def main(argv):
sets = []
use_all = True
if argv[0] == '--USE_MOBILE':
use_all = False
argv = argv[1:]
setnames = []
for fn in argv:
if 'ped' in os.path.basename(fn).lower():
sample = 'Ped'
else:
sample = 'Col'
set_ = load_set(load_transcript_data(open(fn, 'rb'), sample=sample), use_all=use_all)
setname = os.path.basename(fn).replace('_TRANSCRIPTDATA.pickled', '').replace('Sample_', '')
sets.append((setname, set_))
setnames.append(setname)
outfile = '+'.join(setnames)# + '.venn.txt'
if not use_all:
outfile += '.mobile_only'
# outfile.replace('.venn.txt', '.mobile_only.venn.txt')
fo = open(outfile + '.venn.txt', 'w')
fo.write('#SETS = %i\n' % len(sets))
fo.write('#\t'.join(['%s: %i' % (s[0], len(s[1])) for s in sets]) + '\n')
processed = process_sets(sets)
generate_diagram(processed, outfile + '.png')
for id_, set_ in processed:
fo.write('%s\t%s\n' % (id_, len(set_)))
fo.write('\n')
for id_, set_ in processed:
fo.write('%s\t%s\n' % (id_, len(set_)))
for item in set_:
fo.write('%s\n' % item)
fo.close()
pass
def main(argv):
"""
Input EITHER (to generate per-transcript-results from pileup counts)
0. transcript/snp data
1. sample name {Col,Ped}
2. output prefix (output is <prefix>_<DATATYPE>.pickled)
3-n. number of bamfiles
OR (to summarise per-transcript-results)
0. name of a <arbitrary>_TRANSCRIPTDATA.pickled file
1. sample name {Col,Ped}
"""
if len(argv) > 3:
sys.stderr.write('%s: MODE1\n' % get_timestamp())
sys.stderr.write('')
transcript_d, snp_d = read_transcript_data(open(argv[0]))
# show_data(transcript_d, snp_d)
sample = argv[1]
prefix = argv[2]
read_checklist = set([])
for bam_fn in argv[3:]:
sys.stderr.write('%s: Processing file %s...\n' % (get_timestamp(), bam_fn))
process_pileups(pysam.Samfile(bam_fn, 'rb'), snp_d, read_checklist)
# show_data(transcript_d, snp_d)
# break
# print list(read_checklist), len(read_checklist)
ts = get_timestamp()
pickle.dump(snp_d, open(prefix + '_SNPDATA.pickled', 'wb'))
pickle.dump(transcript_d, open(prefix + '_TRANSCRIPTDATA.pickled', 'wb'))
pickle.dump(read_checklist, open(prefix + '_READCHECKLIST.pickled', 'wb'))
# sys.exit(0)
else:
sys.stderr.write('%s: MODE2\n' % get_timestamp())
sys.stderr.write('%s: Loading data from %s.\n' % (get_timestamp(), argv[0]))
# transcript_d = pickle.load(open(argv[0], 'rb'))
transcript_d = load_transcript_data(open(argv[0], 'rb'), sample=argv[1])
sys.stderr.write('%s: Finished loading %s.\n' % (get_timestamp(), argv[0]))
prefix = argv[0].rstrip('TRANSCRIPTDATA.pickled')
# print '======'
#show_data(transcript_d, None, sample=argv[1])
write_data(transcript_d, sample=argv[1], prefix=prefix)
pass