def main():
''' main scripts '''
args = parse_argument()
PromoterList = []
feature = []
print "# loading and reading the promoter of Gene ... "
if args.genefile:
for g in TableIO.parse(args.genefile, "genebed"):
a = g.promoter(args.bp)
PromoterList.append(a)
if args.rna:
for g in TableIO.parse(args.rna, "genebed"):
a = g.promoter(args.bp)
PromoterList.append(a)
if args.feature:
feature = TableIO.parse(args.feature, 'bed')
print "# loading and reading Done !"
PromoterData = readIntoBinIndex(PromoterList)
FeatureData = readIntoBinIndex(feature)
for i in TableIO.parse(args.bed, 'bed'):
overlapGene, overlapFeature, overlap_string = [], [], ''
if i.strand not in ['+', '-']: continue
else:
OverlapGene = getOverlapFeatures(i, PromoterData)
if FeatureData:
overlapFeature = getOverlapFeatures(i, FeatureData)
for g in overlapGene + overlapFeature:
overlap_string += g.id + ';'
print i, "\t", overlap_string
def __init__(self, tabix_file_name,**dict):
'''
wrapped in DBI.init(filename,"tabix")
'''
self.tabix_file_name=tabix_file_name
self.dict=dict
try:
self.data=pysam.Tabixfile(tabix_file_name)
except:
print >>sys.stderr,"WARNING: Can't init the tabix file",tabix_file_name
self.header=None
if dict.has_key("header") and dict["header"]==True:
f=TableIO.parse(tabix_file_name)
h=f.next()
l=len(h)
for i in range(l):
h[i]=h[i].strip()
self.header=h
f.close()
elif dict.has_key("header") and isinstance(dict["header"],list):
self.header=dict["header"]
elif dict.has_key("header") and isinstance(dict["header"],str):
fh=TableIO.parse(dict["header"])
self.header=fh.next()
#print >>sys.stderr,self.header
self.tabix_format="simple"
if self.dict.has_key("tabix"):
self.tabix_format=self.dict["tabix"]
def Main():
global args,out,SHIFTSIZE,data
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
SHIFTSIZE=args.shiftsize
data={}
for x in TableIO.parse(args.chr_length_file,"simple"):
data[x[0].strip()]=[0 for row in range((long(x[1]>>SHIFTSIZE)+1))]
parseAnnotationFile(args.input)
for x in TableIO.parse(args.chr_length_file,"simple"):
chrom=x[0].strip()
length=long(x[1])
for i,bin in enumerate(data[chrom]):
start=i<<SHIFTSIZE
stop=(i+1)<<SHIFTSIZE
if stop > length: stop=length
print >>out,chrom+"\t"+str(start)+"\t"+str(stop)+"\t"+str(bin)
def Main():
global args, out, SHIFTSIZE, data
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
SHIFTSIZE = args.shiftsize
data = {}
for x in TableIO.parse(args.chr_length_file, "simple"):
data[x[0].strip()] = [
0 for row in range((long(x[1] >> SHIFTSIZE) + 1))
]
parseAnnotationFile(args.input)
for x in TableIO.parse(args.chr_length_file, "simple"):
chrom = x[0].strip()
length = long(x[1])
for i, bin in enumerate(data[chrom]):
start = i << SHIFTSIZE
stop = (i + 1) << SHIFTSIZE
if stop > length: stop = length
print >> out, chrom + "\t" + str(start) + "\t" + str(
stop) + "\t" + str(bin)
def main():
''' main scripts '''
args = parse_argument()
PromoterList =[]
feature = []
print "# loading and reading the promoter of Gene ... "
if args.genefile:
for g in TableIO.parse(args.genefile, "genebed"):
a = g.promoter(args.bp)
PromoterList.append(a)
if args.rna:
for g in TableIO.parse(args.rna, "genebed"):
a = g.promoter(args.bp)
PromoterList.append(a)
if args.feature:
feature = TableIO.parse(args.feature, 'bed')
print "# loading and reading Done !"
