From 8ebc08c518d47bdbab9c89b073fe66bc8a0b1f91 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Sat, 10 May 2008 04:32:25 +0000 Subject: [PATCH] make it possible to include all alignments, not just the ones that match chromosomes. --- gaworkflow/util/makebed.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gaworkflow/util/makebed.py b/gaworkflow/util/makebed.py index d2389ba..738b815 100755 --- a/gaworkflow/util/makebed.py +++ b/gaworkflow/util/makebed.py @@ -25,7 +25,9 @@ def make_bed_from_eland_stream(instream, outstream, name, description, chromosom for line in instream: fields = line.split() # we need more than the CHR field, and it needs to match a chromosome - if len(fields) <= CHR or fields[CHR][:3] != chromosome_prefix: + if len(fields) <= CHR or \ + (chromosome_prefix is not None and \ + fields[CHR][:3] != chromosome_prefix): continue start = fields[START] stop = int(start) + len(fields[SEQ]) -- 2.30.2