def __init__(self, samfile, seqfile=None, zerobase=False, use_slider=False):
if isinstance(samfile, basestring):
self.samfile = open(samfile)
else:
self.samfile = samfile
if use_slider:
from rnarry import batchutils
self.samfile = batchutils.slider_file(self.samfile)
self.samfile = QueueableLineReader(self.samfile)
self.seqfile = seqfile
if seqfile is not None:
self.seqidx = GiantFASTAFile(seqfile)
self.zerobase = zerobase
self.seqlen = {}
'%s' % dbinfo['geneName'], '.', '+'
])
else:
print >> bedout, '\t'.join([
nracc, '0',
str(exonlength),
'%s' % dbinfo['geneName'], '.', '+'
])
print >> faout, '>%s %s' % (nracc, dbinfo['geneName'])
faout.write(textwrap(mutatedseq))
if __name__ == '__main__':
refflatdbpath = sys.argv[1]
nrlistpath = sys.argv[2]
genomefastapath = sys.argv[3]
rnaseqgspace = sys.argv[4]
fastaoutpath = sys.argv[5]
bedoutpath = sys.argv[6]
refFlat = shelve.open(refflatdbpath, 'r')
mm9 = GiantFASTAFile(genomefastapath)
rseqarr = MultiTrackSplitBinnedArray(rnaseqgspace)
nrlist = open(nrlistpath).read().split()
bedout = open(bedoutpath, 'w')
faout = open(fastaoutpath, 'w')
process(nrlist)
output.write(name.ljust(32, '\x00'))
output.write(struct.pack('II', len(refseq), len(grp)))
output.write(refseq)
for _, start, end, nreads in grp:
output.write(struct.pack('III', start, end, nreads))
if __name__ == '__main__':
import sys
refseqfile = sys.argv[1] # fasta format
mappingfile = sys.argv[2] # gzipped gmap native format
readerrorfile = sys.argv[3] # python pickle format
packfile = sys.argv[4]
greffile = GiantFASTAFile(refseqfile)
mappingf = gzip.open(mappingfile)
packf = open(packfile, 'w')
print 'Loading read error profile'
profile, maxpos = load_profile(readerrorfile)
print 'Dumping read error profile'
dump_profile(profile, maxpos, packf)
print 'Loading gmap mapping file'
spans = scan_gmap(mappingf)
print 'Dumping mapped reads'
dump_gmap(spans, packf, greffile)
print >> outd, kcnt, refbase, '%.6f' % del_ratio
print >> outm, kcnt, refbase, '%.6f' % mod_ratio
print >> outmd, kcnt, refbase, '%.6f' % moddel_ratio
print >> oute, kcnt, refbase, '%.6f' % sentropy
if __name__ == '__main__':
import sys
mappingfile = sys.argv[1] # gmap native format
greffile = sys.argv[2]
outputprefix = sys.argv[3]
mappingf = gzip.open(mappingfile)
greffile = GiantFASTAFile(greffile)
def opensortedout(fname):
return os.popen(
"sort -k1,1n -k2,2 -k3,3r | uniq -c | "
"awk '{ print $2, $3, $4, $1; }' | gzip - >%s" % fname, 'w')
nonzeroout = gzip.open(outputprefix + 'nonzero.posrcnt.gz', 'w')
distout = {
'D': opensortedout(outputprefix + 'del.real.gz'),
'M': opensortedout(outputprefix + 'mod.real.gz'),
'MD': opensortedout(outputprefix + 'moddel.real.gz'),
'E': opensortedout(outputprefix + 'entropy.real.gz'),
}
spans = scan_gmap(mappingf)
class SAMParser(object):
def __init__(self, samfile, seqfile=None, zerobase=False, use_slider=False):
if isinstance(samfile, basestring):
self.samfile = open(samfile)
else:
self.samfile = samfile
if use_slider:
from rnarry import batchutils
self.samfile = batchutils.slider_file(self.samfile)
self.samfile = QueueableLineReader(self.samfile)
self.seqfile = seqfile
if seqfile is not None:
self.seqidx = GiantFASTAFile(seqfile)
self.zerobase = zerobase
self.seqlen = {}
def getsubseq(self, name, seqfrom, seqto): # [from, to) both 0-base
if self.seqfile is None:
raise ValueError, 'Sequence file is not given.'
return self.seqidx.get(name, seqfrom, seqto)
def __iter__(self):
return self.iteralignments()
# WARNING: 'mapped' coordiates are 1-based, both side inclusive by default
def iteralignments(self, strands='+-', withref=False):
geteditdist= lambda x: x[4]
for line in self.samfile:
fields = line[:-1].split('\t')
if line[0] == '@':
if line[:3] != '@SQ':
continue
sqname = fields[1][3:]
sqlen = [int(fl[3:]) for fl in fields[2:] if fl[:3] == 'LN:'][0]
self.seqlen[sqname] = sqlen
continue
qname = fields[0]
flags = int(fields[1])
rname = fields[2]
pos = int(fields[3]) # 1-based leftmost
mapq = int(fields[4]) # phred-scaled
cigar = fields[5]
seq = fields[9]
options = dict(v.split(':', 1) for v in fields[11:])
if flags & F_REVERSE_STRAND:
strand = '-'
seq = reverse_complement(seq)
else:
strand = '+'
editdist = int(options.get('NM', 'i:-1')[2:])
if rname == '*' or strand not in strands:
mapped = []
else:
reflen, _ = calculate_cigar_length(cigar)
stop = pos + reflen - 1
start = pos - 1 if self.zerobase else pos
mapped = [(rname, start, stop, strand, editdist, cigar)]
for altmatch in options.get('XA', 'Z:')[2:].split(';')[:-1]:
altfields = altmatch.split(',')
strand = altfields[1][0]
pos = int(altfields[1][1:])
rname = altfields[0]
cigar = altfields[2]
editdist = int(altfields[3])
reflen, _ = calculate_cigar_length(cigar)
stop = pos + reflen - 1
start = pos - 1 if self.zerobase else pos
if strand in strands:
mapped.append((rname, start, stop, strand, editdist,
cigar))
# search for alternative reads
for altline in self.samfile:
altfields = altline[:-1].split('\t')
altqname = altfields[0]
altflags = int(altfields[1])
if altqname != qname:
self.samfile.push(altline)
break
altrname = altfields[2]
altpos = int(altfields[3]) # 1-based leftmost
altmapq = int(altfields[4]) # phred-scaled
altcigar = altfields[5]
altseq = altfields[9]
altoptions = dict(v.split(':', 1) for v in altfields[11:])
if altflags & F_REVERSE_STRAND:
altstrand = '-'
altseq = reverse_complement(altseq)
else:
altstrand = '+'
alteditdist = int(altoptions.get('NM', 'i:-1')[2:])
if altrname != '*' and altstrand in strands:
altreflen, _ = calculate_cigar_length(altcigar)
altstop = altpos + altreflen - 1
altstart = altpos - 1 if self.zerobase else altpos
mapped.append((altrname, altstart, altstop, altstrand,
alteditdist, altcigar))
mapped.sort(key=geteditdist)
if withref:
newmapped = []
for m in mapped:
subseq = self.getsubseq(m[0], m[1]-1, m[2])
if m[3] == '-':
subseq = reverse_complement(subseq)
newmapped.append(m + (subseq,))
mapped = newmapped
yield {
'qname': qname,
'flags': flags,
'mapq': mapq,
'seq': seq,
'options': options,
'mapped': mapped, # positions are 1-based
}