PromoterData = readIntoBinIndex(PromoterList)
FeatureData = readIntoBinIndex(feature)
for i in TableIO.parse(args.bed, 'bed'):
overlapGene, overlapFeature, overlap_string = [], [], ''
if i.strand not in ['+','-']: continue
else:
OverlapGene = getOverlapFeatures(i, PromoterData)
if FeatureData:
overlapFeature = getOverlapFeatures(i, FeatureData)
for g in overlapGene + overlapFeature:
overlap_string += g.id+';'
print i, "\t", overlap_string
def __init__(self, tabix_file_name, **dict):
"""
wrapped in DBI.init(filename,"tabix")
"""
self.tabix_file_name = tabix_file_name
self.dict = dict
try:
self.data = pysam.Tabixfile(tabix_file_name)
except:
print >>sys.stderr, "WARNING: Can't init the tabix file", tabix_file_name
self.header = None
if dict.has_key("header") and dict["header"] == True:
f = TableIO.parse(tabix_file_name)
h = f.next()
l = len(h)
for i in range(l):
h[i] = h[i].strip()
self.header = h
f.close()
elif dict.has_key("header") and isinstance(dict["header"], list):
self.header = dict["header"]
elif dict.has_key("header") and isinstance(dict["header"], str):
fh = TableIO.parse(dict["header"])
self.header = fh.next()
# print >>sys.stderr,self.header
self.tabix_format = "simple"
if self.dict.has_key("tabix"):
self.tabix_format = self.dict["tabix"]
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()
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
'''
if args.genome is not None:
chr_sizes={}
for x in TableIO.parse(args.genome):
chr_sizes[x[0]]=int(x[1])
bins=b()
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)
print >>out,"chr\tstart\tstop\tbinindex\tcoverage\tcoverage_nt\tbinlevel\tbinsize "
header=False
if (args.format=="metabed"): header=True
for i,x in enumerate(TableIO.parse(fin,args.format,header=header)):
if i%1000==0:
print >>sys.stderr,"reading %d entries\r"%i,
bins.append(x)
c=b.bin2cov(bins)
for chr in sorted(c.keys()):
for i,x in enumerate(c[chr]):
(start,end)=b.bin2range(i)
if args.genome is not None:
if start > chr_sizes[chr]:
continue
if end > chr_sizes[chr]:
end=chr_sizes[chr]
print >>out,chr,"\t",start,"\t",end,"\t",i,"\t",float(x)/(end-start),"\t",x,"\t",b.bin2level(i),"\t",end-start
def Main():
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
h=[[0,0],[0,0]]
l=[[0,0],[0,0]]
d=Utils.readIntoBinIndex(TableIO.parse(args.centromere,"bed"))
print >>out,"# Coverage Threshold: ",args.t
print >>out,"# Chi2 Threshold:",args.chi2
for i in TableIO.parse(args.input,"oddsratiosnp"):
mark=0
for j in Utils.iterOverlapFeature(i,d):
mark+=1
if mark>1: mark=1
if sum(i.A_nt_dis) > args.t and sum(i.B_nt_dis) > args.t:
if i.odds_ratio > args.chi2:
h[mark][1]+=1
else:
h[mark][0]+=1
print >>out,i,"\tHigh\t",mark
else:
print >>out,i,"\tLow\t",mark
if i.odds_ratio > args.chi2:
l[mark][1]+=1
else:
l[mark][0]+=1
print >>out,"# HighOddsRatio:",h[0][1]+l[0][1]+h[1][1]+l[1][1]
print >>out,"# LowOddsRatio:",h[0][0]+l[0][0]+h[1][0]+l[1][0]
print >>out,"#"
print >>out,"# HighCoverage:",sum(h[1])+sum(h[0])
print >>out,"# LowCoverage :",sum(l[1])+sum(l[0])
print >>out,"#"
print >>out,"# HighCoverage, HighOddsRatio",h[1][1]+h[0][1]
print >>out,"# HighCoverage, LowOddsRatio",h[1][0]+h[0][0]
print >>out,"#"
print >>out,"# HighCoverage, InCentromere",sum(h[1])
print >>out,"# HighCoverage, NotInCentromere",sum(l[1])
print >>out,"#"
print >>out,"# HighCoverage, HighOddsRatio, InCentromere",h[1][1]
print >>out,"# HighCoverage, HighOddsRatio, NotInCentromere",h[0][1]
