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 BamToBed12Iterator(handle,**kwargs):
'''
handle is an bam iterator
need references hash if handle is not filename.
'''
if type(handle)==type("string"):
handle=pysam.Samfile(handle,"rb");
for i in handle:
#print i #debug
if i.tid<0: continue
strand="+"
if i.is_reverse:
strand="-"
score=i.mapq
'''
test
'''
if kwargs.has_key("references"):
if isinstance(kwargs["references"],str):
chr=kwargs["references"]
else:
chr=kwargs["references"][i.tid];
else:
try:
chr=handle.references[i.tid];
except:
chr="chr"
if kwargs.has_key("strand"):
if kwargs["strand"]=="read1" or kwargs["strand"]=="firstMate":
read1=True
else:
read1=False
else:
read1=True
start=i.pos
end=i.aend
name=i.qname
cds_start=start
cds_end=start
itemRgb="0,0,0"
'''
debug
import sys
if i.cigar is None:
print >>sys.stderr,"why cigar is Nonetype?"
print >>sys.stderr,i
exit(0)
end of debug
'''
if i.cigar==None: continue # IGNORE THIS READS?
(block_starts,block_sizes)=Tools.cigar_to_coordinates(i.cigar);
if i.is_read1 and not read1:
strand=Tools.reverse_strand(strand)
elif i.is_read2 and read1:
strand=Tools.reverse_strand(strand)
bed=Bed12([chr,start,end,name,score,strand,cds_start,cds_end,itemRgb,len(block_sizes),block_sizes,block_starts])
yield bed
def BamToBed12Iterator(handle, **kwargs):
'''
handle is an bam iterator
need references hash if handle is not filename.
'''
if type(handle) == type("string"):
handle = pysam.Samfile(handle, "rb")
for i in handle:
#print i #debug
if i.tid < 0: continue
strand = "+"
if i.is_reverse:
strand = "-"
score = i.mapq
'''
test
'''
if kwargs.has_key("references"):
chr = kwargs["references"][i.tid]
else:
try:
chr = handle.references[i.tid]
except:
chr = "chr"
if kwargs.has_key("strand"):
if kwargs["strand"] == "read1" or kwargs["strand"] == "firstMate":
read1 = True
else:
read1 = False
else:
read1 = True
start = i.pos
end = i.aend
name = i.qname
cds_start = start
cds_end = start
itemRgb = "0,0,0"
'''
debug
import sys
if i.cigar is None:
print >>sys.stderr,"why cigar is Nonetype?"
print >>sys.stderr,i
exit(0)
end of debug
'''
if i.cigar == None: continue # IGNORE THIS READS?
(block_starts, block_sizes) = Tools.cigar_to_coordinates(i.cigar)
if i.is_read1 and not read1:
strand = Tools.reverse_strand(strand)
elif i.is_read2 and read1:
strand = Tools.reverse_strand(strand)
bed = Bed12([
chr, start, end, name, score, strand, cds_start, cds_end, itemRgb,
len(block_sizes), block_sizes, block_starts
])
yield bed
def fopen(file,mode="r",**kwargs):
'''
'''
if Tools.guess_format(file)=="bam" and mode=="r":
return pysam.Samfile(file,"rb")
if mode=="w":
return open_output(file)
if mode=="r":
return open_input(file)
return None
def fopen(file, mode="r", **kwargs):
'''
'''
if Tools.guess_format(file) == "bam" and mode == "r":
return pysam.Samfile(file, "rb")
if mode == "w":
return open_output(file)
if mode == "r":
return open_input(file)
return None
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():
global args,out
args=ParseArg()
dict={}
if args.output=="stdout":
out=sys.stdout
else:
try:
out=open(args.output,"w")
except IOError:
print >>sys.stderr,"can't open file ",args.output,"to write. Using stdout instead"
out=sys.stdout
argv=sys.argv
argv[0]=argv[0].split("/")[-1]
print >>out,"# This data was generated by program ",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 :\n#\t"," ".join(argv)
