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mdozmorov / genome_runner

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Filtering by strand and score breaks #36

Closed mdozmorov closed 10 years ago

mdozmorov commented 10 years ago

The "_plus" and "_minus" folders got created, but then:

Filtering GFs by strand and score... Filtering /home/dozmorovm/db_1.00_06.10.2014/grsnp_db/hg19/map/decodeHotSpotMale.bed.gz ... Traceback (most recent call last): File "/usr/lib/python2.7/runpy.py", line 162, in _run_module_as_main "main", fname, loader, pkg_name) File "/usr/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/usr/local/lib/python2.7/dist-packages/GenomeRunner_Web-0.1.0-py2.7.egg/grsnp/dbcreator_ucsc.py", line 632, in filter_by_strand(outputdir,gf_path) File "/usr/local/lib/python2.7/dist-packages/GenomeRunner_Web-0.1.0-py2.7.egg/grsnp/dbcreator_util.py", line 95, in filter_by_strand strand = line.split('\t')[5] IndexError: list index out of range

mdozmorov commented 10 years ago

It looks like checking for strand (and score?) happens always, even the strand column may not be present at all. This breaks GR.

mdozmorov commented 10 years ago

Was fixed