print >>out,"# HighCoverage, LowOddsRatio, InCentromere",h[1][0]
print >>out,"# HighCoverage, LowOddsRatio, NotInCentromere",h[0][0]
print >>out,"# LowCoverage, HighOddsRatio, InCentromere",l[1][1]
print >>out,"# LowCoverage, HighOddsRatio, NotInCentromere",l[0][1]
print >>out,"# LowCoverage, LowOddsRatio, InCentromere",l[1][0]
print >>out,"# LowCoverage, LowOddsRatio, NotInCentromere",l[0][0]
def Main():
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
h = [[0, 0], [0, 0]]
l = [[0, 0], [0, 0]]
d = Utils.readIntoBinIndex(TableIO.parse(args.centromere, "bed"))
print >> out, "# Coverage Threshold: ", args.t
print >> out, "# Chi2 Threshold:", args.chi2
for i in TableIO.parse(args.input, "oddsratiosnp"):
mark = 0
for j in Utils.iterOverlapFeature(i, d):
mark += 1
if mark > 1: mark = 1
if sum(i.A_nt_dis) > args.t and sum(i.B_nt_dis) > args.t:
if i.odds_ratio > args.chi2:
h[mark][1] += 1
else:
h[mark][0] += 1
print >> out, i, "\tHigh\t", mark
else:
print >> out, i, "\tLow\t", mark
if i.odds_ratio > args.chi2:
l[mark][1] += 1
else:
l[mark][0] += 1
print >> out, "# HighOddsRatio:", h[0][1] + l[0][1] + h[1][1] + l[1][1]
print >> out, "# LowOddsRatio:", h[0][0] + l[0][0] + h[1][0] + l[1][0]
print >> out, "#"
print >> out, "# HighCoverage:", sum(h[1]) + sum(h[0])
print >> out, "# LowCoverage :", sum(l[1]) + sum(l[0])
print >> out, "#"
print >> out, "# HighCoverage, HighOddsRatio", h[1][1] + h[0][1]
print >> out, "# HighCoverage, LowOddsRatio", h[1][0] + h[0][0]
print >> out, "#"
print >> out, "# HighCoverage, InCentromere", sum(h[1])
print >> out, "# HighCoverage, NotInCentromere", sum(l[1])
print >> out, "#"
print >> out, "# HighCoverage, HighOddsRatio, InCentromere", h[1][1]
print >> out, "# HighCoverage, HighOddsRatio, NotInCentromere", h[0][1]
print >> out, "# HighCoverage, LowOddsRatio, InCentromere", h[1][0]
print >> out, "# HighCoverage, LowOddsRatio, NotInCentromere", h[0][0]
print >> out, "# LowCoverage, HighOddsRatio, InCentromere", l[1][1]
print >> out, "# LowCoverage, HighOddsRatio, NotInCentromere", l[0][1]
print >> out, "# LowCoverage, LowOddsRatio, InCentromere", l[1][0]
print >> out, "# LowCoverage, LowOddsRatio, NotInCentromere", l[0][0]
def Main():
global args,out
CellLine=["H1"]
HM=("input","H3K27ac","H3K27me3","H3K36me3","H3K4me1","H3K4me3","H3K9me3")
marks=[]
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
for cell in CellLine:
for hm in HM:
mark=cell+"_"+hm
marks.append(mark)
dbi[mark]=DBI.init("/data/zhuxp/bam2x/data/bamlist/"+mark+".bamlist","bamlist")
for i,x in enumerate(TableIO.parse(args.input,args.input_format)):
print >>out,"QR\t",x
if i%100==0: print >>sys.stderr,"query %d entries\r"%i,
for mark in marks:
print >>out,mark,"\t"
for j in DBI.query(x,dbi[mark]):
print >>out,"HT\t",j
def parseIterChrom(fn):
last_chrom= None
fin=open(fn)
positions=[]
x2s=[]
coverage=[]
for x in TableIO.parse(fin,'simple'):
(chrom,pos,snp,x2,x2_matrix,nt_dist)=x
b=x2_matrix.replace("( ","")
b=b.replace(" )","")
a=b.split(" ")
x2_matrix=[]
s=0
for y in a:
s+=int(y)
x2_matrix.append(int(y))
if (last_chrom==None) or (chrom==last_chrom):
coverage.append(s)
positions.append(pos)
x2s.append(x2)
last_chrom=chrom
continue
yield last_chrom,positions,x2s,coverage
positions=[]
x2s=[]
coverage=[]
coverage.append(s)
x2s.append(x2)
positions.append(pos)
last_chrom=chrom
yield last_chrom,positions,x2s,coverage
def Main():
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
count={}