if args.query_method:
dict["method"]=args.query_method
dbi=DBI.init(args.db,args.dbformat)
hits=0
query=0
if args.input=="stdin":
input=sys.stdin
else:
input=args.input
query_length=0
hits_number=0
for (i0,x) in enumerate(TableIO.parse(input,args.input_format)):
if i0%10==0:
print >>sys.stderr,"query ",i0," entries\r",
print >>out,"QR\t",x
hit=0
query+=1
query_length+=len(x)
results=dbi.query(x,**dict)
compatible=0
#print >>sys.stderr,type(results)
if isinstance(results,numpy.ndarray) or isinstance(results,list):
if not args.silence:
print >>out,"HT\t",
for value in results:
print >>out,str(value)+",",
print >>out,""
hit=1
hits_number+=1
elif isinstance(results,str):
if not args.silence:
print >>out,"HT\t",
print >>out,results
hit=1
hits_number+=1
else:
this_query_hits=0
for j in results:
if not args.silence:
print >>out,"HT\t",j,
hit=1
hits_number+=1
this_query_hits+=1
if isinstance(j,xplib.Annotation.Bed12) and isinstance(x,xplib.Annotation.Bed12):
compatible_binary=Tools.compatible_with_transcript(j,x)
if not args.silence:
print >>out,"\tCompatible:",compatible_binary
if compatible_binary:
compatible+=1
else:
if not args.silence:
print >>out,""
print >>out,"HN\t",this_query_hits
if compatible>0:
print >>out,"CP\t",compatible
if args.dbformat=="tabix":
x.chr=x.chr.replace("chr","")
for j in dbi.query(x,**dict):
print >>out,"HT\t",j
hit=1
hits_number+=1
hits+=hit
print >>out,"# Query Number:",query,"\n# Query Have Hits:",hits
print >>out,"# Query Length:",query_length
print >>out,"# Hits Number:",hits_number
def Main():
global args, out
args = ParseArg()
dict = {}
if args.output == "stdout":
out = sys.stdout
else:
try:
out = open(args.output, "w")
except IOError:
print >> sys.stderr, "can't open file ", args.output, "to write. Using stdout instead"
out = sys.stdout
argv = sys.argv
argv[0] = argv[0].split("/")[-1]
print >> out, "# This data was generated by program ", 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 :\n#\t", " ".join(argv)
init_dict = {}
if args.dbformat == "guess":
if Tools.suffix(args.db) == "gz":
args.dbformat = "tabix"
args.tabix_format = Tools.guess_format(args.db)
else:
args.dbformat = Tools.guess_format(args.db)
if args.query_method:
dict["method"] = args.query_method
if args.tabix_format:
init_dict["tabix"] = args.tabix_format
dbi = DBI.init(args.db, args.dbformat, **init_dict)
hits = 0
query = 0
if args.input == "stdin":
input = sys.stdin
else:
input = args.input
query_length = 0
hits_number = 0
if (args.input_format == "guess"):
args.input_format = Tools.guess_format(args.input)
for (i0, x) in enumerate(TableIO.parse(input, args.input_format)):
if i0 % 100 == 0:
print >> sys.stderr, "query ", i0, " entries\r",
print >> out, "QR\t", x
hit = 0
query += 1
query_length += len(x)
#print dbi;#debug
results = dbi.query(x, **dict)
#results=dbi.query(x) #DEBUG
#print >>sys.stderr,type(results)
if isinstance(results, numpy.ndarray) or isinstance(results, list):
print >> out, "HT\t",
for value in results:
print >> out, str(value) + ",",
print >> out, ""
hit = 1
hits_number += 1
elif isinstance(results, str):
print >> out, "HT\t",
print >> out, results
hit = 1
hits_number += 1
else:
for j in results:
print >> out, "HT\t", j
hit = 1
hits_number += 1
if args.dbformat == "tabix":
