def main(readlib, cmapfile, matesfile, out_dir):
LOGFH = open(os.path.join(out_dir, 'parse_mates.LOG'), 'a')
LOGFH.write('Start the program to parse [%s] fragments for [%s] ... %s\n' % (readlib, matesfile, str(datetime.datetime.now())))
LOGFH.flush()
# Initiate the FragmentParser
matesparser = FragmentParser(CHRMAP=cmapfile)
# Parse and write to the output files organized by chromosome
chrs = matesparser.chr_mapping.values()
chrs_fh = generate_fhs(chrs, readlib, out_dir)
for chr, fragment in matesparser.parse_mates(matesfile, readlib):
fout = chrs_fh[chr]
record = fragment.get_bedrecord(chr)
fout.write(record + '\n')
close_fhs(chrs_fh)
LOGFH.write('Finish the program ... %s\n\n' % str(datetime.datetime.now()))
LOGFH.close()
def main(readlib, cmapfile, matesfile, out_dir):
LOGFH = open(os.path.join(out_dir, 'parse_mates.LOG'), 'a')
LOGFH.write(
'Start the program to parse [%s] fragments for [%s] ... %s\n' %
(readlib, matesfile, str(datetime.datetime.now())))
LOGFH.flush()
# Initiate the FragmentParser
matesparser = FragmentParser(CHRMAP=cmapfile)
# Parse and write to the output files organized by chromosome
chrs = matesparser.chr_mapping.values()
chrs_fh = generate_fhs(chrs, readlib, out_dir)
for chr, fragment in matesparser.parse_mates(matesfile, readlib):
fout = chrs_fh[chr]
record = fragment.get_bedrecord(chr)
fout.write(record + '\n')
close_fhs(chrs_fh)
LOGFH.write('Finish the program ... %s\n\n' %
str(datetime.datetime.now()))
LOGFH.close()
LOGFH.flush()
paras = parse_paras(parafile)
# 2. Build CpGs
LOGFH.write('... Build CpG sites ... %s\n' % str(datetime.datetime.now()))
siteparser = SiteParser(chr)
siteparser.parse_sites(cpg_file, 'CpGFull')
cpg_sites = siteparser.get_sites()
# 3. Build RE sites first
LOGFH.write('... Build RE sites ... %s\n' % str(datetime.datetime.now()))
siteparser = SiteParser(chr)
siteparser.parse_sites(re_sitefile, 'RE')
re_sites = siteparser.get_sites()
del siteparser
# 4. Build RE fragments
LOGFH.write('... Build RE fragments ... %s\n' % str(datetime.datetime.now()))
fragparser = FragmentParser()
# Split fragfile into subsets to avoid memory overflow
re_linenum = count_file_lines(re_fragfile)
refh = open(re_fragfile)
re_fraglines = []
pre_count = 0
for count, line in enumerate(refh):
re_fraglines.append(line)
if (count % 10000 == 0 and count != 0) or count + 1 == re_linenum:
re_frags = [fragment for fragment in fragparser.parse_bedfrags(re_fraglines, 'RE')]
# 5. Filter RE fragments, cpg_sites are updated
LOGFH.write('...... Filter RE fragments from lines [%d, %d] ......\n' % (pre_count, count))
refilter = REFilter(re_frags, cpg_sites, re_sites, paras['outlen'], paras['inlen'])
refilter.scan()
# Save information for the passed and failed RE fragments
write_logfiles(out_dir, re_frags, paras, 're')