dbi1=DBI.init(args.db,"bed") # the DBI init file for bed6 file of all kinds of RNA
dbi2=DBI.init(args.db_detail,"bed") # the DBI init file for bed12 file of lincRNA and mRNA with intron, exon, UTR
genome=Genome('mouse', Release=67, account=None)
for bed in TableIO.parse(args.input,args.format):
[typ,name,subtype]=annotation(bed,dbi1,dbi2,genome)
if count.has_key(typ):
count[typ]+=1
else:
count[typ]=1
print >>out, "\t".join (str(f) for f in [bed.chr,bed.start,bed.stop,bed.id,name,bed.strand,typ, subtype])
print >>out, "\n".join ("#"+typ+"\t%d"%(count[typ]) for typ in count.keys())
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():
global args,out
MAX_SCORE=200
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
i=0
x=args.input.split("/")
name=x[-1]
name=name.replace(".OddsRatio.peaks","")
name=name.replace(".LogR.Peaks","")
name=name.replace(".out","")
name=args.prefix+name
for x in TableIO.parse(args.input,"simple"):
if x[0]=="REGION":
i+=1
if x[4]==0:
score=MAX_SCORE
else:
score=-10*math.log(x[4],10)
if score > MAX_SCORE:
score=MAX_SCORE
ID=name+"_ORP_"+str(i)
print >>out,x[1]+"\t"+str(x[2])+"\t"+str(x[3])+"\t"+ID+"\t",
print >>out,"%.2f"%score
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)
h1 = {}
h2 = {}
for i in TableIO.parse(fin):
h1[i[args.c1 - 1]] = i
for j in TableIO.parse(args.input2):
h2[j[args.c2 - 1]] = j
if h1.has_key(j[args.c2 - 1]):
print >> out, TableIO.format_string(
h1[j[args.c2 - 1]]) + "\t" + TableIO.format_string(j)
def main():
''' main scripts '''
args = parse_argument()
bed = args.bed
gene = readIntoBinIndex(TableIO.parse( args.genefile, "genebed") )
for i in TableIO.parse(args.bed, 'bed'):
if i.strand not in ['+','-']: continue
else:
OverlapGene = getOverlapFeatures(i, gene)
Overlap_dict = Classify_Overlap(i, OverlapGene)
overlap_string = ''
for k,v in Overlap_dict.iteritems():
if v:
overlap_string += "".join([ str(k+'_'+each)+';' for each in v])
if not overlap_string:
overlap_string = 'intergenic'
print i, overlap_string
def Main():
global args
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
dbi=DBI.init(args.db,"genebed")
count={}
count["Intergenic"]=0
for x in TableIO.parse(args.input,args.input_format):
flag=0
gene=""
for hit in dbi.query(x):
flag=1
if hit.align_id==gene:
continue
gene=hit.align_id
#print hit
#print hit.cds_start,hit.cds_stop
if (hit.cds_start==hit.cds_stop):
if hit.align_id[0:3]=="Mir":
loc="MiRNA"
else:
loc="Non-coding"
elif hit.strand=="+":
if x.stop<=hit.cds_start:
loc="5-UTR"
elif x.start>=hit.cds_stop:
loc="3-UTR"
else:
loc=judge_exon(x,hit)
else:
if x.stop<=hit.cds_start:
loc="3-UTR"
elif x.start>=hit.cds_stop:
loc="5-UTR"
else:
loc=judge_exon(x,hit)
print >>out,"\t".join (str(f) for f in [x.chr,x.start,x.stop,x.id,x.score,x.strand,hit.align_id,loc])
if count.has_key(loc):
count[loc]+=1
else:
count[loc]=1
if flag==0:
print >>out, "\t".join (str(f) for f in [x.chr,x.start,x.stop,x.id,x.score,x.strand,"None","Intergenic"])
count["Intergenic"]+=1
out2=open(args.output.split(".")[0]+".cisStat","w")
for key in sorted(count.keys()):
print >>out2,key+"\t"+str(count[key])
def Main():
args = ParseArg()
if len(args.data) != len(args.name):
print >> sys.stderr, "ERROR: Number of data is not the same as number of names!"
sys.exit(0)
# store data information
data = {}
total_reads = {}
for i in range(len(args.data)):
temp_name = args.name[i]
print >> sys.stderr, "\n Reading data file:" + temp_name + "..."
