python/GffTranscriptReader.py at master · bmajoros/python · GitHub

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#=========================================================================

# This is OPEN SOURCE SOFTWARE governed by the Gnu General Public

# License (GPL) version 3, as described at www.opensource.org.

#=========================================================================

from __future__ import (absolute_import, division, print_function,

unicode_literals, generators, nested_scopes, with_statement)

from builtins import (bytes, dict, int, list, object, range, str, ascii,

chr, hex, input, next, oct, open, pow, round, super, filter, map, zip)

# The above imports should allow this program to run in both Python 2 and

# Python 3. You might need to update your version of module "future".

from Exon import Exon

from Transcript import Transcript

from Gene import Gene

from Integer import Integer

from Rex import Rex

import re

######################################################################

# Returns a list of Transcripts. For each transcript, the Exons

# will be sorted according to order of translation, so that

# the exon containing the start codon will come before the exon

# containing the stop codon. This means that for the minus strand,

# exon begin coordinates will be decreasing. However, an individual

# exon's begin coordinate is always less than its end coordinate.

# The transcripts themselves are sorted along the chromosome left-to-

# right. Note that although the GFF coordinates are 1-based/base-based

# (1/B), internally all coordinates are stored as 0-based/space-based

# (0/S). This conversion is handled automatically.

# Attributes:

# shouldSortTranscripts

# exonsAreCDS : interpret "exon" features as "CDS" when reading GFF

# Methods:

# reader=GffTranscriptReader()

# reader.setStopCodons({"TAG":1,"TAA":1,"TGA":1})

# transcriptArray=reader.loadGFF(filename)

# geneList=reader.loadGenes(filename)

# hashTable=reader.hashBySubstrate(filename)

# reader.hashBySubstrateInto(filename,hash)

# hashTable=reader.hashGenesBySubstrate(filename)

# hashTable=reader.loadTranscriptIdHash(filename)

# hashTable=reader.loadGeneIdHash(filename)

# reader.doNotSortTranscripts()

######################################################################

class GffTranscriptReader:

def __init__(self):

self.shouldSortTranscripts=True

self.exonsAreCDS=False

self.stopCodons={"TAG":1,"TAA":1,"TGA":1}

def loadGenes(self,filename):

transcripts=self.loadGFF(filename)

genes=set()

for transcript in transcripts:

gene=transcript.getGene()

if(not gene):

raise Exception("transcript "+transcript.getID()+

" has no gene")

genes.add(gene)

genes=list(genes)

genes.sort(key=lambda gene: gene.getBegin())

return genes

def doNotSortTranscripts(self):

self.shouldSortTranscripts=False

def loadTranscriptIdHash(self,filename):

transcriptArray=self.loadGFF(filename)

hash={}

for transcript in transcriptArray:

id=transcript.getID()

hash[id]=transcript

return hash

def loadGeneIdHash(self,filename):

transcriptArray=self.loadGFF(filename)

hash={}

for transcript in transcriptArray:

id=transcript.getGeneId()

array=hash.get(id,None)

if(array is None): array=hash[id]=[]

array.append(transcript)

return hash

def hashBySubstrate(self,filename):

hash={}

self.hashBySubstrateInto(filename,hash)

return hash

def hashBySubstrateInto(self,filename,hash):

transcriptArray=self.loadGFF(filename)

for transcript in transcriptArray:

id=transcript.getSubstrate()

array=hash.get(id,None)

if(array is None): array=hash[id]=[]

array.append(transcript)

def hashGenesBySubstrate(self,filename):

geneArray=self.loadGenes(filename)

hash={}

for gene in geneArray:

id=gene.getSubstrate()

array=hash.get(id,None)

if(array is None): array=hash[id]=[]

array.append(gene)

return hash

def computeFrames(self,transcripts):

for transcript in transcripts:

if(not transcript.areExonTypesSet()): transcript.setExonTypes()

strand=transcript.getStrand()

exons=transcript.exons

frame=0 # fine for both strands

for exon in exons:

exon.frame=frame

length=exon.getLength()

frame=(frame+length)%3 # this is fine, on both strands

def exonContainsPoint(self,exon,point):

return point>=exon.begin and point<=exon.end;

# this '<=' is necessary for the minus strand!

# do not change it back to '<' !!!

def setStopCodons(self,stopCodons):

self.stopCodons=stopCodons

def adjustStartCodons_fw(self,transcript,totalIntronSize):

startCodon=None

exons=transcript.exons

exons.sort(key=lambda exon: exon.begin)

numExons=len(exons)

