[med-svn] [Git][med-team/python-biopython][upstream] bigBed big-endian (#4670)

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / python-biopython


Commits:
6a3c977c by Michiel de Hoon at 2024-03-18T21:43:54+01:00
bigBed big-endian (#4670)

Signed-off-by: Étienne Mollier <emollier at debian.org>

- - - - -


3 changed files:

- + Tests/Blat/bigbed_extended.bigendian.bb
- Tests/Blat/bigbed_extended.bb → Tests/Blat/bigbed_extended.littleendian.bb
- Tests/test_Align_bigbed.py


Changes:

=====================================
Tests/Blat/bigbed_extended.bigendian.bb
=====================================
Binary files /dev/null and b/Tests/Blat/bigbed_extended.bigendian.bb differ


=====================================
Tests/Blat/bigbed_extended.bb → Tests/Blat/bigbed_extended.littleendian.bb
=====================================


=====================================
Tests/test_Align_bigbed.py
=====================================
@@ -2240,8 +2240,9 @@ table bed
 
 
 class TestAlign_extended_bed(unittest.TestCase):
-    # The bigBed file bigbed_extended.bb is a BED9+2 file, with nine predefined
-    # BED fields and 2 extra (custom) fields. It was created by running
+    # The bigBed files bigbed_extended.littleendian.bb and
+    # 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
     #
@@ -2251,12 +2252,23 @@ class TestAlign_extended_bed(unittest.TestCase):
     # and bedExample2.as the associated AutoSQL file, also downloaded from UCSC
     # (https://genome.ucsc.edu/goldenPath/help/examples/bedExample2.as)
     # 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):
         """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(
             str(alignments.declaration),
             """\
@@ -2482,9 +2494,11 @@ table hg18KGchr7
 
     def test_writing(self):
         """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()
-        alignments = Align.parse(self.path, "bigbed")
+        alignments = Align.parse(path, "bigbed")
         with open("Blat/bedExample2.as") as stream:
             autosql_data = stream.read()
         declaration = bigbed.AutoSQLTable.from_string(autosql_data)
@@ -2501,7 +2515,7 @@ table hg18KGchr7
             output.seek(0)
             data = output.read()
         self.assertEqual(correct, data)
-        alignments = Align.parse(self.path, "bigbed")
+        alignments = Align.parse(path, "bigbed")
         targets = alignments.targets
         with tempfile.TemporaryFile() as output:
             Align.write(



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/6a3c977ca14978d9f96ea22f0a2806f4478323b9

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View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/commit/6a3c977ca14978d9f96ea22f0a2806f4478323b9
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