHHHTSCHHHHHHHHHHHHHHHHHHCTTSHHHHHH CS
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Globin 1 qkalvkaswekvkanaeeigaeilkrlfkaypdtkklFkkfgdls.aedlksspkfkahakkvlaaldeavknldnddnlka 81
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+++lv w+kv+a+++ +g+e+l rlfk +p+t ++F kf+ l+ +++k s+++k+h+++vl al+ ++k+ ++ ++a
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gi|4885477|ref|NP_005359.1| 7 EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKsEDEMKASEDLKKHGATVLTALGGILKK---KGHHEA 85
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5789*********************************************************************...6899** PP
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HHHHHHHHHHTT-.--HHHHCCHHHHH CS
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Globin 82 alkklgarHakrg.vdpanfklfgeal 107
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++k l+++Ha+++ ++ ++ + ++e++
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gi|4885477|ref|NP_005359.1| 86 EIKPLAQSHATKHkIPVKYLEFISECI 112
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*********************999998 PP
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Internal pipeline statistics summary:
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-------------------------------------
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Query sequence(s): 1 (154 residues)
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Target model(s): 13672 (2396357 nodes)
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Passed MSV filter: 458 (0.0334991); expected 273.4 (0.02)
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Passed bias filter: 404 (0.0295494); expected 273.4 (0.02)
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Passed Vit filter: 31 (0.00226741); expected 13.7 (0.001)
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Passed Fwd filter: 1 (7.31422e-05); expected 0.1 (1e-05)
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Initial search space (Z): 13672 [actual number of targets]
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Domain search space (domZ): 1 [number of targets reported over threshold]
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# CPU time: 0.33u 0.16s 00:00:00.49 Elapsed: 00:00:00.21
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# Mc/sec: 1757.33
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//
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""" # noqa : W291
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self.check_raw(filename, "gi|4885477|ref|NP_005359.1|", raw)
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def test_hmmer3text_30_multiple_last(self):
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"""Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out)."""
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filename = "Hmmer/text_30_hmmscan_001.out"
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raw = """# hmmscan :: search sequence(s) against a profile database
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# HMMER 3.0 (March 2010); http://hmmer.org/
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# Copyright (C) 2010 Howard Hughes Medical Institute.
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# Freely distributed under the GNU General Public License (GPLv3).
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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# query sequence file: mult.fasta
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# target HMM database: /home/bow/db/hmmer/Pfam-A.hmm
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# output directed to file: hmmer_cases/text_hmmscan_mult.out
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# per-seq hits tabular output: hmmer_cases/tab_hmmscan_mult.out
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# per-dom hits tabular output: hmmer_cases/domtab_hmmscan_mult.out
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Query: gi|125490392|ref|NP_038661.2| [L=352]
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Description: POU domain, class 5, transcription factor 1 isoform 1 [Mus musculus]
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Scores for complete sequence (score includes all domains):
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--- full sequence --- --- best 1 domain --- -#dom-
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E-value score bias E-value score bias exp N Model Description
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------- ------ ----- ------- ------ ----- ---- -- -------- -----------
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7e-37 124.8 0.5 1.4e-36 123.9 0.3 1.5 1 Pou Pou domain - N-terminal to homeobox domain
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2.1e-18 65.5 1.1 4.1e-18 64.6 0.7 1.5 1 Homeobox Homeobox domain
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------ inclusion threshold ------
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0.012 15.6 0.0 0.16 12.0 0.0 2.2 2 HTH_31 Helix-turn-helix domain
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0.039 13.5 0.0 0.095 12.3 0.0 1.6 1 Homeobox_KN Homeobox KN domain
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0.14 10.5 0.1 0.26 9.6 0.1 1.4 1 DUF521 Protein of unknown function (DUF521)
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Domain annotation for each model (and alignments):
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>> Pou Pou domain - N-terminal to homeobox domain
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ! 123.9 0.3 5e-40 1.4e-36 3 75 .] 133 205 .. 131 205 .. 0.97
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Alignments for each domain:
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== domain 1 score: 123.9 bits; conditional E-value: 5e-40
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Pou 3 eldleeleefakefkqrrikLgltqadvgsalgalyGkefsqttIcrFEalqLslknmckLkpllekWLeeae 75
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++ ++ele+fak +kq+ri+Lg+tqadvg +lg+l+Gk+fsqttIcrFEalqLslknmckL+pllekW+eea+
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gi|125490392|ref|NP_038661.2| 133 KALQKELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSLKNMCKLRPLLEKWVEEAD 205
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67899******************************************************************96 PP