#if(transcript.getID()=="ENST00000361390.2"):

# print("adjustStartCodons_fw",numExons,"exons")

if(numExons==0): return None

if(transcript.begin is None) :

transcript.begin=exons[0].begin

if(transcript.end is None):

transcript.end=exons[numExons-1].end

if(transcript.startCodon is not None):

startCodon=transcript.startCodon-transcript.begin

else:

startCodon=0

transcript.startCodon=transcript.begin

transcript.startCodonAbsolute=transcript.begin

for i in range(numExons): exons[i].order=i

for i in range(numExons):

exon=exons[i]

if(i>0):

prevExon=exons[i-1]

intronSize=exon.begin-prevExon.end

totalIntronSize+=intronSize

if(transcript.startCodon is not None and

self.exonContainsPoint(exon,transcript.startCodon)): break

return startCodon

def adjustStartCodons_bw(self,transcript,totalIntronSize):

startCodon=None

exons=transcript.exons

exons.sort(key=lambda exon: exon.begin,reverse=True)

numExons=len(exons)

if(numExons==0): return None

if(transcript.end is None): transcript.end=exons[0].end

if(transcript.begin is None): transcript.begin=exons[numExons-1].begin

if(transcript.startCodon is not None):

startCodon=transcript.end-transcript.startCodon

else:

startCodon=0

transcript.startCodon=transcript.end ###

transcript.startCodonAbsolute=transcript.end ###

for i in range(numExons):

exon=exons[i]

exon.order=i

if(i>0):

prevExon=exons[i-1]

intronSize=prevExon.begin-exon.end

totalIntronSize+=intronSize

if(transcript.startCodon is not None and

self.exonContainsPoint(exon,transcript.startCodon)): break

return startCodon

def adjustStartCodons(self,transcripts):

for transcript in transcripts:

transcript.sortExons()

transcript.adjustOrders()

strand=transcript.strand

startCodon=None

totalIntronSize=Integer(0)

if(strand=="+"):

startCodon=\

self.adjustStartCodons_fw(transcript,totalIntronSize)

else:

startCodon=\

self.adjustStartCodons_bw(transcript,totalIntronSize)

if(startCodon is not None):

startCodon-=int(totalIntronSize)

transcript.startCodon=startCodon

def loadGFF_transcript(self,fields,line,transcriptBeginEnd,GFF,

transcripts,readOrder,genes):

begin=int(fields[3])-1

end=int(fields[4])

rex=Rex()

if(rex.find('transcript_id[:=]?\s*"?([^\s";]+)"?',line)):

transcriptId=rex[1]

transcriptBeginEnd[transcriptId]=[begin,end]

strand=fields[6]

score=fields[5]

transcriptExtraFields=""

for i in range(8,len(fields)):

transcriptExtraFields+=fields[i]+" "

transcript=transcripts.get(transcriptId,None)

if(transcript is None):

transcripts[transcriptId]=transcript= \

Transcript(transcriptId,strand)

transcript.setStopCodons(self.stopCodons)

transcript.readOrder=readOrder;

readOrder+=1

transcript.substrate=fields[0]

transcript.source=fields[1]

transcript.setBegin(begin)

transcript.setEnd(end)

if(transcript.score is None and

score!="."): transcript.score=float(score)

geneId=None

if(rex.find("genegrp=(\S+)",line)): geneId=rex[1]

elif(rex.find('gene_id[:=]?\s*\"?([^\s\;"]+)\"?',line)):

geneId=rex[1]

if(not geneId): raise Exception("can't parse GTF: "+line)

transcript.geneId=geneId

gene=genes.get(geneId,None)

if(not gene): genes[geneId]=gene=Gene(); gene.setId(geneId)

transcript.setGene(gene)

gene.addTranscript(transcript)

transcript.extraFields=transcriptExtraFields

def loadGFF_UTR(self,fields,line,transcriptBeginEnd,GFF,

transcripts,readOrder,genes):

exonBegin=int(fields[3])-1

exonEnd=int(fields[4])

exonScore=fields[5]

strand=fields[6]

frame=fields[7]

transcriptId=None

rex=Rex()

if(rex.find('transgrp[:=]\s*(\S+)',line)): transcriptId=rex[1]

