details: http://www.bx.psu.edu/hg/galaxy/rev/e85a213a347d changeset: 3365:e85a213a347d user: gua110 date: Wed Feb 10 14:14:55 2010 -0500 description: Modified strand column assignment to the NiceReaderWrapper object in basecoverage tool. Previously, if the input had no strand column declared, the object would have a default strand col of 5, and return a coverage of 0 as c5 might not have been a valid strand col. diffstat: tools/new_operations/gops_basecoverage.py | 8 +++----- 1 files changed, 3 insertions(+), 5 deletions(-) diffs (30 lines): diff -r 33b475ccc316 -r e85a213a347d tools/new_operations/gops_basecoverage.py --- a/tools/new_operations/gops_basecoverage.py Wed Feb 10 13:18:45 2010 -0500 +++ b/tools/new_operations/gops_basecoverage.py Wed Feb 10 14:14:55 2010 -0500 @@ -8,7 +8,6 @@ from galaxy import eggs import pkg_resources pkg_resources.require( "bx-python" ) - import sys, traceback, fileinput from warnings import warn from bx.intervals import * @@ -29,15 +28,14 @@ in_fname, out_fname = args except: doc_optparse.exception() - + g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), chrom_col=chr_col_1, start_col=start_col_1, end_col=end_col_1, + strand_col = strand_col_1, fix_strand=True ) - - if strand_col_1 >= 0: - g1.strand_col=strand_col_1 + try: bases = base_coverage(g1) except ParseError, exc: