Example #1
0
File: depth.py Project: SMC1/JK1
def loadExonH():

	exnH = {}

	refFlatH = mygenome.loadRefFlatByChr()

	for chrom in refFlatH.keys():
		
		if chrom not in exnH:
			exnH[chrom] = []

		for tH in refFlatH[chrom]:

			for i in range(len(tH['exnList'])):
				exnH[chrom].append(tH['exnList'][i])

		exnH[chrom] = list(set(exnH[chrom]))

		exnH[chrom].sort(lambda x,y: cmp(x[1],y[1]))
		exnH[chrom].sort(lambda x,y: cmp(x[0],y[0]))


	random.seed()
	tmpN = 'tmp_%d' % random.randint(1, 1000)
	tmpF = open(tmpN,'w')
	for chrom in exnH:
		if len(chrom) > 6:
			continue
		for i in range(len(exnH[chrom])):
			tmpF.write('%s\t%s\t%s\n' % (chrom, int(exnH[chrom][i][0])-1, int(exnH[chrom][i][1])))
	tmpF.flush()
	tmpF.close()
	totalLen = os.popen('%s/NGS/quality/non-overlap.sh %s' % (mysetting.SRC_HOME, tmpN)).readlines()[0].rstrip()
	return exnH, int(totalLen)
Example #2
0
def loadExonH():

    exonH = {}

    refFlatH = mygenome.loadRefFlatByChr()

    for chrom in refFlatH.keys():

        if chrom not in exonH:
            exonH[chrom] = []

        for tH in refFlatH[chrom]:

            for i in range(len(tH['exnList'])):
                exonH[chrom].append(tH['exnList'][i])

    kgH = mygenome.loadKgByChr()

    for chrom in kgH.keys():

        if chrom not in exonH:
            exonH[chrom] = []

        for tH in kgH[chrom]:

            for i in range(len(tH['exnList'])):
                exonH[chrom].append(tH['exnList'][i])

        exonH[chrom] = list(set(exonH[chrom]))

        exonH[chrom].sort(lambda x, y: cmp(x[1], y[1]))
        exonH[chrom].sort(lambda x, y: cmp(x[0], y[0]))

    return exonH
Example #3
0
def loadExonH():

    exonH = {}

    refFlatH = mygenome.loadRefFlatByChr()

    for chrom in refFlatH.keys():

        if chrom not in exonH:
            exonH[chrom] = []

        for tH in refFlatH[chrom]:

            for i in range(len(tH["exnList"])):
                exonH[chrom].append(tH["exnList"][i])

    kgH = mygenome.loadKgByChr()

    for chrom in kgH.keys():

        if chrom not in exonH:
            exonH[chrom] = []

        for tH in kgH[chrom]:

            for i in range(len(tH["exnList"])):
                exonH[chrom].append(tH["exnList"][i])

        exonH[chrom] = list(set(exonH[chrom]))

        exonH[chrom].sort(lambda x, y: cmp(x[1], y[1]))
        exonH[chrom].sort(lambda x, y: cmp(x[0], y[0]))

    return exonH
Example #4
0
def loadAnnot(geneL=[]):

	refFlatH = mygenome.loadRefFlatByChr()

	eiH = {}
	ei_keyH = {}
	juncInfoH = {}

	for chrom in refFlatH.keys():

		eiH[chrom] = {}
		juncInfoH[chrom] = {}

		refFlatL = refFlatH[chrom]

		for tH in refFlatL:

			if geneL!=[] and tH['geneName'] not in geneL:
				continue

			for i in range(len(tH['exnList'])):

				if tH['strand'] == '+':
					pos = tH['exnList'][i][1]
					e_num = i+1
				else:
					pos = tH['exnList'][i][0]
					e_num = len(tH['exnList'])-i

				mybasic.addHash(juncInfoH[chrom], pos, '%s%s:%s:%s/%s' % (tH['strand'], tH['geneName'], tH['refSeqId'], e_num, len(tH['exnList'])))
				eiH[chrom][pos] = 0

		ei_keyH[chrom] = eiH[chrom].keys()
		ei_keyH[chrom].sort()

