def annotatePos(insList, refGenome, outfileName, annotDir, printout):
"""loop through available annotations in annotDir/refgenome"""
namefile = open(annotDir + "/" + refGenome + "/names.txt", 'r')
outfile = open(outfileName, 'w')
# set up each annotator (name, tabix file) present
annDict = {}
for nameline in namefile:
(tname, tfile) = nameline.rstrip().split("\t")
tfile = annotDir + "/" + refGenome + "/" + tfile
annotator = annotate.annotator(tfile, tname, refGenome)
annDict[tname] = annotator
namefile.close()
for ins in insList:
outstring = str(ins)
for annName, ann in annDict.iteritems():
bedline = "\t".join((ins.chr, ins.start, ins.end))
if ins.start > ins.end:
bedline = "\t".join((ins.chr, ins.end, ins.start))
annList = ann.annotate(bedline, refGenome)
annJoin = ",".join(annList)
ins.annot.append(annJoin)
if printout and ins.pseudo == 'False': # exclude overlaps with known pseudogenes
print ins
if ins.pseudo == 'False':
outfile.write(str(ins) + "\n")
outfile.close()
def annotatePos(insList,refGenome,annotDir,outfileName,printout):
namefile = open(annotDir + "/" + refGenome + "/names.txt", 'r')
outfile = open(outfileName, 'w')
# set up each annotator (name, tabix file) present
annDict = {}
for nameline in namefile:
(tname,tfile) = nameline.rstrip().split("\t")
tfile = annotDir + "/" + refGenome + "/" + tfile
annotator = annotate.annotator(tfile, tname, refGenome)
annDict[tname] = annotator
namefile.close()
for ins in insList:
outstring = str(ins)
for annName,ann in annDict.iteritems():
bedline = "\t".join((ins.chr,ins.start,ins.end))
if ins.start > ins.end:
bedline = "\t".join((ins.chr,ins.end,ins.start))
annList = ann.annotate(bedline,refGenome)
annJoin = ",".join(annList)
ins.annot.append(annJoin)
if printout:
print ins
outfile.write(str(ins) + "\n")
outfile.close()
def annotatePos(insList,refGenome,outfileName,annotDir,printout):
"""loop through available annotations in annotDir/refgenome"""
namefile = open(annotDir + "/" + refGenome + "/names.txt", 'r')
outfile = open(outfileName, 'w')
# set up each annotator (name, tabix file) present
annDict = {}
for nameline in namefile:
(tname,tfile) = nameline.rstrip().split("\t")
tfile = annotDir + "/" + refGenome + "/" + tfile
annotator = annotate.annotator(tfile, tname, refGenome)
annDict[tname] = annotator
namefile.close()
for ins in insList:
outstring = str(ins)
for annName,ann in annDict.iteritems():
bedline = "\t".join((ins.chr,ins.start,ins.end))
if ins.start > ins.end:
bedline = "\t".join((ins.chr,ins.end,ins.start))
annList = ann.annotate(bedline,refGenome)
annJoin = ",".join(annList)
ins.annot.append(annJoin)
if printout and ins.pseudo == 'False': # exclude overlaps with known pseudogenes
print ins
if ins.pseudo == 'False':
outfile.write(str(ins) + "\n")
outfile.close()