def parse_gsnap_sam(gsnap_f, ref_path, out_dir, paired_end, write_bin):
fa = Fasta(ref_path)
fc, ft, fmethyltype = \
bin_paths_from_fasta(fa.fasta_name, out_dir)
counts = get_counts(fc, ft, fa)
#chr_lengths = dict((k, len(fa[k])) for k in fa.iterkeys())
print >> sys.stderr, "tabulating methylation for %s" % gsnap_f
for sline in open(gsnap_f):
if sline.startswith("@"):
continue
# the ends didn't map to same spot.
line = sline.split("\t")
sam_flag = int(line[1])
if paired_end:
if line[6] != "=": continue
else:
# no reported alignments.
if sam_flag == 4: continue
seqid = line[2]
aln_seq = line[9]
read_length = len(aln_seq)
bp0 = int(line[3]) - 1
ga = ((sam_flag & 16) != 0) ^ (sam_flag & 128 != 0)
insert_length = int(line[8])
#line[9] = aln_seq
#line[10] = line[10][:len(aln_seq)]
# both ends start at exactly the same place.
if paired_end and insert_length == 0: continue
# handle overlapping reads. one side has + insert, the other is -
if -read_length < insert_length < 0:
insert_length = abs(insert_length)
aln_seq = aln_seq[:-(read_length - insert_length)]
read_length = len(aln_seq)
if paired_end and line[7] == '0': continue
bp1 = bp0 + read_length
ref_seq = (fa[seqid][bp0:bp1]).upper()
letters = 'GA' if ga else 'CT'
read_length = len(ref_seq)
assert read_length > 0, (bp0, bp1)
_update_conversions(ref_seq, aln_seq, bp0, letters, counts[seqid]['c'],
counts[seqid]['t'], 50, read_length, line[5])
write_files(fa.fasta_name, out_dir, counts, write_bin)
cmd = open(out_dir + "/cmd.ran", "w")
import datetime
print >> cmd, "#date:", str(datetime.date.today())
print >> cmd, "#path:", op.abspath(".")
print >> cmd, " ".join(sys.argv)
write_sam_commands(out_dir, fa, "methylcoded.gsnap")
def main(argv):
save = ""
force = False
generate = "log-uniform"
search_mode = "fix-grid-search"
try:
opts, args = getopt.getopt(argv,"vhfo:s:g:",
["verbose","help","force","out=","search=","generate="])
except getopt.GetoptError as getopt_error:
print getopt_error.msg, getopt_error.opt
error()
else:
for opt, arg in opts:
if opt in ("-h", "--help"):
show_help()
sys.exit()
elif opt in ("-v","--verbose"):
global _verbose
_verbose = True
elif opt in ("-f","--force"):
force = True
elif opt in ("-o","--out"):
save = re.sub('.yaml$','',arg)
elif opt in ("-g","--generate"):
if arg not in generation_modes.keys():
print "generate MODE is invalid: " +arg
error()
generate = arg
elif opt in ("-s","--search"):
if arg not in search_modes.keys():
print "search MODE is invalid: " +arg
error()
search_mode = arg
template, hparams = read_args(args)
if not save:
save = re.sub('.yaml$','',args[0])
hpnames, hpvalues = generate_params(hparams,generate,search_mode)
# fill template
template = ''.join(template)
write_files(''.join(open(template,'r')),hpnames,hpvalues,save,force=force)
if _verbose:
print '\n'.join(files)+'\n'
def parse_gsnap_sam(gsnap_f, ref_path, out_dir, paired_end, write_bin):
fa = Fasta(ref_path)
fc, ft, fmethyltype = \
bin_paths_from_fasta(fa.fasta_name, out_dir)
counts = get_counts(fc, ft, fa)
#chr_lengths = dict((k, len(fa[k])) for k in fa.iterkeys())
print >>sys.stderr, "tabulating methylation for %s" % gsnap_f
for sline in open(gsnap_f):
if sline.startswith("@SQ"):
continue
# the ends didn't map to same spot.
line = sline.split("\t")
sam_flag = int(line[1])
if paired_end:
if line[6] != "=": continue
else:
# no reported alignments.
if sam_flag == 4: continue
seqid = line[2]
aln_seq = line[9]
read_length = len(aln_seq)
bp0 = int(line[3]) - 1
ga = ((sam_flag & 16) != 0) ^ (sam_flag & 128 != 0)
insert_length = int(line[8])
#line[9] = aln_seq
#line[10] = line[10][:len(aln_seq)]
# both ends start at exactly the same place.
if paired_end and insert_length == 0: continue
# handle overlapping reads. one side has + insert, the other is -
if -read_length < insert_length < 0:
insert_length = abs(insert_length)
aln_seq = aln_seq[:-(read_length - insert_length)]
read_length = len(aln_seq)
if paired_end and line[7] == '0': continue
bp1 = bp0 + read_length
ref_seq = (fa[seqid][bp0:bp1]).upper()
letters = 'GA' if ga else 'CT'
read_length = len(ref_seq)
assert read_length > 0, (bp0, bp1)
_update_conversions(ref_seq, aln_seq, bp0, letters,
counts[seqid]['c'], counts[seqid]['t'],
50, read_length, line[5])
write_files(fa.fasta_name, out_dir, counts, write_bin)
cmd = open(out_dir +"/cmd.ran", "w")
import datetime
print >>cmd, "#date:", str(datetime.date.today())
print >>cmd, "#path:", op.abspath(".")
print >>cmd, " ".join(sys.argv)
write_sam_commands(out_dir, fa, "methylcoded.gsnap")