total_reads[temp_name] = 0
if args.format[i] == "bam":
total_reads[temp_name] = reduce(lambda x, y: x + y, [
int(l.rstrip('\n').split('\t')[2])
for l in pysam.idxstats(args.data[i])
])
else:
Format = "bed"
for b in TableIO.parse(args.data[i], Format):
total_reads[temp_name] += 1
if total_reads[temp_name] % 50000 == 0:
print >> sys.stderr, " reading %d reads..\r" % (
total_reads[temp_name]),
data[temp_name] = DBI.init(args.data[i], args.format[i])
output = open(args.output, 'w')
Input = open(args.input, 'r')
lines = Input.read().split("\n")
# header
header = ["chr", "start", "end", "type", "name", "subtype", "count"
] + data.keys()
print >> output, "\t".join(g + "_%d" % (f) for f in [1, 2]
for g in header) + "\tinteraction\tp-value"
num = 0
print >> sys.stderr, "Start process interactions:"
for l in lines:
if l.strip() == '': continue
l = l.strip().split('\t')
num = num + 1
if l[0] == "chrM" or l[7] == "chrM": continue
C1 = Bed([l[0], int(l[1]), int(l[2])])
C2 = Bed([l[7], int(l[8]), int(l[9])])
rpkm1 = "\t".join(
str(f) for f in
[RPKM(C1, data[n], total_reads[n], n) for n in data.keys()])
rpkm2 = "\t".join(
str(f) for f in
[RPKM(C2, data[n], total_reads[n], n) for n in data.keys()])
print >> output, "\t".join(
str(f) for f in l[:7] + [rpkm1] + l[7:14] + [rpkm2, l[14], l[15]])
if num % 1000 == 0:
print >> sys.stderr, " Output interaction: %d\r" % (num),
def main():
''' main scripts '''
args = parse_argument()
bed = args.bed
gene = readIntoBinIndex(TableIO.parse(args.genefile, "genebed"))
for i in TableIO.parse(args.bed, 'bed'):
if i.strand not in ['+', '-']: continue
else:
OverlapGene = getOverlapFeatures(i, gene)
Overlap_dict = Classify_Overlap(i, OverlapGene)
overlap_string = ''
for k, v in Overlap_dict.iteritems():
if v:
overlap_string += "".join(
[str(k + '_' + each) + ';' for each in v])
if not overlap_string:
overlap_string = 'intergenic'
print i, overlap_string
def toBed12Tuple(self,chr="chr",strand="read2"):
'''
test now
'''
from xplib import TableIO
x=list()
for i in TableIO.parse(self.reads,"bam2bed12tuple",references=chr,strand=strand):
x.append(i)
return x
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)
enhancer_dbi = DBI.init(args.enhancer_tabix,
"tabix",
tabix="metabed",
header=re.sub(".gz$", ".header",
args.enhancer_tabix))
promoter_dbi = DBI.init(args.promoter_tabix,
"tabix",
tabix="metabed",
header=re.sub(".gz$", ".header",
args.promoter_tabix))
for i in TableIO.parse(fin, args.format):
tss = i.tss()
tss.start -= args.size
tss.stop += args.size
if tss.start < 0: tss.start = 0
tss.id += "_near" + str(args.size)
print "QR\t", tss
for e in enhancer_dbi.query(tss):
print "EH\t", e
for p in promoter_dbi.query(tss):
print "PM\t", p
def query(self,x,**kwargs):
'''
yield the overlap feature in tabix index files
'''
try:
for item in TableIO.parse(self.data.fetch(x.chr,x.start,x.stop),format=self.tabix_format,header=self.header):
yield item
except:
raise StopIteration
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)
h1={}
h2={}
for i in TableIO.parse(fin):
h1[i[args.c1-1]]=i
for j in TableIO.parse(args.input2):
h2[j[args.c2-1]]=j
if h1.has_key(j[args.c2-1]):
print >>out,TableIO.format_string(h1[j[args.c2-1]])+"\t"+TableIO.format_string(j)
def __init__(self,file,**dict):
'''
Wrapped in xplib.DBI.init()
'''
if type(file)==type([1,2,3]):
f=file
else:
format=dict['format']
f=TableIO.parse(file,format)
self.data=binindex(f)
def __init__(self,file,**dict):
'''
Wrapped in xplib.DBI.init()
'''
if type(file)==type([1,2,3]):
f=file
else:
format=dict['format']
f=TableIO.parse(file,format)
self.data=binindex(f)
def test():
if len(sys.argv)==1:
print >>sys.stderr,"Usage: Utils.py file.bed"
exit()
a=TableIO.parse(sys.argv[1],'bed')
data=readIntoBinIndex(a)
bed=Bed(["chr1",100000,200000,".",".","."])
g=getOverlapFeatures(bed,data)
print "Overlap with",bed
for i in g:
print i
def test():
if len(sys.argv) == 1:
print >> sys.stderr, "Usage: Utils.py file.bed"
exit()
a = TableIO.parse(sys.argv[1], 'bed')
data = readIntoBinIndex(a)
bed = Bed(["chr1", 100000, 200000, ".", ".", "."])
