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make it possible to include all alignments, not just the ones that match
author
Diane Trout
<diane@caltech.edu>
Sat, 10 May 2008 04:32:25 +0000
(
04:32
+0000)
committer
Diane Trout
<diane@caltech.edu>
Sat, 10 May 2008 04:32:25 +0000
(
04:32
+0000)
chromosomes.
gaworkflow/util/makebed.py
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diff --git
a/gaworkflow/util/makebed.py
b/gaworkflow/util/makebed.py
index d2389ba0441fb2a7154d8c48919106efa59edd32..738b815b270d2d8352d6157a7b5e1948b437e3a3 100755
(executable)
--- 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])