details: http://www.bx.psu.edu/hg/galaxy/rev/fe853d8e062d changeset: 3136:fe853d8e062d user: Kelly Vincent kpvincent@bx.psu.edu date: Tue Dec 01 16:18:25 2009 -0500 description: Added some error checking to pileup_parser tool so that it exits with a meaningful message if the user tries to do some 6-column work on a 10-column file, or vice versa.
diffstat:
tools/samtools/pileup_interval.py | 16 ++++++++++++++-- 1 files changed, 14 insertions(+), 2 deletions(-)
diffs (40 lines):
diff -r eb317734e391 -r fe853d8e062d tools/samtools/pileup_interval.py --- a/tools/samtools/pileup_interval.py Tue Dec 01 11:49:07 2009 -0500 +++ b/tools/samtools/pileup_interval.py Tue Dec 01 16:18:25 2009 -0500 @@ -1,7 +1,7 @@ #! /usr/bin/python
""" -Creates a pileup file from a bam file and a reference. +Condenses pileup format into ranges of bases.
usage: %prog [options] -i, --input=i: Input pileup file @@ -18,6 +18,7 @@ from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) from bx.cookbook import doc_optparse +import sys
def stop_err( msg ): sys.stderr.write( msg ) @@ -56,7 +57,18 @@ bases = [] while inLine.strip() != '': lineParts = inLine.split('\t') - seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex]) + try: + seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex]) + except IndexError, ei: + if options.format == 'ten': + stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) ) + else: + stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) ) + except ValueError, ev: + if options.format == 'six': + stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) ) + else: + stop_err( 'There appears to be something wrong with your column index values.\n' + str( ev ) ) # strout += str(startLoc) + '\n' # strout += str(bases) + '\n' # strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov)