def Main():
'''
IO TEMPLATE
'''
global args,out
args=ParseArg()
fin=IO.fopen(args.input,"r")
out=IO.fopen(args.output,"w")
'''
END OF IO TEMPLATE
'''
print >>out,"# This data was generated by program ",sys.argv[0]," (version: %s)"%VERSION,
print >>out,"in bam2x ( https://github.com/nimezhu/bam2x )"
print >>out,"# Date: ",time.asctime()
print >>out,"# The command line is :"
print >>out,"#\t"," ".join(sys.argv)
dbi=[];
for i,bam in enumerate(args.bams):
print >>out,"# SAMPLE_"+str(i+1)+" BAM File:",bam
dbi.append(DBI.init(bam,"bam"))
print >>out,"#",VCF.header(),
for i,bam in enumerate(args.bams):
print >>out,"\t","Sample_"+str(i+1),
print >>out,""
for i,vcf in enumerate(TableIO.parse(fin,"vcf")):
vcf.chr=args.chr_prefix+vcf.chr
if(i%100==0):
print >>sys.stderr,"processing",i,"vcf\r",
print >>out,vcf,
for d in dbi:
print >>out,"\t",
for r in d.query(vcf):
print >>out,format(r),
print >>out,""
def Main():
'''
IO TEMPLATE
'''
global args,out
args=ParseArg()
fin=IO.fopen(args.input,"r")
out=IO.fopen(args.output,"w")
'''
END OF IO TEMPLATE
'''
print >>out,"# This data was generated by program ",sys.argv[0]," (version: %s)"%VERSION,
print >>out,"in bam2x ( https://github.com/nimezhu/bam2x )"
print >>out,"# Date: ",time.asctime()
print >>out,"# The command line is :"
print >>out,"#\t"," ".join(sys.argv)
dbi=DBI.init(args.db,Tools.guess_format(args.db))
references=dbi.bamfiles[0].references
for i in TableIO.parse(fin,args.format):
print i
n=0
c_count=0
reads=dbi.query(i,args.method)
for read in reads:
compatible=Tools.compatible_with_transcript(read,i,references=references,strand=args.strand)
print "HT:"
for i0,r in enumerate(TableIO.parse(read.reads,"bam2bed12",references=references)):
print "READ"+str(i0)+"\t",r
print "COMPATIBLE:",compatible,"\n\n"
if compatible: c_count+=1
n+=1
print "COMPATIBLE / ALL OVERLAP READS = ",c_count,"/",n
print "RATIO\t%.4f"%float(c_count)/n
def Main():
'''
This program is a test for TableIO.parse(file.bam,"bam2bed")
'''
global args,out
args=ParseArg()
fin=IO.fopen(args.input,"r")
out=IO.fopen(args.output,"w")
if args.format=="guess":
args.format=Tools.guess_format(args.input)
s=TableIO.parse(args.input,args.format)
for i in s:
print >>out,i
def Main():
'''
IO TEMPLATE
'''
global args,out
args=ParseArg()
fin=IO.fopen(args.input,"r")
out=IO.fopen(args.output,"w")
'''
END OF IO TEMPLATE
'''
print >>out,"# This data was generated by program ",sys.argv[0]," (version: %s)"%VERSION,
print >>out,"in bam2x ( https://github.com/nimezhu/bam2x )"
print >>out,"# Date: ",time.asctime()
print >>out,"# The command line is :"
print >>out,"#\t"," ".join(sys.argv)
for i in TableIO.parse(fin,args.format):
print >>out,i
def Main():
'''
IO TEMPLATE
'''
global args, out
args = ParseArg()
fin = IO.fopen(args.input, "r")
out = IO.fopen(args.output, "w")
'''
END OF IO TEMPLATE
'''
print >> out, "# This data was generated by program ", sys.argv[
0], " (version: %s)" % VERSION,
print >> out, "in bam2x ( https://github.com/nimezhu/bam2x )"
print >> out, "# Date: ", time.asctime()
print >> out, "# The command line is :"
print >> out, "#\t", " ".join(sys.argv)
for i in TableIO.parse(fin, args.format):
print >> out, i
def Main():
'''
IO TEMPLATE
'''
global args, out
args = ParseArg()
fin = IO.fopen(args.input, "r")
out = IO.fopen(args.output, "w")
'''
END OF IO TEMPLATE
'''
print >> out, "# This data was generated by program ", sys.argv[
0], " (version: %s)" % VERSION,
print >> out, "in bam2x ( https://github.com/nimezhu/bam2x )"
print >> out, "# Date: ", time.asctime()
print >> out, "# The command line is :"
print >> out, "#\t", " ".join(sys.argv)
dbi = DBI.init(args.db, Tools.guess_format(args.db))
references = dbi.bamfiles[0].references
for i in TableIO.parse(fin, args.format):
print i
n = 0
c_count = 0
reads = dbi.query(i, args.method)
for read in reads:
compatible = Tools.compatible_with_transcript(
read, i, references=references, strand=args.strand)
print "HT:"
for i0, r in enumerate(