x.chr = x.chr.replace("chr", "")
for j in dbi.query(x, **dict):
print >> out, "HT\t", j
hit = 1
hits_number += 1
hits += hit
print >> out, "# Query Number:", query, "\n# Query Have Hits:", hits
print >> out, "# Query Length:", query_length
print >> out, "# Hits Number:", hits_number
def compare_reads(isoforms):
# global dbi,out
isoforms_set=[]
chr=isoforms[0].chr
min_start=isoforms[0].start
max_stop=isoforms[0].stop
for i in isoforms:
if i.start < min_start: min_start=i.start
if i.stop > max_stop: max_stop=i.stop
isoforms_set.append(i)
# print >>sys.stderr,"debug",i
transcript_region=Bed([chr,min_start,max_stop]);
print >>out,"REGION\t",chr,"\t",min_start,"\t",max_stop
print >>out,"ISOFORM_INPUT_NUMBER\t",len(isoforms_set)
'''
reading all the reads in this transcript region
'''
reads_set=[]
reads_num=0
for i in dbi.query(transcript_region,method="fetch12"):
reads_set.append(i)
reads_num+=1
'''
compare two sets
'''
l=len(isoforms_set)
bincodes={}
total=reads_num
if total==0: total=0.001
for i in reads_set:
bincode=0
for j in isoforms_set:
k=Tools.compatible_with_transcript(i,j)
if k:
bincode = (bincode<<1)+1
else:
bincode = bincode<<1
if bincodes.has_key(bincode):
bincodes[bincode]+=1
else:
bincodes[bincode]=1
init=[ 1.0/l for i in range(l) ]
proportion=init
'''
EM Initialize
'''
'''
E step
'''
totals=[0.0 for i in range(l)]
new_proportion=[0.0 for i in range(l)]
iterate_time=0;
while(1):
totals=[0.0 for i in range(l)]
for code in bincodes.keys():
row_total=0.0
for j in range(l):
if get_bit_n(j,l,code):
row_total+=proportion[j]
for j in range(l):
if get_bit_n(j,l,code):
totals[j]+=bincodes[code] * proportion[j] / row_total
for i in range(l):
new_proportion[i]=totals[i]/total
'''
M step
'''
#print >>sys.stderr,"proportion",proportion #debug
#print >>sys.stderr,"new_proportion",new_proportion #debug
#print >>sys.stderr,"total",total #debug
#print >>sys.stderr,"totals",totals #debug
dis=distance(proportion,new_proportion)
proportion=new_proportion
iterate_time+=1
if(dis<1e-05): break;
if(args.BYY and iterate_time > 10): break;
'''
BYY Hard Cut Algorithm
'''
while(args.BYY):
totals=[0.0 for i in range(l)]
for code in bincodes.keys():
maxj=-1
for j in range(l):
if get_bit_n(j,l,code):
# totals[j]+=bincodes[code] * proportion[j] / row_total
if maxj==-1: maxj=j
elif proportion[j] > proportion[maxj]: maxj=j
if maxj!=-1: totals[maxj]+=bincodes[code]
#new_proportion=[0.0 for i in range(l)]
for i in range(l):
new_proportion[i]=totals[i]/total
'''
M step
'''
dis=distance(proportion,new_proportion)
if(dis<1e-05): break;
proportion=new_proportion
# print >>out,proportion
'''
print isoforms
'''
for i,x in enumerate(isoforms_set):
if proportion[i] > args.threshold:
if x.score==0.0:
x.score=proportion[i]
print >>out,"HT\t",x,"\t",proportion[i]
else:
print >>out,"HT\t",x,"\t",proportion[i]
else:
if not args.hits_only:
if x.score==0.0:
x.score=proportion[i]
print >>out,"NT\t",x,"\t",proportion[i]
else:
print >>out,"NT\t",x,"\t",proportion[i]
print >>out,"//"
def Main():
'''
IO TEMPLATE
'''
global args,out
args=ParseArg()
if args.output=="stdout":
out=sys.stdout
else:
try:
out=open(args.output,"w")
except IOError:
print >>sys.stderr,"can't open file ",args.output,"to write. Using stdout instead"
out=sys.stdout
if args.input=="stdin":
fin=sys.stdin
else:
try:
x=args.input.split(".")