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>> Homeobox Homeobox domain
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ! 64.6 0.7 1.5e-21 4.1e-18 1 57 [] 224 280 .. 224 280 .. 0.98
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Alignments for each domain:
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== domain 1 score: 64.6 bits; conditional E-value: 1.5e-21
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SS--SS--HHHHHHHHHHCCTSSS--HHHHHHHHHH----HHHHHHHHHHHHHHHHH CS
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Homeobox 1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57
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+rkRt++++ Le +F k+++ps ++++++A++lgL++++V+vWF+NrR+k k+
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gi|125490392|ref|NP_038661.2| 224 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 280
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79****************************************************997 PP
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>> HTH_31 Helix-turn-helix domain
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ? 12.0 0.0 5.7e-05 0.16 1 35 [. 141 181 .. 141 184 .. 0.96
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2 ? 0.8 0.0 0.19 5.2e+02 39 62 .. 245 268 .. 243 270 .. 0.86
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Alignments for each domain:
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== domain 1 score: 12.0 bits; conditional E-value: 5.7e-05
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HTH_31 1 aLGarLralReraGLtqeevAerlg......vSastlsrlE 35
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+++ +L++ R + G tq++v+ lg +S++t++r E
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gi|125490392|ref|NP_038661.2| 141 QFAKLLKQKRITLGYTQADVGLTLGvlfgkvFSQTTICRFE 181
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6999***********************************99 PP
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== domain 2 score: 0.8 bits; conditional E-value: 0.19
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HTH_31 39 rgrpsaavlaalaralgldpaera 62
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++ ps+++++ +a+ lgl+ + ++
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gi|125490392|ref|NP_038661.2| 245 CPKPSLQQITHIANQLGLEKDVVR 268
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678**************9988765 PP
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>> Homeobox_KN Homeobox KN domain
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ? 12.3 0.0 3.5e-05 0.095 7 39 .. 244 276 .. 241 277 .. 0.91
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Alignments for each domain:
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== domain 1 score: 12.3 bits; conditional E-value: 3.5e-05
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Homeobox_KN 7 hnPYPskevkeelakqTglsrkqidnWFiNaRr 39
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+ P Ps +++ +a+q gl + + WF N R
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gi|125490392|ref|NP_038661.2| 244 KCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 276
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56779*************************996 PP
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>> DUF521 Protein of unknown function (DUF521)
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ? 9.6 0.1 9.4e-05 0.26 273 334 .. 221 280 .. 197 294 .. 0.77
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Alignments for each domain:
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== domain 1 score: 9.6 bits; conditional E-value: 9.4e-05
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DUF521 273 adlaavleelnkakkeevdlvvlGcPhlsleeleelaellkgrkkkvsvelvvttsravlsk 334
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+ +++ + +++++ +++ ++l cP sl++++++a++l +k v+++ + r+ ++
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gi|125490392|ref|NP_038661.2| 221 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEK--DVVRVWFCNRRQKGKR 280
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345666667778888899************************99..9999999988876554 PP
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Internal pipeline statistics summary:
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-------------------------------------
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Query sequence(s): 1 (352 residues)
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Target model(s): 13672 (2396357 nodes)
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Passed MSV filter: 603 (0.0441047); expected 273.4 (0.02)
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Passed bias filter: 465 (0.0340111); expected 273.4 (0.02)
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Passed Vit filter: 44 (0.00321826); expected 13.7 (0.001)
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Passed Fwd filter: 5 (0.000365711); expected 0.1 (1e-05)
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Initial search space (Z): 13672 [actual number of targets]
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Domain search space (domZ): 5 [number of targets reported over threshold]
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# CPU time: 0.51u 0.15s 00:00:00.66 Elapsed: 00:00:00.23
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# Mc/sec: 3667.47
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//
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""" # noqa : W291
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self.check_raw(filename, "gi|125490392|ref|NP_038661.2|", raw)
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def test_hmmer3text_30_single(self):
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"""Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out)."""
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filename = "Hmmer/text_30_hmmscan_003.out"
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raw = """# hmmscan :: search sequence(s) against a profile database
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# HMMER 3.0 (March 2010); http://hmmer.org/
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# Copyright (C) 2010 Howard Hughes Medical Institute.
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# Freely distributed under the GNU General Public License (GPLv3).
