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# 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)
|
