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bigBed big-endian (#4670)

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Co-authored-by: Michiel de Hoon <mdehoon@tkx249.genome.gsc.riken.jp>
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mdehoon
2024-03-18 11:55:25 +09:00
committed by GitHub
parent bfc7b2ca5d
commit c50d27df11
3 changed files with 22 additions and 8 deletions
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Tests/Blat/bigbed_extended.bigendian.bb Normal file
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Tests/Blat/bigbed_extended.bb → Tests/Blat/bigbed_extended.littleendian.bb
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30
Tests/test_Align_bigbed.py
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@ -2240,8 +2240,9 @@ table bed
class TestAlign_extended_bed(unittest.TestCase): class TestAlign_extended_bed(unittest.TestCase):
# The bigBed file bigbed_extended.bb is a BED9+2 file, with nine predefined # The bigBed files bigbed_extended.littleendian.bb and
# BED fields and 2 extra (custom) fields. It was created by running # bigbed_extended.bigendian.bb are BED9+2 files, with nine predefined BED
# fields and 2 extra (custom) fields. It was created by running
# #
# bedToBigBed -as=bedExample2.as -type=bed9+2 -extraIndex=name,geneSymbol bedExample2.bed hg18.chrom.sizes bigbed_extended.bb # bedToBigBed -as=bedExample2.as -type=bed9+2 -extraIndex=name,geneSymbol bedExample2.bed hg18.chrom.sizes bigbed_extended.bb
# #
@ -2251,12 +2252,23 @@ class TestAlign_extended_bed(unittest.TestCase):
# and bedExample2.as the associated AutoSQL file, also downloaded from UCSC # and bedExample2.as the associated AutoSQL file, also downloaded from UCSC
# (https://genome.ucsc.edu/goldenPath/help/examples/bedExample2.as) # (https://genome.ucsc.edu/goldenPath/help/examples/bedExample2.as)
# declaring the nine predefined BED fields and the two extra fields # declaring the nine predefined BED fields and the two extra fields
#
path = "Blat/bigbed_extended.bb" # The bigBed file bigbed_extended.littleendian.bb was generated on a
# little-endian machine; the bigBed file bigbed_extended.bigendian.bb was
# generated on a big-endian machine.
def test_reading(self): def test_reading(self):
"""Test parsing bigbed_extended.bb.""" """Test parsing bigbed_extended.bb."""
alignments = Align.parse(self.path, "bigbed") path = "Blat/bigbed_extended.littleendian.bb"
alignments = Align.parse(path, "bigbed")
self.assertEqual(alignments.byteorder, "<")
self.check_alignments(alignments)
path = "Blat/bigbed_extended.bigendian.bb"
alignments = Align.parse(path, "bigbed")
self.assertEqual(alignments.byteorder, ">")
self.check_alignments(alignments)
def check_alignments(self, alignments):
self.assertEqual( self.assertEqual(
str(alignments.declaration), str(alignments.declaration),
"""\ """\
@ -2482,9 +2494,11 @@ table hg18KGchr7
def test_writing(self): def test_writing(self):
"""Test writing bigbed_extended.bb.""" """Test writing bigbed_extended.bb."""
with open(self.path, "rb") as stream: byteorder = sys.byteorder # "little" or "big"
path = f"Blat/bigbed_extended.{byteorder}endian.bb"
with open(path, "rb") as stream:
correct = stream.read() correct = stream.read()
alignments = Align.parse(self.path, "bigbed") alignments = Align.parse(path, "bigbed")
with open("Blat/bedExample2.as") as stream: with open("Blat/bedExample2.as") as stream:
autosql_data = stream.read() autosql_data = stream.read()
declaration = bigbed.AutoSQLTable.from_string(autosql_data) declaration = bigbed.AutoSQLTable.from_string(autosql_data)
@ -2501,7 +2515,7 @@ table hg18KGchr7
output.seek(0) output.seek(0)
data = output.read() data = output.read()
self.assertEqual(correct, data) self.assertEqual(correct, data)
alignments = Align.parse(self.path, "bigbed") alignments = Align.parse(path, "bigbed")
targets = alignments.targets targets = alignments.targets
with tempfile.TemporaryFile() as output: with tempfile.TemporaryFile() as output:
Align.write( Align.write(