	ei_cntH = {}
	for chrom in juncInfoH.keys():
		ei_cntH[chrom] = {}
		i = 0
		for pos in sorted(juncInfoH[chrom].keys()):
			i += 1
			ei_cntH[chrom][pos] = i

	return eiH,ei_keyH,juncInfoH,ei_cntH
Example #5
0
def loadAnnot(geneL=[]):

	refFlatH = mygenome.loadRefFlatByChr()

	eiH = {}
	ei_keyH = {}
	juncInfoH = {}

	for chrom in refFlatH.keys():

		eiH[chrom] = {}
		juncInfoH[chrom] = {}

		refFlatL = refFlatH[chrom]

		for tH in refFlatL:

			if geneL!=[] and tH['geneName'] not in geneL:
				continue

			for i in range(len(tH['exnList'])):

				if tH['strand'] == '+':
					pos = tH['exnList'][i][1]
					e_num = i+1
				else:
					pos = tH['exnList'][i][0]
					e_num = len(tH['exnList'])-i

				mybasic.addHash(juncInfoH[chrom], pos, '%s%s:%s:%s/%s' % (tH['strand'], tH['geneName'], tH['refSeqId'], e_num, len(tH['exnList'])))
				eiH[chrom][pos] = 0

				cursor.execute('replace into temp_table (chrom,pos) values ("%s",%s)' % (chrom,pos))

		ei_keyH[chrom] = eiH[chrom].keys()
		ei_keyH[chrom].sort()

	return eiH,ei_keyH,juncInfoH
Example #6
0
def loadExonH():

    exnH = {}

    refFlatH = mygenome.loadRefFlatByChr()

    for chrom in refFlatH.keys():

        if chrom not in exnH:
            exnH[chrom] = []

        for tH in refFlatH[chrom]:

            for i in range(len(tH['exnList'])):
                exnH[chrom].append(tH['exnList'][i])

        exnH[chrom] = list(set(exnH[chrom]))

        exnH[chrom].sort(lambda x, y: cmp(x[1], y[1]))
        exnH[chrom].sort(lambda x, y: cmp(x[0], y[0]))

    random.seed()
    tmpN = 'tmp_%d' % random.randint(1, 1000)
    tmpF = open(tmpN, 'w')
    for chrom in exnH:
        if len(chrom) > 6:
            continue
        for i in range(len(exnH[chrom])):
            tmpF.write(
                '%s\t%s\t%s\n' %
                (chrom, int(exnH[chrom][i][0]) - 1, int(exnH[chrom][i][1])))
    tmpF.flush()
    tmpF.close()
    totalLen = os.popen('%s/NGS/quality/non-overlap.sh %s' %
                        (mysetting.SRC_HOME, tmpN)).readlines()[0].rstrip()
    return exnH, int(totalLen)
Example #7
0
data = {}

filePathPrefix = bedgraphFileN.split('.bedgraph')[0]
split = filePathPrefix.split('/')
sampN = split[len(split) - 1]

#if 'D-' in sampN:
#	DorW='D'
#elif 'SOLiD' in sampN:
#	DorW='W-SOLiD'
#else:
#	DorW='W'

bedgraph = open(bedgraphFileN, 'r')
refFlat = mygenome.loadRefFlatByChr(refFlatFileN)

for line in bedgraph:
    l = line.split('\t')
    chr_sample = l[0]
    if refFlat.has_key(chr_sample):
        s = int(l[1])
        e = int(l[2])
        d = int(l[3])
        for gene in refFlat[chr_sample]:
            GeneN = gene['geneName']
            if not data.has_key(GeneN):
                data.update({GeneN: {}})
            SeqId = gene['refSeqId']
            if not data[GeneN].has_key(SeqId):
                data[GeneN].update(
Example #8
0
File: 1s1gene.py Project: SMC1/JK1
data={}

filePathPrefix = bedgraphFileN.split('.bedgraph')[0]
split=filePathPrefix.split('/')
sampN = split[len(split)-1]