elif(rex.find('transcript_id[:=]?\s*"?([^\s";]+)"?',line)):

transcriptId=rex[1]

elif(rex.find('Parent=([^;,\s]+)',line)): transcriptId=rex[1]

geneId=None

if(rex.find('genegrp=(\S+)',line)): geneId=rex[1]

elif(rex.find('gene_id[:=]?\s*"?([^\s\;"]+)"?',line)): geneId=rex[1]

if(transcriptId is None): transcriptId=geneId

if(geneId is None): geneId=transcriptId

if(transcriptId is None):

raise Exception(line+" : no transcript ID found")

if(rex.find("(\S+);$",transcriptId)): transcriptId=rex[1]

if(rex.find("(\S+);$",geneId)): geneId=rex[1]

extra=""

for i in range(8,len(fields)): extra+=fields[i]+" "

if(exonBegin>exonEnd): (exonBegin,exonEnd)=(exonEnd,exonBegin)

transcript=transcripts.get(transcriptId,None)

if(not transcript):

transcripts[transcriptId]=transcript= \

Transcript(transcriptId,strand)

transcript.setStopCodons(self.stopCodons)

transcript.readOrder=readOrder

readOrder+=1

transcript.substrate=fields[0]

transcript.source=fields[1]

if(transcriptBeginEnd.get(transcriptId,None) is not None):

(begin,end)=transcriptBeginEnd[transcriptId]

transcript.setBegin(begin)

transcript.setEnd(end)

else:

transcript.setBegin(exonBegin)

transcript.setEnd(exonEnd)

transcript.geneId=geneId

gene=genes.get(geneId,None)

if(gene is None):

genes[geneId]=gene=Gene(); gene.setId(geneId)

transcript.setGene(gene)

exon=Exon(exonBegin,exonEnd,transcript)

exon.extraFields=extra

if(transcript.rawExons is not None):

exon.frame=frame

exon.score=exonScore

exon.type=fields[2]

transcript.rawExons.append(exon)

elif(not transcript.exonOverlapsExon(exon)):

exon.frame=frame

exon.score=exonScore

exon.type=fields[2]

transcript.UTR.append(exon) # OK -- we sort later

gene.addTranscript(transcript)

def loadGFF_exon(self,fields,line,transcriptBeginEnd,GFF,

transcripts,readOrder,genes):

exonBegin=int(fields[3])-1

exonEnd=int(fields[4])

exonScore=fields[5]

strand=fields[6]

frame=fields[7]

transcriptId=None

rex=Rex()

if(rex.find("transgrp[:=]\s*(\S+)",line)): transcriptId=rex[1]

elif(rex.find('transcript_id[:=]?\s*"?([^\s";]+)"?',line)):

transcriptId=rex[1]

elif(rex.find('Parent=([^;,\s]+)',line)): transcriptId=rex[1]

geneId=None

if(rex.find("genegrp=(\S+)",line)): geneId=rex[1]

elif(rex.find('gene_id[:=]?\s*"?([^\s\;"]+)"?',line)): geneId=rex[1]

if(transcriptId is None): transcriptId=geneId

if(geneId is None): geneId=transcriptId

if(rex.find("(\S+);$",transcriptId)): transcriptId=rex[1]

if(rex.find("(\S+);$",geneId)): geneId=rex[1]

extra=""

for i in range(8,len(fields)): extra+=fields[i]+" "

if(exonBegin>exonEnd): (exonBegin,exonEnd)=(exonEnd,exonBegin)

transcript=transcripts.get(transcriptId,None)

if(transcript is None):

transcripts[transcriptId]=transcript= \

Transcript(transcriptId,strand)

transcript.setStopCodons(self.stopCodons)

transcript.readOrder=readOrder

readOrder+=1

transcript.substrate=fields[0]

transcript.source=fields[1]

if(transcriptBeginEnd.get(transcriptId,None) is not None):

