Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

341 lines (280 sloc) 18.719 kb
# 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
//
"""
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
//
"""
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
//
"""
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)
Jump to Line
Something went wrong with that request. Please try again.