if x[-1]=="gz":
fin=gzip.open(args.input,"r")
else:
fin=open(args.input,"r")
except IOError:
print >>sys.stderr,"can't read file",args.input
fin=sys.stdin
'''
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)
gene=DBI.init(args.genetab,args.gene_format);
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,"bed")
downstream=DBI.init(downstream_list,"bed")
exons=DBI.init(exons_list,"bed")
introns=DBI.init(introns_list,"bed")
utr3=DBI.init(utr3_list,"genebed")
utr5=DBI.init(utr5_list,"genebed")
if args.format=="guess":
args.format=Tools.guess_format(args.input)
for (i0,i) in enumerate(TableIO.parse(fin,args.format)):
if i0==0:
if isinstance(i,Bed12):
print >>out,"#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"
elif isinstance(i,GeneBed):
print >>out,"#name\tchr\tstrand\tstart\tend\tcds_start\texon_count\texon_starts\texont_ends\tgene\tupstream\tdownstream\texon\tintron\tutr3\tutr5"
else:
print >>out,"#chr\tstart\tend\tname\tscore\tstrand\tgene\tupstream\tdownstream\texon\tintron\tutr3\tutr5"
print >>out,i,
print >>out,"\t",toIDs(gene.query(i)),
print >>out,"\t",toIDs(upstream.query(i)),
print >>out,"\t",toIDs(downstream.query(i)),
print >>out,"\t",toIDs(exons.query(i)),
print >>out,"\t",toIDs(introns.query(i)),
print >>out,"\t",toIDs(utr3.query(i)),
print >>out,"\t",toIDs(utr5.query(i))
def Main():
global args, out
args = ParseArg()
dict = {}
if args.output == "stdout":
out = sys.stdout
else:
try:
out = open(args.output, "w")
except IOError:
print >> sys.stderr, "can't open file ", args.output, "to write. Using stdout instead"
out = sys.stdout
argv = sys.argv
argv[0] = argv[0].split("/")[-1]
print >> out, "# This data was generated by program ", 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 :\n#\t", " ".join(argv)
if args.query_method:
dict["method"] = args.query_method
dbi = DBI.init(args.db, args.dbformat)
hits = 0
query = 0
if args.input == "stdin":
input = sys.stdin
else:
input = args.input
query_length = 0
hits_number = 0
for (i0, x) in enumerate(TableIO.parse(input, args.input_format)):
if i0 % 10 == 0:
print >> sys.stderr, "query ", i0, " entries\r",
print >> out, "QR\t", x
hit = 0
query += 1
query_length += len(x)
results = dbi.query(x, **dict)
compatible = 0
#print >>sys.stderr,type(results)
if isinstance(results, numpy.ndarray) or isinstance(results, list):
if not args.silence:
print >> out, "HT\t",
for value in results:
print >> out, str(value) + ",",
print >> out, ""
hit = 1
hits_number += 1
elif isinstance(results, str):
if not args.silence:
print >> out, "HT\t",
print >> out, results
hit = 1
hits_number += 1
else:
this_query_hits = 0
for j in results:
if not args.silence:
print >> out, "HT\t", j,
hit = 1
hits_number += 1
this_query_hits += 1
if isinstance(j, xplib.Annotation.Bed12) and isinstance(
x, xplib.Annotation.Bed12):
compatible_binary = Tools.compatible_with_transcript(j, x)
if not args.silence:
print >> out, "\tCompatible:", compatible_binary
if compatible_binary:
compatible += 1
else:
if not args.silence:
print >> out, ""
print >> out, "HN\t", this_query_hits
if compatible > 0:
print >> out, "CP\t", compatible
if args.dbformat == "tabix":
x.chr = x.chr.replace("chr", "")
for j in dbi.query(x, **dict):
print >> out, "HT\t", j
hit = 1
hits_number += 1
hits += hit
print >> out, "# Query Number:", query, "\n# Query Have Hits:", hits
print >> out, "# Query Length:", query_length
print >> out, "# Hits Number:", hits_number
def Main():
"""
IO TEMPLATE
"""
global args, out
args = ParseArg()
if args.output == "stdout":
out = sys.stdout
else:
try:
out = open(args.output, "w")
except IOError:
print >>sys.stderr, "can't open file ", args.output, "to write. Using stdout instead"
out = sys.stdout
if args.input == "stdin":
fin = sys.stdin
else:
try:
x = args.input.split(".")
