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