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# 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 InterproscanIO parsers."""
import os
import sys
import unittest
import warnings
from Bio import BiopythonParserWarning
from Bio.SearchIO import parse
# test case files are in the Blast directory
TEST_DIR = "InterProScan"
FMT = "interproscan-xml"
def get_file(filename):
"""Return the path of a test file."""
return os.path.join(TEST_DIR, filename)
class InterproscanXmlCases(unittest.TestCase):
def test_xml_001(self):
xml_file = get_file("test_001.xml")
qresults = parse(xml_file, FMT)
counter = 0
# test each qresult's attributes
qresult = next(qresults)
counter += 1
self.assertEqual("5.26-65.0", qresult.version)
# test parsed values of qresult
self.assertEqual("AT5G23090.4", qresult.id)
self.assertEqual(
"pacid=19665592 transcript=AT5G23090.4 locus=AT5G23090 "
"ID=AT5G23090.4.TAIR10 annot-version=TAIR10",
qresult.description,
)
self.assertEqual(4, len(qresult))
hit = qresult[0]
self.assertEqual("PF00808", hit.id)
self.assertEqual(
"Histone-like transcription factor (CBF/NF-Y) and archaeal histone",
hit.description,
)
self.assertEqual("PFAM", hit.attributes["Target"])
self.assertEqual("31.0", hit.attributes["Target version"])
self.assertEqual("hmmer3", hit.attributes["Hit type"])
self.assertEqual(2, len(hit))
hsp = hit.hsps[0]
self.assertEqual(76.7, hsp.bitscore)
self.assertEqual(1.1e-21, hsp.evalue)
self.assertEqual(13, hsp.query_start)
self.assertEqual(79, hsp.query_end)
self.assertEqual(0, hsp.hit_start)
self.assertEqual(65, hsp.hit_end)
self.assertEqual(66, hsp.aln_span)
self.assertEqual(
"MDPMDIVGKSKEDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEH"
"VLKALQVLGFGEYIEEVYAAYEQHKYETMDTQRSVKWNPGAQMTEEEAAAEQQRMFAEARARMNGGVSVPQPEH"
"PETDQRSPQS",
str(hsp.query.seq),
)
# parse last hit
hit = qresult[-1]
self.assertEqual("SSF47113", hit.id)
self.assertEqual(1, len(hit))
self.assertEqual("IPR:IPR009072", hit.dbxrefs[0])
self.assertEqual("GO:0046982", hit.dbxrefs[1])
hsp = hit.hsps[0]
self.assertEqual(11, hsp.query_start)
self.assertEqual(141, hsp.query_end)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