if x[-1] == "gz":
fin = gzip.open(args.input, "r")
else:
fin = open(args.input, "r")
except IOError:
print >>sys.stderr, "can't read file", args.input
fin = sys.stdin
"""
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)
gene = DBI.init(args.genetab, args.gene_format)
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, "bed")
downstream = DBI.init(downstream_list, "bed")
exons = DBI.init(exons_list, "bed")
introns = DBI.init(introns_list, "bed")
utr3 = DBI.init(utr3_list, "genebed")
utr5 = DBI.init(utr5_list, "genebed")
if args.format == "guess":
args.format = Tools.guess_format(args.input)
for (i0, i) in enumerate(TableIO.parse(fin, args.format)):
if i0 == 0:
if isinstance(i, Bed12):
print >> out, "#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"
elif isinstance(i, GeneBed):
print >> out, "#name\tchr\tstrand\tstart\tend\tcds_start\texon_count\texon_starts\texont_ends\tgene\tupstream\tdownstream\texon\tintron\tutr3\tutr5"
else:
print >> out, "#chr\tstart\tend\tname\tscore\tstrand\tgene\tupstream\tdownstream\texon\tintron\tutr3\tutr5"
print >> out, i,
print >> out, "\t", toIDs(gene.query(i)),
print >> out, "\t", toIDs(upstream.query(i)),
print >> out, "\t", toIDs(downstream.query(i)),
print >> out, "\t", toIDs(exons.query(i)),
print >> out, "\t", toIDs(introns.query(i)),
print >> out, "\t", toIDs(utr3.query(i)),
print >> out, "\t", toIDs(utr5.query(i))
def query(self,x,method='pileup'):
if method=='fetch':
for bamfile in self.bamfiles:
for read in bamfile.fetch(x.chr,x.start,x.stop):
if read.tid<0:continue
if read.mapq==0:continue
strand='+'
if read.is_reverse:
strand='-'
score=read.mapq
bed=Bed([bamfile.references[read.tid],read.pos,read.aend,read.qname,score,strand])
yield bed
elif method=='fetch12':
'''
test version
still test Tools.cigar_to_coordinates
'''
for bamfile in self.bamfiles:
for read in bamfile.fetch(x.chr,x.start,x.stop):
if read.tid<0:continue
if read.mapq==0:continue
chr=bamfile.references[read.tid]
strand='+'
if read.is_reverse:
strand='-'
score=read.mapq
start=read.pos
end=read.aend
name=read.qname
cds_start=start
cds_end=start
itemRgb="0,0,0"
(block_starts,block_sizes)=Tools.cigar_to_coordinates(read.cigar);
bed=Bed12([chr,start,end,name,score,strand,cds_start,cds_end,itemRgb,len(block_sizes),block_sizes,block_starts])
yield bed
elif method=="paired_end":
for bamfile in self.bamfiles:
for fragment in TableIO.parse(bamfile.fetch(x.chr,x.start,x.stop),"bam2fragment",bam=bamfile):
yield fragment
elif method=='pileup':
s=[[0,0,0,0] for row in range(x.stop-x.start)]
for bamfile in self.bamfiles:
try:
A=bamfile.pileup(x.chr,x.start,x.stop)
except:
print >>sys.stderr,"Can't pile up",x.chr,x.start,x.stop
raise StopIteration
for pileupcolumn in A:
j=pileupcolumn.pos-x.start
if j<0: continue
if j>x.stop-x.start: break
for pileupread in pileupcolumn.pileups:
try:
if pileupread.is_del: continue
if pileupread.indel!=0: continue
nt=pileupread.alignment.seq[pileupread.qpos]
if BamI.hNtToNum.has_key(nt):
k=BamI.hNtToNum[nt]
s[j][k]+=1
except:
pass
for i in s:
yield i
def Main():
'''
IO TEMPLATE
'''
global args,out,isoforms_set,selected_isoforms_set,reads_set,selected_reads_set,dbi
args=ParseArg()
if args.output=="stdout":
out=sys.stdout
else:
try:
out=open(args.output,"w")
except IOError:
print >>sys.stderr,"can't open file ",args.output,"to write. Using stdout instead"
out=sys.stdout
if args.input=="stdin":
fin=sys.stdin
else:
try:
x=args.input.split(".")
