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From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Test Tabix index contents, not the compression
Fixes: https://github.com/samtools/htslib/issues/827
--- python-pysam.orig/tests/tabix_test.py
+++ python-pysam/tests/tabix_test.py
@@ -14,8 +14,6 @@
import subprocess
import glob
import re
-import copy
-import tempfile
from TestUtils import check_url, load_and_convert, TABIX_DATADIR, get_temp_filename
IS_PYTHON3 = sys.version_info[0] >= 3
@@ -64,6 +62,17 @@
return found
+def checkGZBinaryEqual(filename1, filename2):
+ '''return true if the two files are binary equal.'''
+ with gzip.open(filename1, "rb") as infile1:
+ d1 = infile1.read()
+ with gzip.open(filename2, "rb") as infile2:
+ d2 = infile2.read()
+ if d1 == d2:
+ return True
+ return False
+
+
class TestIndexing(unittest.TestCase):
filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
filename_idx = os.path.join(TABIX_DATADIR, "example.gtf.gz.tbi")
@@ -77,7 +86,7 @@
'''test indexing via preset.'''
pysam.tabix_index(self.tmpfilename, preset="gff")
- self.assertTrue(checkBinaryEqual(
+ self.assertTrue(checkGZBinaryEqual(
self.tmpfilename + ".tbi", self.filename_idx))
def test_indexing_to_custom_location_works(self):
@@ -86,7 +95,7 @@
index_path = get_temp_filename(suffix='custom.tbi')
pysam.tabix_index(self.tmpfilename, preset="gff",
index=index_path, force=True)
- self.assertTrue(checkBinaryEqual(index_path, self.filename_idx))
+ self.assertTrue(checkGZBinaryEqual(index_path, self.filename_idx))
os.unlink(index_path)
def test_indexing_with_explict_columns_works(self):
@@ -98,7 +107,7 @@
end_col=4,
line_skip=0,
zerobased=False)
- self.assertTrue(checkBinaryEqual(
+ self.assertTrue(checkGZBinaryEqual(
self.tmpfilename + ".tbi", self.filename_idx))
def test_indexing_with_lineskipping_works(self):
@@ -109,7 +118,7 @@
end_col=4,
line_skip=1,
zerobased=False)
- self.assertFalse(checkBinaryEqual(
+ self.assertFalse(checkGZBinaryEqual(
self.tmpfilename + ".tbi", self.filename_idx))
def tearDown(self):
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