(begin,end)=transcriptBeginEnd[transcriptId]

transcript.setBegin(begin)

transcript.setEnd(end)

else:

transcript.setBegin(exonBegin)

transcript.setEnd(exonEnd)

transcript.geneId=geneId

gene=genes.get(geneId,None)

if(gene is None):

genes[geneId]=gene=Gene(); gene.setId(geneId)

transcript.setGene(gene)

exon=Exon(exonBegin,exonEnd,transcript)

exon.extraFields=extra

exon.score=exonScore

exon.type=fields[2]

if(transcript.rawExons is None): transcript.rawExons=[]

transcript.rawExons.append(exon)

gene.addTranscript(transcript)

def loadGFF_CDS(self,fields,line,transcriptBeginEnd,GFF,

transcripts,readOrder,genes):

exonBegin=int(fields[3])-1

exonEnd=int(fields[4])

exonScore=fields[5]

strand=fields[6]

frame=fields[7]

transcriptId=None

rex=Rex()

if(rex.find('transgrp[:=]\s*(\S+)',line)): transcriptId=rex[1]

elif(rex.find('transcript_id[:=]?\s*"?([^\s";]+)"?',line)):

transcriptId=rex[1]

elif(rex.find('Parent=([^;,\s]+)',line)): transcriptId=rex[1]

geneId=None

if(rex.find('genegrp=(\S+)',line)): geneId=rex[1]

elif(rex.find('gene_id[:=]?\s*"?([^\s\;"]+)"?',line)): geneId=rex[1]

if(transcriptId is None): transcriptId=geneId

if(geneId is None): geneId=transcriptId

if(transcriptId is None):

raise Exception(line+" : no transcript ID found")

if(rex.find('(\S+);$',transcriptId)): transcriptId=rex[1]

if(rex.find('(\S+);$',geneId)): geneId=rex[1]

extra=""

for i in range(8,len(fields)): extra+=fields[i]+" "

if(exonBegin>exonEnd): (exonBegin,exonEnd)=(exonEnd,exonBegin)

transcript=transcripts.get(transcriptId,None)

if(transcript is None):

transcripts[transcriptId]=transcript= \

Transcript(transcriptId,strand)

transcript.setStopCodons(self.stopCodons)

transcript.readOrder=readOrder

readOrder+=1

transcript.substrate=fields[0]

transcript.source=fields[1]

if(transcriptBeginEnd.get(transcriptId,None) is not None):

(begin,end)=transcriptBeginEnd[transcriptId]

transcript.setBegin(begin)

transcript.setEnd(end)

else:

transcript.setBegin(exonBegin)

transcript.setEnd(exonEnd)

transcript.geneId=geneId

gene=genes.get(geneId,None)

if(gene is None):

genes[geneId]=gene=Gene(); gene.setId(geneId)

transcript.setGene(gene)

exon=Exon(exonBegin,exonEnd,transcript)

exon.extraFields=extra

if(not transcript.exonOverlapsExon(exon)):

exon.frame=frame

exon.score=exonScore

exon.type=fields[2]

transcript.exons.append(exon) # OK -- we sort later

gene.addTranscript(transcript)

def loadGFF(self,gffFilename):

transcripts={}

genes={}

readOrder=Integer(1)

GFF=open(gffFilename,"r")

transcriptBeginEnd={}

while(True):

line=GFF.readline()

if(not line): break

if(not re.search("\S+",line)): continue

if(re.search("^\s*\#",line)): continue

fields=line.split("\t") ### \t added 3/24/2017

if(len(fields)<8): raise Exception("can't parse GTF:"+line)

if(fields[2]=="transcript" or fields[2]=="mRNA"):

self.loadGFF_transcript(fields,line,transcriptBeginEnd,GFF,

transcripts,readOrder,genes)

elif("UTR" in fields[2] or "utr" in fields[2]):

self.loadGFF_UTR(fields,line,transcriptBeginEnd,GFF,

transcripts,readOrder,genes)

elif(fields[2]=="exon"):

if(self.exonsAreCDS):

self.loadGFF_CDS(fields,line,transcriptBeginEnd,GFF,

transcripts,readOrder,genes)

else:

self.loadGFF_exon(fields,line,transcriptBeginEnd,GFF,

transcripts,readOrder,genes)

elif("CDS" in fields[2] or "-exon" in fields[2]):

self.loadGFF_CDS(fields,line,transcriptBeginEnd,GFF,

transcripts,readOrder,genes)

GFF.close()

transcripts=list(transcripts.values())

for transcript in transcripts: transcript.parseRawExons()

self.adjustStartCodons(transcripts)

self.computeFrames(transcripts);

if(self.shouldSortTranscripts):

transcripts.sort(key=lambda t: t.substrate+" "+str(t.begin)+" "+

str(t.end))

else:

transcripts.sort(key=lambda t: t.readOrder)

return transcripts

python/GffTranscriptReader.py at master · bmajoros/python · GitHub

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