#if 'D-' in sampN:
#	DorW='D'
#elif 'SOLiD' in sampN:
#	DorW='W-SOLiD'
#else:
#	DorW='W'

bedgraph=open(bedgraphFileN,'r')
refFlat=mygenome.loadRefFlatByChr(refFlatFileN)


for line in bedgraph:
	l=line.split('\t')
	chr_sample=l[0]
	if refFlat.has_key(chr_sample):
		s=int(l[1])
		e=int(l[2])
		d=int(l[3])
		for gene in refFlat[chr_sample]:
			GeneN=gene['geneName']
			if not data.has_key(GeneN):
				data.update({GeneN:{}})
			SeqId=gene['refSeqId']
			if not data[GeneN].has_key(SeqId):
Example #9
0
def exonSkip_proc(inGsnapFileName, outGsnapFileName, outReportFileName, sampN):

    geneNameH = mygenome.geneNameH()
    geneSetH = mygenome.geneSetH()
    geneInfoH = mygenome.geneInfoH(geneNameH, geneSetH)
    refFlatH = mygenome.loadRefFlatByChr()

    result = mygsnap.gsnapFile(inGsnapFileName, False)

    juncHH = {}

    for r in result:

        match = r.matchL()[0]

        if not '(transloc)' in r.pairRel:
            raise Exception

        if len(match.segL) != 2:
            raise Exception

        splice_type = re.search('splice_type:([^,\t]*)',
                                match.segL[0][3]).group(1)
        direction = re.search('dir:([^,\t]*)', match.segL[0][3]).group(1)
        offset = int(re.search('\.\.([0-9]*)', match.segL[0][1]).group(1))

        transcript1 = re.search('label_[12]:([^,\t]*)', match.segL[0][3])
        gene1 = set()

        if transcript1:

            transcript1 = tuple(
                [x.split('.exon')[0] for x in transcript1.group(1).split('|')])

            for t in transcript1:

                g = mygenome.gene(t, geneNameH, geneSetH, geneInfoH)

                if g.geneName:
                    gene1.add(g.geneName)

        else:

            transcript1 = ()

        transcript2 = re.search('label_[12]:([^,\t]*)', match.segL[1][3])
        gene2 = set()

        if transcript2:

            transcript2 = tuple(
                [x.split('.exon')[0] for x in transcript2.group(1).split('|')])

            for t in transcript2:

                g = mygenome.gene(t, geneNameH, geneSetH, geneInfoH)

                if g.geneName:
                    gene2.add(g.geneName)

        else:

            transcript2 = ()

        s1 = match.segL[0][2]
        s2 = match.segL[1][2]

        bp1 = re.match('([+-])([^:]+):[0-9]+..([0-9]+)', s1)
        bp2 = re.match('([+-])([^:]+):([0-9]+)..[0-9]+', s2)

        if (bp1.group(1), direction) in (('+', 'sense'), ('-', 'antisense')):
            trans_strand1 = '+'
        elif (bp1.group(1), direction) in (('+', 'antisense'), ('-', 'sense')):
            trans_strand1 = '-'
        else:
            raise Exception

        if (bp2.group(1), direction) in (('+', 'sense'), ('-', 'antisense')):
            trans_strand2 = '+'
        elif (bp2.group(1), direction) in (('+', 'antisense'), ('-', 'sense')):
            trans_strand2 = '-'
        else:
            raise Exception

        bp_gene1 = mygenome.locus(
            '%s:%s-%s%s' % (bp1.group(2), int(bp1.group(3)) - 1, bp1.group(3),
                            trans_strand1)).overlappingGeneL(
                                refFlatH=refFlatH, strand_sensitive=True)
        bp_gene2 = mygenome.locus(
            '%s:%s-%s%s' % (bp2.group(2), int(bp2.group(3)) - 1, bp2.group(3),
                            trans_strand2)).overlappingGeneL(
                                refFlatH=refFlatH, strand_sensitive=True)

        if direction == 'sense':
            key = (bp1.groups()[1:], bp2.groups()[1:])
            transcript = (transcript1, transcript2)
            gene = (tuple(gene1), tuple(gene2))
            bp_gene = (bp_gene1, bp_gene2)
        elif direction == 'antisense':
            key = (bp2.groups()[1:], bp1.groups()[1:])
            transcript = (transcript2, transcript1)
            gene = (tuple(gene2), tuple(gene1))
            bp_gene = (bp_gene2, bp_gene1)
        else:
            raise Exception

