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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-tab indexing."""
import os
import unittest
from search_tests_common import CheckRaw, CheckIndex
class Hmmer3TabRawCases(CheckRaw):
fmt = 'hmmer3-tab'
def test_hmmer3tab_30_multiple_first(self):
"""Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out)"""
filename = os.path.join('Hmmer', 'tab_30_hmmscan_001.out')
raw = """Globin PF00042.17 gi|4885477|ref|NP_005359.1| - 6e-21 74.6 0.3 9.2e-21 74.0 0.2 1.3 1 0 0 1 1 1 1 Globin
"""
self.check_raw(filename, "gi|4885477|ref|NP_005359.1|", raw)
def test_hmmer3tab_30_multiple_middle(self):
"""Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out)"""
filename = os.path.join('Hmmer', 'tab_30_hmmscan_001.out')
raw = """Ig_3 PF13927.1 gi|126362951:116-221 - 1.4e-09 38.2 0.4 2.1e-09 37.6 0.3 1.3 1 0 0 1 1 1 1 Immunoglobulin domain
Ig_2 PF13895.1 gi|126362951:116-221 - 3.5e-05 23.7 0.1 4.3e-05 23.4 0.1 1.1 1 0 0 1 1 1 1 Immunoglobulin domain
"""
self.check_raw(filename, "gi|126362951:116-221", raw)
def test_hmmer3tab_30_multiple_last(self):
"""Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out)"""
filename = os.path.join('Hmmer', 'tab_30_hmmscan_001.out')
raw = """Pou PF00157.12 gi|125490392|ref|NP_038661.2| - 7e-37 124.8 0.5 1.4e-36 123.9 0.3 1.5 1 0 0 1 1 1 1 Pou domain - N-terminal to homeobox domain
Homeobox PF00046.24 gi|125490392|ref|NP_038661.2| - 2.1e-18 65.5 1.1 4.1e-18 64.6 0.7 1.5 1 0 0 1 1 1 1 Homeobox domain
HTH_31 PF13560.1 gi|125490392|ref|NP_038661.2| - 0.012 15.6 0.0 0.16 12.0 0.0 2.2 2 0 0 2 2 2 0 Helix-turn-helix domain
Homeobox_KN PF05920.6 gi|125490392|ref|NP_038661.2| - 0.039 13.5 0.0 0.095 12.3 0.0 1.6 1 0 0 1 1 1 0 Homeobox KN domain
DUF521 PF04412.8 gi|125490392|ref|NP_038661.2| - 0.14 10.5 0.1 0.26 9.6 0.1 1.4 1 0 0 1 1 1 0 Protein of unknown function (DUF521)
"""
self.check_raw(filename, "gi|125490392|ref|NP_038661.2|", raw)
def test_hmmer3tab_30_single(self):
"""Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out)"""
filename = os.path.join('Hmmer', 'tab_30_hmmscan_004.out')
raw = """Ig_3 PF13927.1 gi|126362951:116-221 - 1.4e-09 38.2 0.4 2.1e-09 37.6 0.3 1.3 1 0 0 1 1 1 1 Immunoglobulin domain
Ig_2 PF13895.1 gi|126362951:116-221 - 3.5e-05 23.7 0.1 4.3e-05 23.4 0.1 1.1 1 0 0 1 1 1 1 Immunoglobulin domain
"""
self.check_raw(filename, "gi|126362951:116-221", raw)
class Hmmer3TabIndexCases(CheckIndex):
fmt = 'hmmer3-tab'
def test_hmmer3tab_30_hmmscan_001(self):
"""Test hmmer3-tab indexing, HMMER 3.0, multiple queries"""
filename = os.path.join('Hmmer', 'tab_30_hmmscan_001.out')
self.check_index(filename, self.fmt)
def test_hmmer3tab_30_hmmscan_002(self):
"""Test hmmer3-tab indexing, HMMER 3.0, single query, no hits"""
filename = os.path.join('Hmmer', 'tab_30_hmmscan_002.out')
self.check_index(filename, self.fmt)
def test_hmmer3tab_30_hmmscan_003(self):
"""Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits"""
filename = os.path.join('Hmmer', 'tab_30_hmmscan_003.out')
self.check_index(filename, self.fmt)
def test_hmmer3tab_30_hmmscan_004(self):
"""Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments"""
filename = os.path.join('Hmmer', 'tab_30_hmmscan_004.out')
self.check_index(filename, self.fmt)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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