if x[-1]=="gz":
fin=gzip.open(args.input,"r")
else:
fin=open(args.input,"r")
except IOError:
print >>sys.stderr,"can't read file",args.input
fin=sys.stdin
'''
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.bam,args.format)
'''
reading all the isoforms
'''
isoforms=[]
iterator=TableIO.parse(fin,"bed")
beds=[]
for i in iterator:
beds.append(i)
beds.sort()
if len(beds)==0:
print >>sys.stderr,"error in reading file",args.input
exit(1)
bed=beds[0]
chr=bed.chr
min_start=bed.start
max_stop=bed.stop
j=0
for i in beds:
j+=1
if (j%10==0): print >>sys.stderr,"processed %d entries\r"%j,
if Tools.overlap(bed,i):
if bed.stop < i.stop:
bed.stop=i.stop
isoforms.append(i)
else:
compare(isoforms)
isoforms=[i]
bed=i
if len(isoforms)>0:
compare(isoforms)
def Main():
global args,out
args=ParseArg()
dict={}
if args.output=="stdout":
out=sys.stdout
else:
try:
out=open(args.output,"w")
except IOError:
print >>sys.stderr,"can't open file ",args.output,"to write. Using stdout instead"
out=sys.stdout
argv=sys.argv
argv[0]=argv[0].split("/")[-1]
print >>out,"# This data was generated by program ",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 :\n#\t"," ".join(argv)
init_dict={}
if args.dbformat=="guess":
if Tools.suffix(args.db)=="gz":
args.dbformat="tabix"
args.tabix_format=Tools.guess_format(args.db)
else:
args.dbformat=Tools.guess_format(args.db)
if args.query_method:
dict["method"]=args.query_method
if args.tabix_format:
init_dict["tabix"]=args.tabix_format
dbi=DBI.init(args.db,args.dbformat,**init_dict)
hits=0
query=0
if args.input=="stdin":
input=sys.stdin
else:
input=args.input
query_length=0
hits_number=0
if (args.input_format=="guess"):
args.input_format=Tools.guess_format(args.input)
for (i0,x) in enumerate(TableIO.parse(input,args.input_format)):
if i0%100==0:
print >>sys.stderr,"query ",i0," entries\r",
print >>out,"QR\t",x
hit=0
query+=1
query_length+=len(x)
#print dbi;#debug
results=dbi.query(x,**dict)
#results=dbi.query(x) #DEBUG
#print >>sys.stderr,type(results)
if isinstance(results,numpy.ndarray) or isinstance(results,list):
print >>out,"HT\t",
for value in results:
print >>out,str(value)+",",
print >>out,""
hit=1
hits_number+=1
elif isinstance(results,str):
print >>out,"HT\t",
print >>out,results
hit=1
hits_number+=1
else:
for j in results:
print >>out,"HT\t",j
hit=1
hits_number+=1
if args.dbformat=="tabix":
x.chr=x.chr.replace("chr","")
for j in dbi.query(x,**dict):
print >>out,"HT\t",j
hit=1
hits_number+=1
hits+=hit
print >>out,"# Query Number:",query,"\n# Query Have Hits:",hits
print >>out,"# Query Length:",query_length
print >>out,"# Hits Number:",hits_number
def query(self, x=None, method="pileup", **dict):
if type(x) == type("str"):
x = x.split(":")
chrom = x[0]
start = None
end = None
if len(x) > 1:
b = x[1].split("-")
if len(b) == 2:
start = int(b[0]) - 1
end = int(b[1])
elif isinstance(x, tuple):
chrom = x[CHROM]
start = x[CHROMSTART]
end = x[CHROMEND]
elif x is not None:
chrom = x.chr
start = x.start
end = x.stop
if method == "fetch":
for bamfile in self.bamfiles:
for read in bamfile.fetch(chrom, start, end):
if read.tid < 0:
continue
if read.mapq == 0:
continue
strand = "+"
if read.is_reverse:
strand = "-"
score = read.mapq
bed = Bed([bamfile.references[read.tid], read.pos, read.aend, read.qname, score, strand])
yield bed
elif method == "fetch12":
"""
test version
still test Tools.cigar_to_coordinates
"""
for bamfile in self.bamfiles:
for read in bamfile.fetch(chrom, start, end):
if read.tid < 0:
continue
if read.mapq == 0:
continue
chr = bamfile.references[read.tid]
strand = "+"
if read.is_reverse:
strand = "-"
score = read.mapq
start = read.pos
end = read.aend
name = read.qname
cds_start = start
cds_end = start
itemRgb = "0,0,0"
(block_starts, block_sizes) = Tools.cigar_to_coordinates(read.cigar)
bed = Bed12(
[
chr,
start,
end,
name,
score,
strand,
cds_start,
cds_end,
itemRgb,
len(block_sizes),
block_sizes,
block_starts,
]
)
yield bed
elif method == "bam1":
# fetch read from paired end with strand information
for bamfile in self.bamfiles:
strand = "read1"
if dict.has_key("strand"): # TODO: if bamfiles have different read1 or read2 ?