        if key in juncHH:

            juncHH[key]['match'].append(r)
            juncHH[key]['seq'].append(r.seq())
            juncHH[key]['reg'].append((direction, offset))

        else:

            juncHH[key] = {
                'match': [r],
                'splice_type': splice_type,
                'seq': [r.seq()],
                'reg': [(direction, offset)],
                'transcript': transcript,
                'gene': gene,
                'bp_gene': bp_gene
            }

    juncKH = juncHH.items()
    juncKH.sort(lambda x, y: cmp(len(set(y[1]['reg'])), len(set(x[1]['reg']))))

    outGsnapFile = open(outGsnapFileName, 'w')
    outReportFile = open(outReportFileName, 'w')

    for (key, juncH) in juncKH:

        if key[0][0] == key[1][0]:
            type = 'intra'
        else:
            type = 'inter'

        geneInfo1 = []
        censusInfo1 = []

        for geneName in juncH['gene'][0]:
            gene = mygenome.gene(geneName, geneNameH, geneSetH, geneInfoH)
            geneInfo1.append(
                '%s:%s:%s' %
                (geneName, gene.getAttr('desc'), gene.getAttr('summary')))
            censusInfo1.append('%s:%s:%s:%s' %
                               (gene.getAttr('census_somatic'),
                                gene.getAttr('census_germline'),
                                gene.getAttr('census_mutType'),
                                gene.getAttr('census_translocPartners')))

        geneInfo2 = []
        censusInfo2 = []

        for geneName in juncH['gene'][1]:
            gene = mygenome.gene(geneName, geneNameH, geneSetH, geneInfoH)
            geneInfo2.append(
                '%s:%s:%s' %
                (geneName, gene.getAttr('desc'), gene.getAttr('summary')))
            censusInfo2.append('%s:%s:%s:%s' %
                               (gene.getAttr('census_somatic'),
                                gene.getAttr('census_germline'),
                                gene.getAttr('census_mutType'),
                                gene.getAttr('census_translocPartners')))

        outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
         (type, juncH['splice_type'], sampN, ':'.join(key[0]), ':'.join(key[1]), \
         ';'.join(juncH['transcript'][0]), ';'.join(juncH['transcript'][1]), ';'.join(juncH['gene'][0]), ';'.join(juncH['gene'][1]), ';'.join(geneInfo1), ';'.join(geneInfo2), \
         ';'.join(censusInfo1), ';'.join(censusInfo2), ','.join(juncH['bp_gene'][0]), ','.join(juncH['bp_gene'][1]), \
         len(juncH['match']) ,len(set(juncH['seq'])), len(set(juncH['reg']))))

        for m in juncH['match']:
            outGsnapFile.write(m.rawText() + '\n')
Example #10
0
def gsnap_process_junction(inGsnapFileName,outGsnapFileName,outReportFileName,sampN):

	geneNameH = mygenome.geneNameH()
	geneSetH = mygenome.geneSetH()
	geneInfoH = mygenome.geneInfoH(geneNameH,geneSetH)
	refFlatH = mygenome.loadRefFlatByChr()

	result = mygsnap.gsnapFile(inGsnapFileName,False)

	juncHH = {}

	for r in result:

		match = r.matchL()[0]

		if not '(transloc)' in r.pairRel:
			raise Exception

		if len(match.segL) != 2:
			raise Exception

		splice_type = re.search('splice_type:([^,\t]*)', match.segL[0][3]).group(1)
		direction = re.search('dir:([^,\t]*)', match.segL[0][3]).group(1)
		offset = int(re.search('\.\.([0-9]*)', match.segL[0][1]).group(1))

		rm = re.search('label_[12]:([^,\t]*)', match.segL[0][3])
		gene1 = set()

		if rm:

			trans_exon1 = rm.group(1).split('|')

			for t in trans_exon1:

				g = mygenome.gene(t.split('.exon')[0],geneNameH,geneSetH,geneInfoH)

