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mdozmorov / genome_runner

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DCC score calculations not working. We need to use the truncated name as the key. #30

Closed lkscara closed 9 years ago

mdozmorov commented 10 years ago

Remains to be tested

mdozmorov commented 10 years ago

Apparently, it breaks on tables that do not have strand:

MinMax stats for Helas3Pk: Min=0.0, Max=1000.0, 25 pct_thresh=250.0 MinMax stats for Helas3Pk: Min=0.0, Max=1000.0, 75 pct_thresh=750.0 MinMax stats for Helas3Pk: Min=0.0, Max=1000.0, 50 pct_thresh=500.0 Filtering /home/dozmorovm/db_1.00_06.10.2014/grsnp_db/hg19/wgEncodeOpenChromSynth/NhekPk.bed.gz ... Filtering /home/dozmorovm/db_1.00_06.10.2014/grsnp_db/hg19/wgEncodeOpenChromSynth/Gm19239Pk.bed.gz ... Filtering /home/dozmorovm/db_1.00_06.10.2014/grsnp_db/hg19/wgEncodeOpenChromSynth/PanisletsPk.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 "/home/dozmorovm/genome_runner/grsnp/dbcreator_encodeDCC.py", line 342, in filter_by_strand(outputdir,gf_path) File "/home/dozmorovm/genome_runner/grsnp/dbcreator_util.py", line 94, in filter_by_strand strand = line.split('\t')[5] IndexError: list index out of range

mdozmorov commented 9 years ago

We are not pursuing DDC data processing