strand = dict["strand"]
for bed in TableIO.parse(
bamfile.fetch(chrom, start, end), "bam2bed12", references=chrom, strand=strand
):
yield bed
elif method == "paired_end":
for bamfile in self.bamfiles:
for fragment in TableIO.parse(bamfile.fetch(chrom, start, end), "bam2fragment", bam=bamfile):
yield fragment
elif method == "bam2": # yield bed12
for bamfile in self.bamfiles:
for fragment in TableIO.parse(bamfile.fetch(chrom, start, end), "bam2fragment", bam=bamfile):
if dict.has_key("strand"):
yield fragment.toBed12(chr=chrom, strand=dict["strand"])
else:
yield fragment.toBed12(chr=chrom)
elif method == "bam1tuple":
for bamfile in self.bamfiles:
strand = "read1"
if dict.has_key("strand"): # TODO: if bamfiles have different read1 or read2 ?
strand = dict["strand"]
for bed in TableIO.parse(
bamfile.fetch(chrom, start, end), "bam2bed12tuple", references=chrom, strand=strand
):
yield bed
elif method == "bam2tuple":
for bamfile in self.bamfiles:
for fragment in TableIO.parse(bamfile.fetch(chrom, start, end), "bam2fragment", bam=bamfile):
if dict.has_key("strand"):
yield fragment.toBed12Tuple(chr=chrom, strand=dict["strand"])
else:
yield fragment.toBed12Tuple(chr=chrom)
elif method == "bam2tuple_fast":
for bamfile in self.bamfiles:
for fragment in TableIO.parse(bamfile.fetch(chrom, start, end), "bam2fragment"):
if dict.has_key("strand"):
yield fragment.toBed12Tuple(chr=chrom, strand=dict["strand"])
else:
yield fragment.toBed12Tuple(chr=chrom)
elif method == "pileup":
s = [[0, 0, 0, 0] for row in range(end - start)]
for bamfile in self.bamfiles:
try:
A = bamfile.pileup(chrom, start, end)
except:
print >>sys.stderr, "Can't pile up", chrom, start, end
raise StopIteration
for pileupcolumn in A:
j = pileupcolumn.pos - start
if j < 0:
continue
if j > end - start:
break
for pileupread in pileupcolumn.pileups:
try:
if pileupread.is_del:
continue
if pileupread.indel != 0:
continue
nt = pileupread.alignment.seq[pileupread.qpos]
if BamI.hNtToNum.has_key(nt):
k = BamI.hNtToNum[nt]
s[j][k] += 1
except:
pass
for i in s:
yield i
elif method == "count":
s = 0
for bamfile in self.bamfiles:
s += bamfile.count(chrom, start, end)
yield s
elif method == "count_fragment":
s = 0
for bamfile in self.bamfiles:
for fragment in TableIO.parse(bamfile.fetch(chrom, start, end), "bam2fragment", bam=bamfile):
s += 1
yield s
elif method == "references":
for i in self.bamfiles[0].references:
yield i
elif method == "lengths":
for i in self.bamfiles[0].lengths:
yield i