				if g.geneName:
					gene1.add(g.geneName)

		else:

			trans_exon1 = ()

		rm = re.search('label_[12]:([^,\t]*)', match.segL[0][3])
		gene2 = set()

		if rm:

			trans_exon2 = rm.group(1).split('|')

			for t in trans_exon2:

				g = mygenome.gene(t.split('.exon')[0],geneNameH,geneSetH,geneInfoH)

				if g.geneName:
					gene2.add(g.geneName)

		else:

			trans_exon2 = ()


		s1 = match.segL[0][2]
		s2 = match.segL[1][2]

		bp1 = re.match('([+-])([^:]+):[0-9]+..([0-9]+)',s1)
		bp2 = re.match('([+-])([^:]+):([0-9]+)..[0-9]+',s2)

		if (bp1.group(1),direction) in (('+','sense'),('-','antisense')):
			trans_strand1 = '+'
		elif (bp1.group(1),direction) in (('+','antisense'),('-','sense')):
			trans_strand1 = '-'
		else:
			raise Exception

		if (bp2.group(1),direction) in (('+','sense'),('-','antisense')):
			trans_strand2 = '+'
		elif (bp2.group(1),direction) in (('+','antisense'),('-','sense')):
			trans_strand2 = '-'
		else:
			raise Exception

		locus1 = mygenome.locus('%s:%s-%s%s' % (bp1.group(2),int(bp1.group(3))-1,bp1.group(3),trans_strand1))
		bp_gene1 = list(set(locus1.overlappingGeneL(refFlatH=refFlatH,strand_sensitive=True)).difference(gene1))

		locus2 = mygenome.locus('%s:%s-%s%s' % (bp2.group(2),int(bp2.group(3))-2,bp2.group(3),trans_strand2))
		bp_gene2 = list(set(locus2.overlappingGeneL(refFlatH=refFlatH,strand_sensitive=True)).difference(gene2))

		if direction=='sense':
			key = (bp1.groups()[1:],bp2.groups()[1:])
			trans_exon = (trans_exon1,trans_exon2)
			gene = (list(gene1),list(gene2))
			bp_gene = (bp_gene1,bp_gene2)
		elif direction=='antisense':
			key = (bp2.groups()[1:],bp1.groups()[1:])
			trans_exon = (trans_exon2,trans_exon1)
			gene = (list(gene2),list(gene1))
			bp_gene = (bp_gene2,bp_gene1)
		else:
			raise Exception

		if key in juncHH:

			juncHH[key]['match'].append(r)
			juncHH[key]['seq'].append(r.seq())
			juncHH[key]['reg'].append((direction,offset))

		else:

			juncHH[key] = {'match':[r], 'splice_type':splice_type, 'seq':[r.seq()], 'reg':[(direction,offset)], 'trans_exon':trans_exon, 'gene':gene, 'bp_gene':bp_gene}

	juncKH = juncHH.items()
	juncKH.sort(lambda x,y: cmp(len(set(y[1]['reg'])),len(set(x[1]['reg']))))

	outGsnapFile = open(outGsnapFileName,'w')
	outReportFile = open(outReportFileName,'w')

	for (key, juncH) in juncKH:

		if key[0][0] == key[1][0]:
			type = 'intra'
		else:
			type = 'inter'

		geneInfo1 = []
		censusInfo1 = []

		for geneName in juncH['gene'][0]+juncH['bp_gene'][0]:
			gene = mygenome.gene(geneName,geneNameH,geneSetH,geneInfoH)
			geneInfo1.append('%s:%s:%s' % (geneName,gene.getAttr('desc'),gene.getAttr('summary')))
			censusInfo1.append('%s:%s:%s:%s' % (gene.getAttr('census_somatic'),gene.getAttr('census_germline'),gene.getAttr('census_mutType'),gene.getAttr('census_translocPartners')))

		geneInfo2 = []
		censusInfo2 = []

