track_name = os.path.splitext(os.path.basename(infile))[0]
track_description = track_name
outfile = os.path.splitext(os.path.basename(infile))[0] + ".bed"
print "Output file: %s" % outfile
# Read in data
data = BedMaker(infile,column_names=('chr','start','stop','strand','transcript',
'fold_change','p_value'))
# Fix chromosome name
if fix_chromosome_name:
print "Prepending 'chr' to chromosome names where it's missing"
prependChromosomeName(data,'chr')
# Subtract one from end position
if correct_stop_position:
print "Correcting 'stop' position by subtracting one base"
adjustStopPosition(data)
# Set name and RBG values
data.computeColumn('name',lambda line: "%s_fc%s" % (line['transcript'],line['fold_change']))
data.computeColumn('RGB',lambda line: computeRGB(line['p_value']))
# Write out lines to BED
print "Writing data to BED file"
data.makeBedFile(outfile,track_name,track_description,column_names=('chr','start','stop',
'name','p_value',
'strand','start','stop',
'RGB'))
print "Finished"
print "Output file: %s" % outfile
# Read in data
data = BedMaker(infile,column_names=('chr','start','stop','sample_id','length',
'average_coverage'))
# Fix chromosome name
if fix_chromosome_name:
print "Prepending 'chr' to chromosome names where it's missing"
prependChromosomeName(data,'chr')
# Subtract one from end position
if correct_stop_position:
print "Correcting 'stop' position by subtracting one base"
adjustStopPosition(data)
# Set name, strand, score and RBG values
data.computeColumn('name',lambda line: "%s_%sbp" % (line['sample_id'],line['length']))
data.computeColumn('strand',lambda line: "+")
data.computeColumn('score',lambda line: min(int(line['average_coverage']),1000))
data.computeColumn('RGB',lambda line: computeRGBUnexplained(line['length'],
line['average_coverage']))
# Write out lines to BED
print "Writing data to BED file"
data.makeBedFile(outfile,track_name,track_description,column_names=('chr','start','stop',
'name','score',
'strand','start','stop',
'RGB'))
print "Finished"
