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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
223 lines
9.2 KiB
Python
223 lines
9.2 KiB
Python
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
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# 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 writing."""
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import os
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import unittest
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from search_tests_common import SearchTestBaseClass
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from Bio import SearchIO
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class WriteCases(SearchTestBaseClass):
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def tearDown(self):
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if os.path.exists(self.out):
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os.remove(self.out)
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def parse_write_and_compare(
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self, source_file, source_format, out_file, out_format, **kwargs
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):
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"""Compare parsed QueryResults after they have been written to a file."""
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source_qresults = list(SearchIO.parse(source_file, source_format, **kwargs))
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SearchIO.write(source_qresults, out_file, out_format, **kwargs)
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out_qresults = list(SearchIO.parse(out_file, out_format, **kwargs))
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for source, out in zip(source_qresults, out_qresults):
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self.compare_search_obj(source, out)
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def read_write_and_compare(
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self, source_file, source_format, out_file, out_format, **kwargs
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):
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"""Compare read QueryResults after it has been written to a file."""
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source_qresult = SearchIO.read(source_file, source_format, **kwargs)
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SearchIO.write(source_qresult, out_file, out_format, **kwargs)
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out_qresult = SearchIO.read(out_file, out_format, **kwargs)
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self.compare_search_obj(source_qresult, out_qresult)
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class BlastXmlWriteCases(WriteCases):
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fmt = "blast-xml"
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out = os.path.join("Blast", "test_write.xml")
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def test_write_single_from_blastxml(self):
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"""Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml)."""
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source = os.path.join("Blast", "xml_2226_blastp_004.xml")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
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self.read_write_and_compare(source, self.fmt, self.out, self.fmt)
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def test_write_multiple_from_blastxml(self):
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"""Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml)."""
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source = os.path.join("Blast", "xml_2226_blastp_001.xml")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
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class BlastTabWriteCases(WriteCases):
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fmt = "blast-tab"
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out = os.path.join("Blast", "test_write.txt")
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def test_write_single_from_blasttab(self):
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"""Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt)."""
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source = os.path.join("Blast", "tab_2226_tblastn_004.txt")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
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self.read_write_and_compare(source, self.fmt, self.out, self.fmt)
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def test_write_multiple_from_blasttab(self):
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"""Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt)."""
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source = os.path.join("Blast", "tab_2226_tblastn_001.txt")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
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def test_write_single_from_blasttabc(self):
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"""Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt)."""
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source = os.path.join("Blast", "tab_2226_tblastn_008.txt")
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self.parse_write_and_compare(
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source, self.fmt, self.out, self.fmt, comments=True
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)
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self.read_write_and_compare(source, self.fmt, self.out, self.fmt, comments=True)
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def test_write_multiple_from_blasttabc(self):
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"""Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt)."""
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source = os.path.join("Blast", "tab_2226_tblastn_005.txt")
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self.parse_write_and_compare(
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source, self.fmt, self.out, self.fmt, comments=True
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)
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def test_write_multiple_from_blasttabc_allfields(self):
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"""Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt)."""
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source = os.path.join("Blast", "tab_2228_tblastx_001.txt")
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fields = [
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"qseqid",
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"qgi",
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"qacc",
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"qaccver",
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"qlen",
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"sseqid",
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"sallseqid",
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"sgi",
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"sallgi",
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"sacc",
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"saccver",
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"sallacc",
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"slen",
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"qstart",
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"qend",
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"sstart",
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"send",
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"qseq",
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"sseq",
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"evalue",
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"bitscore",
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"score",
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"length",
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"pident",
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"nident",
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"mismatch",
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"positive",
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"gapopen",
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"gaps",
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"ppos",
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"frames",
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"qframe",
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"sframe",
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"btop",
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"staxids",
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"sscinames",
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"scomnames",
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"sblastnames",
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"sskingdoms",
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"stitle",
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"salltitles",
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"sstrand",
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"qcovs",
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"qcovhsp",
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]
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self.parse_write_and_compare(
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source, self.fmt, self.out, self.fmt, comments=True, fields=fields
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)
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class HmmerTabWriteCases(WriteCases):
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fmt = "hmmer3-tab"
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out = os.path.join("Hmmer", "test_write.txt")
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def test_write_single_from_hmmertab(self):
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"""Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out)."""
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source = os.path.join("Hmmer", "tab_30_hmmscan_004.out")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
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self.read_write_and_compare(source, self.fmt, self.out, self.fmt)
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def test_write_multiple_from_hmmertab(self):
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"""Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out)."""
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source = os.path.join("Hmmer", "tab_30_hmmscan_001.out")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
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class HmmerDomtabWriteCases(WriteCases):
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out = os.path.join("Hmmer", "test_write.txt")
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def test_write_single_from_hmmscandomtab(self):
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"""Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out)."""
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source = os.path.join("Hmmer", "domtab_30_hmmscan_004.out")
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fmt = "hmmscan3-domtab"
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self.parse_write_and_compare(source, fmt, self.out, fmt)
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self.read_write_and_compare(source, fmt, self.out, fmt)
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def test_write_multiple_from_hmmscandomtab(self):
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"""Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out)."""
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source = os.path.join("Hmmer", "domtab_30_hmmscan_001.out")
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fmt = "hmmscan3-domtab"
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self.parse_write_and_compare(source, fmt, self.out, fmt)
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def test_write_single_from_hmmsearchdomtab(self):
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"""Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out)."""
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source = os.path.join("Hmmer", "domtab_30_hmmsearch_001.out")
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fmt = "hmmsearch3-domtab"
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self.parse_write_and_compare(source, fmt, self.out, fmt)
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self.read_write_and_compare(source, fmt, self.out, fmt)
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class BlatPslWriteCases(WriteCases):
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fmt = "blat-psl"
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out = os.path.join("Blat", "test_write.txt")
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def test_write_single_from_blatpsl(self):
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"""Test blat-psl writing from blat-psl, single query (psl_34_004.psl)."""
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source = os.path.join("Blat", "psl_34_004.psl")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
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self.read_write_and_compare(source, self.fmt, self.out, self.fmt)
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def test_write_single_from_blatpsl_protein_query(self):
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"""Test blat-psl writing from blat-psl, single query (psl_35_002.psl)."""
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source = os.path.join("Blat", "psl_35_002.psl")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
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self.read_write_and_compare(source, self.fmt, self.out, self.fmt)
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def test_write_multiple_from_blatpsl(self):
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"""Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl)."""
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source = os.path.join("Blat", "psl_34_001.psl")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
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def test_write_single_from_blatpslx(self):
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"""Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx)."""
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source = os.path.join("Blat", "pslx_34_004.pslx")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt, pslx=True)
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self.read_write_and_compare(source, self.fmt, self.out, self.fmt, pslx=True)
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def test_write_single_from_blatpslx_protein_query(self):
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"""Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx)."""
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source = os.path.join("Blat", "pslx_35_002.pslx")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt, pslx=True)
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self.read_write_and_compare(source, self.fmt, self.out, self.fmt, pslx=True)
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def test_write_multiple_from_blatpslx(self):
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"""Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx)."""
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source = os.path.join("Blat", "pslx_34_001.pslx")
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self.parse_write_and_compare(source, self.fmt, self.out, self.fmt, pslx=True)
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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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