g = getOverlapFeatures(bed, data)
print "Overlap with", bed
for i in g:
print i
def query(self,x):
'''
yield the overlap feature in tabix index files
'''
f="simple"
if self.dict.has_key("tabix"):
f=self.dict["tabix"]
try:
for item in TableIO.parse(self.data.fetch(x.chr,x.start,x.stop),format=f,header=self.header):
yield item
except:
raise StopIteration
def parseIterRegion(fn):
'''
yield each region ( gap < args.gap)
'''
last_chrom = None
last_position = 0
fin = open(fn)
positions = []
x2s = []
snps = []
matrix_x2 = []
for x in TableIO.parse(fin, 'simple'):
(chrom, pos, snp, x2, x2_matrix, nt_dist) = x
'''
add filter here
'''
b = x2_matrix.replace("( ", "")
b = b.replace(" )", "")
a = b.split(" ")
x2_matrix = []
for y in a:
x2_matrix.append(int(y))
t = x2_matrix
CV = int(t[0]) + int(t[1]) + int(t[2]) + int(t[3])
MR = (float(t[1]) + float(t[3])) / CV
if (CV > args.reads or MR < 0.05): continue
# end of filter
if (last_chrom == None) or (chrom == last_chrom
and pos - last_position < args.gap):
matrix_x2.append(x2_matrix)
positions.append(pos)
x2s.append(x2)
snps.append(snp)
last_chrom = chrom
last_position = pos
continue
yield last_chrom, positions, x2s, matrix_x2, snps
positions = []
x2s = []
matrix_x2 = []
snps = []
matrix_x2.append(x2_matrix)
x2s.append(x2)
positions.append(pos)
snps.append(snp)
last_chrom = chrom
last_position = pos
yield last_chrom, positions, x2s, matrix_x2, snps
def Main():
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
for i in TableIO.parse(args.input, "oddsratiosnp"):
print i
def parseAnnotationFile(fn):
format=args.format
if format=="bam":
format="bam2bed"
for x in TableIO.parse(fn,format):
if not data.has_key(x.chr):
print >>sys.stderr,"ignore",x
print >>sys.stderr,"since this chromosome size is not in ",args.chr_length_file
continue
bin_start=x.start>>SHIFTSIZE
bin_stop=x.stop>>SHIFTSIZE
for bin in range(bin_start,bin_stop+1):
data[x.chr][bin]+=1
def parseAnnotationFile(fn):
format = args.format
if format == "bam":
format = "bam2bed"
for x in TableIO.parse(fn, format):
if not data.has_key(x.chr):
print >> sys.stderr, "ignore", x
print >> sys.stderr, "since this chromosome size is not in ", args.chr_length_file
continue
bin_start = x.start >> SHIFTSIZE
bin_stop = x.stop >> SHIFTSIZE
for bin in range(bin_start, bin_stop + 1):
data[x.chr][bin] += 1
def Main():
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
for i in TableIO.parse(args.input,'transunit'):
print >>out,i
def parseIterRegion(fn):
'''
yield each region ( gap < args.gap)
'''
last_chrom= None
last_position = 0
fin=open(fn)
positions=[]
x2s=[]
snps=[]
matrix_x2=[]
for x in TableIO.parse(fin,'simple'):
(chrom,pos,snp,x2,x2_matrix,nt_dist)=x
'''
add filter here
'''
b=x2_matrix.replace("( ","")
b=b.replace(" )","")
a=b.split(" ")
x2_matrix=[]
for y in a:
x2_matrix.append(int(y))
t=x2_matrix
CV=int(t[0])+int(t[1])+int(t[2])+int(t[3])
MR=(float(t[1])+float(t[3]))/CV
if(CV>args.reads or MR<0.05):continue
# end of filter
if (last_chrom==None) or (chrom==last_chrom and pos-last_position < args.gap):
matrix_x2.append(x2_matrix)
positions.append(pos)
x2s.append(x2)
snps.append(snp)
last_chrom=chrom
last_position=pos
continue
yield last_chrom,positions,x2s,matrix_x2,snps
positions=[]
x2s=[]
matrix_x2=[]
snps=[]
matrix_x2.append(x2_matrix)
x2s.append(x2)
positions.append(pos)
snps.append(snp)
last_chrom=chrom
last_position=pos
yield last_chrom,positions,x2s,matrix_x2,snps
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 test():
if len(sys.argv)==1:
print >>sys.stderr,"Usage: Utils.py file.bed"
exit()
a=TableIO.parse(sys.argv[1],'genebed')
data=readIntoBinIndex(a)
bed=Bed( ["chr12", 54380000, 54392000, "HOXC", 0, "+"] )
g=getOverlapFeatures(bed,data)