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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# query sequence file: s01.fasta
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# target HMM database: /home/bow/db/hmmer/Pfam-A.hmm
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# output directed to file: hmmer_cases/text_hmmscan_s01.out
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# per-seq hits tabular output: hmmer_cases/tab_hmmscan_s01.out
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# per-dom hits tabular output: hmmer_cases/domtab_hmmscan_s01.out
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# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Query: gi|4885477|ref|NP_005359.1| [L=154]
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Description: myoglobin [Homo sapiens]
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Scores for complete sequence (score includes all domains):
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--- full sequence --- --- best 1 domain --- -#dom-
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E-value score bias E-value score bias exp N Model Description
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------- ------ ----- ------- ------ ----- ---- -- -------- -----------
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6e-21 74.6 0.3 9.2e-21 74.0 0.2 1.3 1 Globin Globin
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Domain annotation for each model (and alignments):
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>> Globin Globin
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# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
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--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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1 ! 74.0 0.2 6.7e-25 9.2e-21 1 107 [. 7 112 .. 7 113 .. 0.97
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Alignments for each domain:
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== domain 1 score: 74.0 bits; conditional E-value: 6.7e-25
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HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHSGGGGGGGCCCTTTT.HHHHHTSCHHHHHHHHHHHHHHHHHHCTTSHHHHHH CS
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Globin 1 qkalvkaswekvkanaeeigaeilkrlfkaypdtkklFkkfgdls.aedlksspkfkahakkvlaaldeavknldnddnlka 81
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+++lv w+kv+a+++ +g+e+l rlfk +p+t ++F kf+ l+ +++k s+++k+h+++vl al+ ++k+ ++ ++a
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gi|4885477|ref|NP_005359.1| 7 EWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKsEDEMKASEDLKKHGATVLTALGGILKK---KGHHEA 85
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5789*********************************************************************...6899** PP
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HHHHHHHHHHTT-.--HHHHCCHHHHH CS
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Globin 82 alkklgarHakrg.vdpanfklfgeal 107
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++k l+++Ha+++ ++ ++ + ++e++
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gi|4885477|ref|NP_005359.1| 86 EIKPLAQSHATKHkIPVKYLEFISECI 112
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*********************999998 PP
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Internal pipeline statistics summary:
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-------------------------------------
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Query sequence(s): 1 (154 residues)
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Target model(s): 13672 (2396357 nodes)
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Passed MSV filter: 458 (0.0334991); expected 273.4 (0.02)
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Passed bias filter: 404 (0.0295494); expected 273.4 (0.02)
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Passed Vit filter: 31 (0.00226741); expected 13.7 (0.001)
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Passed Fwd filter: 1 (7.31422e-05); expected 0.1 (1e-05)
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Initial search space (Z): 13672 [actual number of targets]
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Domain search space (domZ): 1 [number of targets reported over threshold]
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# CPU time: 0.28u 0.17s 00:00:00.45 Elapsed: 00:00:00.21
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# Mc/sec: 1757.33
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//
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""" # noqa : W291
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self.check_raw(filename, "gi|4885477|ref|NP_005359.1|", raw)
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class Hmmer3TextIndexCases(CheckIndex):
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fmt = "hmmer3-text"
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def test_hmmertext_text_30_hmmscan_001(self):
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"""Test hmmer3-text indexing, HMMER 3.0, multiple queries."""
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filename = "Hmmer/text_30_hmmscan_001.out"
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self.check_index(filename, self.fmt)
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def test_hmmertext_text_30_hmmscan_002(self):
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"""Test hmmer3-text indexing, HMMER 3.0, single query, no hits."""
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filename = "Hmmer/text_30_hmmscan_002.out"
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self.check_index(filename, self.fmt)
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def test_hmmertext_text_30_hmmscan_006(self):
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"""Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits."""
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filename = "Hmmer/text_30_hmmscan_006.out"
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self.check_index(filename, self.fmt)
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def test_hmmertext_text_30_hmmscan_007(self):
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"""Test hmmer3-text indexing, HMMER 3.0, single query, no alignments."""
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filename = "Hmmer/text_30_hmmscan_007.out"
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self.check_index(filename, self.fmt)
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def test_hmmertext_text_30_hmmscan_008(self):
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"""Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width."""
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filename = "Hmmer/text_30_hmmscan_008.out"
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self.check_index(filename, self.fmt)
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def test_hmmertext_text_30_hmmsearch_005(self):
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"""Test hmmer3-text indexing, HMMER 3.0, multiple queries."""
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filename = "Hmmer/text_30_hmmsearch_005.out"
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self.check_index(filename, self.fmt)
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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