1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/aa8298344ed5/ changeset: aa8298344ed5 user: inithello date: 2013-01-23 18:32:05 summary: Make wrapper compatible with python 2.5. affected #: 1 file
diff -r da970ef6075702286d47b9ccf83942092eaac27d -r aa8298344ed5b5f7c209a4341999815d25a2e305 tools/evolution/add_scores.py --- a/tools/evolution/add_scores.py +++ b/tools/evolution/add_scores.py @@ -17,11 +17,11 @@
def open_or_die( filename, mode='r', message=None ): if message is None: - message = 'Error opening {0}'.format( filename ) + message = 'Error opening %s' % filename try: fh = open( filename, mode ) except IOError, err: - die( '{0}: {1}'.format( message, err.strerror ) ) + die( '%s: %s' % ( message, err.strerror ) ) return fh
################################################################################ @@ -48,16 +48,16 @@ if not line.startswith( self.comment_chars ): elems = line.split( self.delimiter ) if len( elems ) <= self.key_column: - die( 'Location file {0} line {1}: less than {2} columns'.format( self.filename, line_number, self.key_column + 1 ) ) + die( 'Location file %s line %d: less than %d columns' % ( self.filename, line_number, self.key_column + 1 ) ) else: key = elems.pop( self.key_column ) if key in self._map: if self._map[key] != elems: - die( 'Location file {0} line {1}: duplicate key "{2}"'.format( self.filename, line_number, key ) ) + die( 'Location file %s line %d: duplicate key "%s"' % ( self.filename, line_number, key ) ) else: self._map[key] = elems except IOError, err: - die( 'Error opening location file {0}: {1}'.format( self.filename, err.strerror ) ) + die( 'Error opening location file %s: %s' % ( self.filename, err.strerror ) )
def get_values( self, key ): if key in self._map: @@ -67,7 +67,7 @@ else: return rval else: - die( 'key "{0}" not found in location file {1}'.format( key, self.filename ) ) + die( 'key "%s" not found in location file %s' % ( key, self.filename ) )
################################################################################
@@ -77,10 +77,10 @@ # open input, output, and bigwig files location_file = LocationFile( loc_filename ) bigwig_filename = location_file.get_values( loc_key ) - bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file {0}'.format( bigwig_filename ) ) + bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file %s' % bigwig_filename ) bw = BigWigFile( file=bwfh ) - ifh = open_or_die( input_filename, message='Error opening input file {0}'.format( input_filename ) ) - ofh = open_or_die( output_filename, mode='w', message='Error opening output file {0}'.format( output_filename ) ) + ifh = open_or_die( input_filename, message='Error opening input file %s' % input_filename ) + ofh = open_or_die( output_filename, mode='w', message='Error opening output file %s' % output_filename )
# make column numbers 0-based chrom_col = int( chrom_col ) - 1 @@ -101,11 +101,11 @@ score_list_len = len( score_list ) if score_list_len == 1: beg, end, score = score_list[0] - score_val = '{0:1.3f}'.format( score ) + score_val = '%1.3f' % score elif score_list_len == 0: score_val = 'NA' else: - die( '{0} line {1}: chrom={2}, start={3}, score_list_len = {4}'.format( input_filename, line_number, chrom, start, score_list_len ) ) + die( '%s line %d: chrom=%s, start=%d, score_list_len = %d' % ( input_filename, line_number, chrom, start, score_list_len ) ) print >> ofh, '\t'.join( [line, score_val] ) else: print >> ofh, line
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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