Overlap_dict = Classify_Overlap(bed, g)
overlap_string = ''
for k, v in Overlap_dict.iteritems():
if v:
overlap_string += "".join([ str(k+'_'+each)+';' for each in v])
print bed, overlap_string
def test():
if len(sys.argv) == 1:
print >> sys.stderr, "Usage: Utils.py file.bed"
exit()
a = TableIO.parse(sys.argv[1], 'genebed')
data = readIntoBinIndex(a)
bed = Bed(["chr12", 54380000, 54392000, "HOXC", 0, "+"])
g = getOverlapFeatures(bed, data)
Overlap_dict = Classify_Overlap(bed, g)
overlap_string = ''
for k, v in Overlap_dict.iteritems():
if v:
overlap_string += "".join(
[str(k + '_' + each) + ';' for each in v])
print bed, overlap_string
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)
enhancer_dbi=DBI.init(args.enhancer_tabix,"tabix",tabix="metabed",header=re.sub(".gz$",".header",args.enhancer_tabix))
promoter_dbi=DBI.init(args.promoter_tabix,"tabix",tabix="metabed",header=re.sub(".gz$",".header",args.promoter_tabix))
for i in TableIO.parse(fin,args.format):
tss=i.tss()
tss.start-=args.size
tss.stop+=args.size
if tss.start<0: tss.start=0
tss.id+="_near"+str(args.size)
print "QR\t",tss
for e in enhancer_dbi.query(tss):
print "EH\t",e
for p in promoter_dbi.query(tss):
print "PM\t",p
def Main():
args=ParseArg()
if len(args.data)!=len(args.name):
print >> sys.stderr, "ERROR: Number of data is not the same as number of names!"
sys.exit(0)
# store data information
data={}
total_reads={}
for i in range(len(args.data)):
temp_name=args.name[i]
print >> sys.stderr, "\n Reading data file:"+temp_name+"..."
total_reads[temp_name]=0
if args.format[i]=="bam":
total_reads[temp_name] = reduce(lambda x, y: x + y, [ int(l.rstrip('\n').split('\t')[2]) for l in pysam.idxstats(args.data[i])])
else:
Format="bed"
for b in TableIO.parse(args.data[i],Format):
total_reads[temp_name]+=1
if total_reads[temp_name]%50000==0:
print >> sys.stderr, " reading %d reads..\r"%(total_reads[temp_name]),
data[temp_name]=DBI.init(args.data[i],args.format[i])
output=open(args.output,'w')
Input=open(args.input,'r')
lines=Input.read().split("\n")
# header
header=["chr","start","end","type","name","subtype","count"]+data.keys()
print >> output, "\t".join(g+"_%d"%(f) for f in [1,2] for g in header)+"\tinteraction\tp-value"
num=0
print >> sys.stderr, "Start process interactions:"
for l in lines:
if l.strip()=='': continue
l=l.strip().split('\t')
num=num+1
if l[0]=="chrM" or l[7]=="chrM": continue
C1=Bed([l[0],int(l[1]),int(l[2])])
C2=Bed([l[7],int(l[8]),int(l[9])])
rpkm1="\t".join (str(f) for f in [RPKM(C1,data[n],total_reads[n],n) for n in data.keys()])
rpkm2="\t".join (str(f) for f in [RPKM(C2,data[n],total_reads[n],n) for n in data.keys()])
print >> output, "\t".join(str(f) for f in l[:7]+[rpkm1]+l[7:14]+[rpkm2,l[14],l[15]])
if num%1000==0:
print >> sys.stderr, " Output interaction: %d\r"%(num),
def __init__(self,bamfiles,**dict):
'''
'''
if type(bamfiles)==type("string"):
filename=bamfiles
bamfiles=[]
for i in TableIO.parse(filename,"simple"):
bamfiles.append(i[0])
self.bamfiles=[]
for bamfile in bamfiles:
if type(bamfile)==type("str"):
try:
bamfile=pysam.Samfile(bamfile,"rb")
except:
print >>sys.stderr,"WARNING: Can't init the bam file",bamfile
self.bamfiles.append(bamfile)
def __init__(self,bamfiles,**dict):
'''
'''
if type(bamfiles)==type("string"):
filename=bamfiles
bamfiles=[]
for i in TableIO.parse(filename,"simple"):
bamfiles.append(i[0])
self.bamfiles=[]
for bamfile in bamfiles:
if type(bamfile)==type("str"):
try:
bamfile=pysam.Samfile(bamfile,"rb")
except:
print >>sys.stderr,"WARNING: Can't init the bam file",bamfile
self.bamfiles.append(bamfile)
def ParseInput(fin):
flag=0
for x in TableIO.parse(fin):
if x[0]=="VCF":
if flag==1:
yield (vcf,hm,hits)