		for geneName in juncH['gene'][1]+juncH['bp_gene'][1]:
			gene = mygenome.gene(geneName,geneNameH,geneSetH,geneInfoH)
			geneInfo2.append('%s:%s:%s' % (geneName,gene.getAttr('desc'),gene.getAttr('summary')))
			censusInfo2.append('%s:%s:%s:%s' % (gene.getAttr('census_somatic'),gene.getAttr('census_germline'),gene.getAttr('census_mutType'),gene.getAttr('census_translocPartners')))

		outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s;%s\t%s;%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
			(type, juncH['splice_type'], sampN, ':'.join(key[0]), ':'.join(key[1]), \
			','.join(juncH['trans_exon'][0]), ','.join(juncH['trans_exon'][1]), \
			','.join(juncH['gene'][0]), ','.join(juncH['bp_gene'][0]), ','.join(juncH['gene'][1]), ','.join(juncH['bp_gene'][1]), \
			';'.join(geneInfo1), ';'.join(geneInfo2), ';'.join(censusInfo1), ';'.join(censusInfo2), \
			len(juncH['match']) ,len(set(juncH['seq'])), len(set(juncH['reg']))))

		for m in juncH['match']:
			outGsnapFile.write(m.rawText()+'\n')
Example #11
0
	inFileName = sys.argv[1]
	outFileName = sys.argv[2]
else: # this is default file, analysis specific files should be indicated as commandline arguments
	inFileName = 'GH_ft.txt'
	outFileName = 'GH_ft_process.txt'


refFlatFileName = '/home/gye_hyeon/RNASeq/code_jk/refFlat_hg19.txt'
resolveGene = False


result = mygsnap.gsnapFile(inFileName)
outFile = open(outFileName, 'w')

if resolveGene:
	refFlatH = mygenome.loadRefFlatByChr(refFlatFileName)

for rL in result:

	for i in (0,1):

		outFile.write(','.join([x.toString() for x in rL[i].matchL()[0].mergedLocusL()]) + '\t')

		if resolveGene:

			overlappingGeneL = []

			for loc in rL[i].locusMergedL:
				overlappingGeneL += loc.overlappingGeneL(refFlatH=refFlatH)

			outFile.write(','.join(overlappingGeneL))
Example #12
0
def fusion_proc_annot(inReportFileName,outReportFileName,inCnaGctFileName=None):

	geneDB = mygenome.getGeneDB()
	frameInfoH = mygenome.getFrameInfoH()
	refFlatH = mygenome.loadRefFlatByChr()

	if inCnaGctFileName:
		cnaDB = mygenome.tcgaCnaDB(inCnaGctFileName)
	else:
		cnaDB = None

	outReportFile = open(outReportFileName,'w')

	for line in open(inReportFileName):

		(splice_type,sampN,bp1,bp2,teStr1,teStr2,nmatch,nseq,nreg) = line[:-1].split('\t')

		if inCnaGctFileName:
			indivId = re.match('.*(TCGA-[0-9]{2}-[0-9]{4}).*',sampN).group(1)

		geneStatL = []

		for (bp,teStr) in ((bp1,teStr1),(bp2,teStr2)):

			geneS = set()
			teL = []

			for te in teStr.split(','):

				rm = re.match('(.*)\.exon([0-9]*)/[0-9]*',te)

				if rm:

					t = rm.group(1)
					e = int(rm.group(2))

					g = mygenome.gene(t,geneDB=geneDB)

					if g.geneName:
						geneS.add(g.geneName)

					teL.append((t,e))

			rm = re.match('([+-])(chr[^:]*):([0-9]*)',bp)

			bp_geneS = set(mygenome.locus('%s:%s-%s%s' % (rm.group(2),int(rm.group(3))-1,rm.group(3),rm.group(1))).overlappingGeneL(refFlatH=refFlatH,strand_sensitive=True))
			bp_geneS = bp_geneS.difference(geneS)

			cnaInfo = []
			geneInfo = []
			censusInfo = []

			goInfoS = set()
			keggInfoS = set()
			biocartaInfoS = set()

			for geneName in list(geneS) + list(bp_geneS):

				gene = mygenome.gene(geneName,geneDB=geneDB)

				if cnaDB:
					cnaInfo.append('%s:%s' % (geneName,cnaDB.query(indivId,geneName)))

