Unverified Commit 48bb29f6 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #12001 from mvdbeek/liftover_fix 

[21.01] Open input file in read mode in liftover wrapper
parents 4ec02d1b bbbfde85

tools/extract/liftOver_wrapper.py

+1 −1
Original line number Diff line number Diff line
@@ -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