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Merge pull request #12001 from mvdbeek/liftover_fix

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[21.01] Open input file in read mode in liftover wrapper
This commit is contained in:
Marius van den Beek
2021-05-19 13:03:35 +02:00
committed by GitHub
parent 4ec02d1b6c bbbfde85ef
commit 48bb29f6be
1 changed files with 1 additions and 1 deletions
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tools/extract/liftOver_wrapper.py
+1 -1
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@@ -25,7 +25,7 @@ def safe_bed_file(infile):
https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013561.html
"""
fix_pat = re.compile("^(track|browser)")
with tempfile.NamedTemporaryFile(mode='w', delete=False) as out_handle, open(infile, 'w') as in_handle:
with tempfile.NamedTemporaryFile(mode='w', delete=False) as out_handle, open(infile, 'r') as in_handle:
for line in in_handle:
if fix_pat.match(line):
line = "#" + line