				geneInfo.append('%s:%s:%s' % (geneName,gene.getAttr('desc'),gene.getAttr('summary')))
				censusInfo.append('%s:%s:%s:%s' % (gene.getAttr('census_somatic'),gene.getAttr('census_germline'),gene.getAttr('census_mutType'),gene.getAttr('census_translocPartners')))
				goInfoS = goInfoS.union(set(gene.getAttr('go')))
				keggInfoS = keggInfoS.union(set(gene.getAttr('kegg')))
				biocartaInfoS = biocartaInfoS.union(set(gene.getAttr('biocarta')))

			geneStatL.append((bp1.split(':')[0],bp,teStr,teL,geneS,bp_geneS,cnaInfo,geneInfo,censusInfo,goInfoS,keggInfoS,biocartaInfoS))


		(chrom1,bp1,teStr1,teL1,geneS1,bp_geneS1,cnaInfo1,geneInfo1,censusInfo1,goInfoS1,keggInfoS1,biocartaInfoS1) = geneStatL[0]
		(chrom2,bp2,teStr2,teL2,geneS2,bp_geneS2,cnaInfo2,geneInfo2,censusInfo2,goInfoS2,keggInfoS2,biocartaInfoS2) = geneStatL[1]


		if chrom1 == chrom2:
			type = 'intra'
		else:
			type = 'inter'


		frameL = []

		for (t1,e1) in teL1:

			for (t2,e2) in teL2:

				cons = mygenome.frameCons(t1,e1, t2,e2, frameInfoH)

				if cons=='Y':
					frameL.append('%s.%s-%s.%s:%s' % (t1,e1,t2,e2,cons))

		outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
			(sampN, splice_type, type, bp1,bp2, teStr1,teStr2, ','.join(frameL), ','.join(cnaInfo1), ','.join(cnaInfo2), \
			'%s;%s' % (','.join(geneS1),','.join(bp_geneS1)), ';'.join(geneInfo1), ';'.join(censusInfo1), \
			';'.join(map(str,goInfoS1)), ';'.join(map(str,keggInfoS1)), ';'.join(map(str,biocartaInfoS1)), 
			'%s;%s' % (','.join(geneS2),','.join(bp_geneS2)), ';'.join(geneInfo2), ';'.join(censusInfo2), \
			';'.join(map(str,goInfoS2)), ';'.join(map(str,keggInfoS2)), ';'.join(map(str,biocartaInfoS2)), 
			nmatch,nseq,nreg))
Example #13
0
if len(sys.argv) >= 3:
    inFileName = sys.argv[1]
    outFileName = sys.argv[2]
else:  # this is default file, analysis specific files should be indicated as commandline arguments
    inFileName = 'GH_ft.txt'
    outFileName = 'GH_ft_process.txt'

refFlatFileName = '/home/gye_hyeon/RNASeq/code_jk/refFlat_hg19.txt'
resolveGene = False

result = mygsnap.gsnapFile(inFileName)
outFile = open(outFileName, 'w')

if resolveGene:
    refFlatH = mygenome.loadRefFlatByChr(refFlatFileName)

for rL in result:

    for i in (0, 1):

        outFile.write(
            ','.join([x.toString()
                      for x in rL[i].matchL()[0].mergedLocusL()]) + '\t')

        if resolveGene:

            overlappingGeneL = []

            for loc in rL[i].locusMergedL:
                overlappingGeneL += loc.overlappingGeneL(refFlatH=refFlatH)
Example #14
0
def fusion_proc_annot(inReportFileName,
                      outReportFileName,
                      inCnaGctFileName=None):

    geneDB = mygenome.getGeneDB()
    frameInfoH = mygenome.getFrameInfoH()
    refFlatH = mygenome.loadRefFlatByChr()

    if inCnaGctFileName:
        cnaDB = mygenome.tcgaCnaDB(inCnaGctFileName)
    else:
        cnaDB = None

    outReportFile = open(outReportFileName, 'w')

    for line in open(inReportFileName):