TableIO.parse(read.reads,
"bam2bed12",
references=references)):
print "READ" + str(i0) + "\t", r
print "COMPATIBLE:", compatible, "\n\n"
if compatible: c_count += 1
n += 1
print "COMPATIBLE / ALL OVERLAP READS = ", c_count, "/", n
print "RATIO\t%.4f" % float(c_count) / n
def Main():
"""
IO TEMPLATE
"""
global args, out
args = ParseArg()
fin = IO.fopen(args.input, "r")
out = IO.fopen(args.output, "w")
"""
END OF IO TEMPLATE
"""
print >> out, "# This data was generated by program ", sys.argv[0], " (version: %s)" % VERSION,
print >> out, "in bam2x ( https://github.com/nimezhu/bam2x )"
print >> out, "# Date: ", time.asctime()
print >> out, "# The command line is :"
print >> out, "#\t", " ".join(sys.argv)
hSites = {}
donorSites = {}
acceptorSites = {}
if args.genome is not None:
genome = DBI.init(args.genome, "genome")
else:
genome = None
j = 0
for j, i in enumerate(TableIO.parse(fin, "bam2bed12", references=fin.references, strand=args.strand)):
# print >>out,i
if j % 1000 == 0:
print >>sys.stderr, "processing ", j, "reads \r",
for intron in i.Introns():
if len(intron) < args.intron_min_length:
continue
donor = intron.head()
# print >>sys.stderr,intron
# print >>sys.stderr,donor
donorID = bedToID(donor)
if donorSites.has_key(donorID):
donorSites[donorID] += 1
else:
donorSites[donorID] = 1
acceptor = intron.tail()
acceptorID = bedToID(acceptor)
if acceptorSites.has_key(acceptorID):
acceptorSites[acceptorID] += 1
else:
acceptorSites[acceptorID] = 1
"""
if genome is not None:
s=genome.query(intron.head()).upper()+".."+genome.query(intron.tail()).upper()
if hSites.has_key(s):
hSites[s]+=1
else:
hSites[s]=1
"""
donors = []
for key in donorSites.keys():
a = key.split("\t")
donors.append(Bed([a[0], a[1], a[2], "noname_donor", donorSites[key], a[3]]))
donors.sort()
for i, x in enumerate(donors):
x.id = "donor_" + str(i)
print >> out, x, "\t", genome.query(x).upper()
acceptors = []
for key in acceptorSites.keys():
a = key.split("\t")
acceptors.append(Bed([a[0], a[1], a[2], "noname_acceptor", acceptorSites[key], a[3]]))
acceptors.sort()
for i, x in enumerate(acceptors):
x.id = "acceptor_" + str(i)
print >> out, x, "\t", genome.query(x).upper()
def Main():
'''
IO TEMPLATE
'''
global args,out
args=ParseArg()
fin=IO.fopen(args.input,"r")
out=IO.fopen(args.output,"w")
'''
END OF IO TEMPLATE
'''
print >>out,"# This data was generated by program ",sys.argv[0]," (version: %s)"%VERSION,
print >>out,"in bam2x ( https://github.com/nimezhu/bam2x )"
print >>out,"# Date: ",time.asctime()
print >>out,"# The command line is :"
print >>out,"#\t"," ".join(sys.argv)
hSites={};
donorSites={};
acceptorSites={}
if args.genome is not None:
genome=DBI.init(args.genome,"genome")
else:
genome=None
j=0
for j,i in enumerate(TableIO.parse(fin,"bam2bed12",references=fin.references,strand=args.strand)):
#print >>out,i
if j%1000==0: print >>sys.stderr,"processing ",j,"reads \r",
for intron in i.Introns():
if len(intron)< args.intron_min_length: continue
donor=intron.head();
#print >>sys.stderr,intron
#print >>sys.stderr,donor
donorID=bedToID(donor)
if(donorSites.has_key(donorID)):
donorSites[donorID]+=1
else:
donorSites[donorID]=1
acceptor=intron.tail();
acceptorID=bedToID(acceptor)
if(acceptorSites.has_key(acceptorID)):
acceptorSites[acceptorID]+=1
else:
acceptorSites[acceptorID]=1
'''
if genome is not None:
s=genome.query(intron.head()).upper()+".."+genome.query(intron.tail()).upper()
if hSites.has_key(s):
hSites[s]+=1
else:
hSites[s]=1
'''
donors=[]
for key in donorSites.keys():
a=key.split("\t")
donors.append(Bed([a[0],a[1],a[2],"noname_donor",donorSites[key],a[3]]));
donors.sort()
for i,x in enumerate(donors):
x.id="donor_"+str(i)
print >>out,x,"\t",genome.query(x).upper()
acceptors=[]
for key in acceptorSites.keys():
a=key.split("\t")
acceptors.append(Bed([a[0],a[1],a[2],"noname_acceptor",acceptorSites[key],a[3]]));
acceptors.sort()
for i,x in enumerate(acceptors):
x.id="acceptor_"+str(i)
print >>out,x,"\t",genome.query(x).upper()