def inferUTRort(self):
'''
Infers a UTR record based on strand and coordinates compare between UTR and cds
'''
if not self.utr: return
self.cds = sortArr(self.cds,0)
firstcdsStart, firstcdsEnd = self.cds[0]
for utrs,utre in self.utr:
if self.strand == "+":
if utrs < firstcdsStart:
self.fp_utr.append([utrs,utre])
else:
self.tp_utr.append([utrs,utre])
else:
if utrs < firstcdsStart:
self.tp_utr.append([utrs,utre])
else:
self.fp_utr.append([utrs,utre])
self.fp_utr=sortArr(self.fp_utr,0)
self.tp_utr=sortArr(self.tp_utr,0)
return True
def inferUTR(self):
'''
This method would try to infer FP_UTR and TP_UTR
even without UTR annotation for a transcript. Exons and CDSs are suffcient.
'''
if self.fp_utr and self.tp_utr: return
if not self.cds: return
self.cds = sortArr(self.cds,0)
self.exons = sortArr(self.exons,0)
CDSstart,CDSend = (self.cds[0][0],self.cds[-1][-1]) if self.strand == "+" else (self.cds[-1][-1],self.cds[0][0])
for tmps,tmpe in self.exons:
if self.strand == "+":
if tmpe < CDSstart:
self.fp_utr.append([tmps,tmpe])
elif tmps < CDSstart < tmpe:
self.fp_utr.append([tmps,CDSstart])
elif tmps > CDSend:
self.tp_utr.append([tmps,tmpe])
elif tmps < CDSend < tmpe:
self.tp_utr.append([CDSend,tmpe])
else:
pass
#raise Exception("ERROR: could not determine this exon [%d,%d] is a UTR or not" % (tmps,tmpe,))
else:
if tmps > CDSstart:
self.fp_utr.append([tmps,tmpe])
elif tmps < CDSstart < tmpe:
self.fp_utr.append([CDSstart,tmpe])
elif tmpe < CDSend:
self.tp_utr.append([tmps,tmpe])
elif tmps < CDSend < tmpe:
self.tp_utr.append([tmps,CDSend])
else:
pass
#raise Exception("ERROR: could not determine this exon [%d,%d] is a UTR or not" % (tmps,tmpe,))
self.fp_utr = sortArr(rmExtra(self.fp_utr),0)
self.tp_utr = sortArr(rmExtra(self.tp_utr),0)
return True
def inferIntron(self):
'''Returns a list of duples containing start/end positions of introns in this transcript.'''
self.introns = []
if self.exons:
intervals = self.exons
elif self.cds:
intervals = self.cds
else:
return
for i in xrange(1,len(intervals)) :
intron = [exons[i-1].end(), exons[i].start()]
self.introns.append(intron)
self.introns = sortArr(self.introns,0)
return True
class transcript(BaseFeature):
"""
An mRNA acts like an isoform in that it is associated with a parent gene
and contains a number of coding sequences (CDS).
"""
def __init__(self, chromosome, start, end, strand, feature, id, attr={}):
BaseFeature.__init__(self, chromosome, start, end, strand, feature, attr)
self.id = id
self.exons = []
self.biotype = attr['biotype']
self.feature = feature
self.cds = []
self.cdsMap = {}
self.start_codon = None
self.stop_codon = None
self.utr = []
self.fp_utr = []
self.tp_utr = []
self.utrMap = {}
self.exonMap = {}
self.introns = []
self.attrs = attr
self.length = self.end - self.start
def addexon(self,exon):
if exon.strand != self.strand:
raise Exception("ERROR: strand '%s' of exon from transcript %s does not match gene strand '%s'" % (exon.strand, exon.parent, self.strand))
if exon.chromosome != self.chromosome:
raise Exception("ERROR: chromosome '%s' of exon from transcript %s does not match gene chromosome '%s'" % (exon.chromosome, exon.parent, self.chromosome))
exonTuple = (exon.start,exon.end)
try :
ignore = self.exonMap[exonTuple]
return False
except KeyError,e:
self.exonMap[exonTuple] = exon
self.exons.append(list(exonTuple))
self.exons = sortArr(self.exons,0,1)
return True
def getCDSs(self):
if self.CDSStartStat is 'unk' or self.CDSEndStat is 'unk':
# in this case, CDSStart is equal to CDSEnd , so we will not try to infer cds boundrary
return
for exonStart,exonEnd in self.exons:
if exonEnd < self.CDSStart:
self.utr.append([exonStart,exonEnd])
continue
elif exonStart < self.CDSStart < exonEnd:
tmpStart = self.CDSStart if self.strand=='+' else self.CDSStart -3
self.utr.append([exonStart,tmpStart])
self.cds.append([self.CDSStart,exonEnd])
elif self.CDSStart < exonEnd < self.CDSEnd:
self.cds.append([exonStart,exonEnd])
elif exonStart < self.CDSEnd < exonEnd:
tmpEnd = self.CDSEnd+3 if self.strand=='+' else self.CDSEnd
self.utr.append([tmpEnd,exonEnd])
self.cds.append([exonStart,self.CDSEnd])
else:
self.utr.append([exonStart,exonEnd])
continue
self.cds = sortArr(self.cds,0)
return True
self.exons = sortArr(self.exons,0,1)
return True
def addCDS(self, cds):
if cds.strand != self.strand:
raise Exception("ERROR: strand '%s' of CDS from transcript %s does not match gene strand '%s'" % (cds.strand, cds.parent, self.strand))
if cds.chromosome != self.chromosome:
raise Exception("ERROR: chromosome '%s' of CDS from transcript %s does not match gene chromosome '%s'" % (cds.chromosome, cds.parent, self.chromosome))
cdsTuple = (cds.start,cds.end)
try :
ignore = self.cdsMap[cdsTuple]
return False
except KeyError,e:
self.cdsMap[cdsTuple] = cds
self.cds.append(list(cdsTuple))
self.cds = sortArr(self.cds,0,1)
return True
def addUTR(self,utr):
if utr.strand != self.strand:
raise Exception("ERROR: strand '%s' of UTR from transcript %s does not match gene strand '%s'" % (cds.strand, cds.parent, self.strand))
if utr.chromosome != self.chromosome :
raise Exception("ERROR: chromosome '%s' of UTR from transcript %s does not match gene chromosome '%s'" % (cds.chromosome, cds.parent, self.chromosome))
utrTuple = (utr.start,utr.end)
try :
ignore = self.utrMap[utrTuple]
return False
except KeyError,e:
self.utrMap[utrTuple] = utr
self.utr.append(list(utrTuple))
return True
def getIntrons(self):
for i in range(self.txExonCount-1):
self.introns.append([self.txExonsEnd[i],self.txExonsStart[i+1]-1])
self.introns=sortArr(self.introns,0)
return True
#print a
#print b
sys.exit(0)
import bamio
'''
idx=bamio.Tabix(sys.argv[1])
for item in idx.fetch('1',3100,5000):
print item
idx.close()
a,b,c,d,e,f,g=bamio.mappingstat(sys.argv[1])
print a,b,c,d,e,f,g
#matplot.densityplot([a1,a2,a3,a4,a5,a6,a7,a8],['s','e','f','g','h','a','b','c'])
'''
arr = [['1', 42, 52], ['11', 45, 78], ['2', 25, 100], ['1', 23, 78],
['1', 56, 89]]
print utils.sortArr(arr, 0, 1)
from format import *
f = sys.argv[1]
recs = fasta_itr(f)
print dir(recs)
print type(recs)
for rec in recs:
print rec.id
print rec.seq