        (splice_type, sampN, bp1, bp2, teStr1, teStr2, nmatch, nseq,
         nreg) = line[:-1].split('\t')

        if inCnaGctFileName:
            indivId = re.match('.*(TCGA-[0-9]{2}-[0-9]{4}).*', sampN).group(1)

        geneStatL = []

        for (bp, teStr) in ((bp1, teStr1), (bp2, teStr2)):

            geneS = set()
            teL = []

            for te in teStr.split(','):

                rm = re.match('(.*)\.exon([0-9]*)/[0-9]*', te)

                if rm:

                    t = rm.group(1)
                    e = int(rm.group(2))

                    g = mygenome.gene(t, geneDB=geneDB)

                    if g.geneName:
                        geneS.add(g.geneName)

                    teL.append((t, e))

            rm = re.match('([+-])(chr[^:]*):([0-9]*)', bp)

            bp_geneS = set(
                mygenome.locus('%s:%s-%s%s' %
                               (rm.group(2), int(rm.group(3)) - 1, rm.group(3),
                                rm.group(1))).overlappingGeneL(
                                    refFlatH=refFlatH, strand_sensitive=True))
            bp_geneS = bp_geneS.difference(geneS)

            cnaInfo = []
            geneInfo = []
            censusInfo = []

            goInfoS = set()
            keggInfoS = set()
            biocartaInfoS = set()

            for geneName in list(geneS) + list(bp_geneS):

                gene = mygenome.gene(geneName, geneDB=geneDB)

                if cnaDB:
                    cnaInfo.append('%s:%s' %
                                   (geneName, cnaDB.query(indivId, geneName)))

                geneInfo.append(
                    '%s:%s:%s' %
                    (geneName, gene.getAttr('desc'), gene.getAttr('summary')))
                censusInfo.append('%s:%s:%s:%s' %
                                  (gene.getAttr('census_somatic'),
                                   gene.getAttr('census_germline'),
                                   gene.getAttr('census_mutType'),
                                   gene.getAttr('census_translocPartners')))
                goInfoS = goInfoS.union(set(gene.getAttr('go')))
                keggInfoS = keggInfoS.union(set(gene.getAttr('kegg')))
                biocartaInfoS = biocartaInfoS.union(
                    set(gene.getAttr('biocarta')))

            geneStatL.append(
                (bp1.split(':')[0], bp, teStr, teL, geneS, bp_geneS, cnaInfo,
                 geneInfo, censusInfo, goInfoS, keggInfoS, biocartaInfoS))

        (chrom1, bp1, teStr1, teL1, geneS1, bp_geneS1, cnaInfo1, geneInfo1,
         censusInfo1, goInfoS1, keggInfoS1, biocartaInfoS1) = geneStatL[0]
        (chrom2, bp2, teStr2, teL2, geneS2, bp_geneS2, cnaInfo2, geneInfo2,
         censusInfo2, goInfoS2, keggInfoS2, biocartaInfoS2) = geneStatL[1]

        if chrom1 == chrom2:
            type = 'intra'
        else:
            type = 'inter'

        frameL = []

        for (t1, e1) in teL1:

            for (t2, e2) in teL2:

                cons = mygenome.frameCons(t1, e1, t2, e2, frameInfoH)

                if cons == 'Y':
                    frameL.append('%s.%s-%s.%s:%s' % (t1, e1, t2, e2, cons))

        outReportFile.write('%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
         (sampN, splice_type, type, bp1,bp2, teStr1,teStr2, ','.join(frameL), ','.join(cnaInfo1), ','.join(cnaInfo2), \
         '%s;%s' % (','.join(geneS1),','.join(bp_geneS1)), ';'.join(geneInfo1), ';'.join(censusInfo1), \
         ';'.join(map(str,goInfoS1)), ';'.join(map(str,keggInfoS1)), ';'.join(map(str,biocartaInfoS1)),
         '%s;%s' % (','.join(geneS2),','.join(bp_geneS2)), ';'.join(geneInfo2), ';'.join(censusInfo2), \
         ';'.join(map(str,goInfoS2)), ';'.join(map(str,keggInfoS2)), ';'.join(map(str,biocartaInfoS2)),
         nmatch,nseq,nreg))