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)
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():
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 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():
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