def run(args):
fin=IO.fopen(args.input,"r")
out=IO.fopen(args.output,"w")
if args.format=="guess":
args.format=IO.guess_format(args.input)
s=TableIO.parse(args.input,args.format)
for i in s:
print(i,file=out)
def run(local_args):
'''
IO TEMPLATE
'''
global args,out
args=local_args
out=IO.fopen(args.output,"w")
fin=IO.fopen(args.input,"r")
print("# This data was generated by program ",sys.argv[0]," (version: %s)"%VERSION,file=out)
print("# in bam2x ( https://github.com/nimezhu/bam2x )",file=out)
print("# Date: ",time.asctime(),file=out)
print("# The command line is :",file=out)
print("#\t"," ".join(sys.argv),file=out)
gene=DBI.init(args.genetab,"binindex",cls="bed12");
upstream_list=[]
downstream_list=[]
exons_list=[]
introns_list=[]
utr3_list=[]
utr5_list=[]
for g in gene:
upstream_list.append(g.upstream(args.upstream));
downstream_list.append(g.downstream(args.downstream));
for e in g.Exons():
exons_list.append(e)
for i in g.Introns():
introns_list.append(i)
if not (g.utr3() is None):
utr3_list.append(g.utr3())
if not (g.utr5() is None):
utr5_list.append(g.utr5())
upstream=DBI.init(upstream_list,"binindex",cls="bed6")
downstream=DBI.init(downstream_list,"binindex",cls="bed6")
exons=DBI.init(exons_list,"binindex",cls="bed6")
introns=DBI.init(introns_list,"binindex",cls="bed6")
utr3=DBI.init(utr3_list,"binindex",cls="bed6")
utr5=DBI.init(utr5_list,"binindex",cls="bed6")
if args.format=="guess":
args.format=IO.guess_format(args.input)
for (i0,i) in enumerate(TableIO.parse(fin,args.format)):
if i0==0:
if isinstance(i,Bed12):
print("#chr\tstart\tend\tname\tscore\tstrand\tthick_start\tthick_end\titem_rgb\tblock_count\tblock_sizes\tblock_starts\tgene\tupstream\tdownstream\texon\tintron\tutr3\tutr5",file=out)
else:
print("#chr\tstart\tend\tname\tscore\tstrand\tgene\tupstream\tdownstream\texon\tintron\tutr3\tutr5",file=out)
print(i,file=out,end="")
print("\t",toIDs(gene.query(i)),file=out,end="")
print("\t",toIDs(upstream.query(i)),file=out,end="")
print("\t",toIDs(downstream.query(i)),file=out,end="")
print("\t",toIDs(exons.query(i)),file=out,end="")
print("\t",toIDs(introns.query(i)),file=out,end="")
print("\t",toIDs(utr3.query(i)),file=out,end="")
print("\t",toIDs(utr5.query(i)),file=out)
def run(args):
fin=IO.fopen(args.input,"r")
out=IO.fopen(args.output,"w")
if args.format=="guess":
args.format=IO.guess_format(args.input)
s=TableIO.parse(args.input,args.format)
l=[]
for i,x in enumerate(s):
if i/10000==0:
logging.info("reading %s entrys in %s",i,args.input)
l.append(x)
logging.info("begin sorting")
l.sort()
logging.info("sorting done")
for i in l:
print(i,file=out)
logging.info("completed")