vcf=VCF(x[1:])
hm=[]
hits=[]
flag=1
elif x[0]=="HM ":
hm=x[1:]
elif x[0]=="DIS ":
hits=x[1:]
yield (vcf,hm,hits)
def Main():
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
extend=args.extend
f=open(args.input)
for bed in TableIO.parse(f,"bed"):
bed.start-=extend
bed.stop+=extend
bed.id+=str("_extend_"+str(extend)+"bp")
print >>out,bed
def parse(fin):
flag=0
for x in TableIO.parse(fin):
if x[0]=="QR":
if flag==1:
yield (vcf,sorted(HM.keys()),hits)
vcf=VCF(x[1:])
HM={}
hits={}
flag=1
elif x[0]=="HT":
hit=eval(x[1])
hits[hm]=hit
else:
(cell,hm)=x[0].split("_")
if not HM.has_key(hm):
HM[hm]=1
yield (vcf,sorted(HM.keys()),hits)
def Main():
'''
This program is a test for TableIO.parse(file.bam,"bam2bed")
'''
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
s = TableIO.parse(args.input, "bam2bed")
for i in s:
print >> out, i
def Main():
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
extend = args.extend
f = open(args.input)
for bed in TableIO.parse(f, "bed"):
bed.start -= extend
bed.stop += extend
bed.id += str("_extend_" + str(extend) + "bp")
print >> out, bed
def Main():
args = ParseArg()
#store bed files with indexing and count information:
bed = {}
print >> sys.stderr, "Starting index bed files:"
for i in range(len(args.beds)):
temp_name = args.name[i]
print >> sys.stderr, " #Indexing for bed file of", temp_name, "\r",
bed[temp_name] = DBI.init(args.beds[i], 'bed')
half_len = int(args.len)
print >> sys.stderr
print >> sys.stderr, "Reading nucleosome peak xls file from Danpos."
nucleosomes = TableIO.parse(args.nucleosome, 'metabed', header=True)
print >> sys.stderr, "Start Counting..."
count_matrix = []
out = open(args.output, "w")
line_head = open(args.nucleosome, 'r').readline().strip()
line_head = line_head + "\t" + "\t".join(str(f) for f in args.name)
print >> out, line_head
for i in nucleosomes:
chrom = i.chr
if chrom == 'chrY' or chrom == 'chrX' or chrom == 'chrM':
continue
center = int(i.start + i.end) / 2
count = np.zeros(len(args.beds), dtype="float")
line = str(i)
for k, name in enumerate(bed.keys()):
for j in bed[name].query(
Bed([
chrom, center - ma - (half_len - 75),
center + ma + (half_len - 75)
])):
j_center = find_center(j, half_len)
weight = max(min(1, (ma - abs(j_center - center)) / 25.0), 0)
count[k] += weight
line = line + "\t" + "\t".join(str(f) for f in count)
print >> out, line
count_matrix.append(count)
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)
genome = GenomeI(args.genome)
for i in TableIO.parse(fin, args.format):
print >> out, ">" + i.id + "_cDNA"
if args.line:
print >> out, genome.get_cdna_seq(i)
else:
print >> out, seq_wrapper(genome.get_cdna_seq(i))
def Main():
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
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)
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
query_sets=[]
for x in TableIO.parse(input,args.input_format):
query_sets.append(x)
length=len(query_sets)
size=length/args.thread
#results=[[] for i in range(args.thread)]
for i in range(args.thread):
end= (i+1)*size if (i+1)*size < length else length
end= end if (i+1)!=args.thread else length
querys=query_sets[i*size:end]
# print i*size,end
# for j in querys: print j
thread.start_new_thread(fquery,(querys,dbi,i))
def __init__(self,handle=None,**kwargs):
self.data={}
if handle is not None:
self.read(handle)
'''
init from file
Example:
data=binindex(file="file.bed")
or
data=binindex(file="file.vcf",format="vcf")
'''
if kwargs.has_key("format"):
format=kwargs["format"]
del kwargs["format"]
else:
format="bed"
if kwargs.has_key("file"):
f=kwargs["file"]
del kwargs["file"]
self.read(TableIO.parse(f,format,**kwargs))
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
