# Copyright (C)2016 William H. Majoros ([email protected]). #========================================================================= 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 GffTranscriptReader import GffTranscriptReader #filename="/home/bmajoros/1000G/assembly/local-genes.gff" #filename="/home/bmajoros/1000G/assembly/tmp.gff" #filename="test/data/tmp.gff" filename="test/data/local-genes.gff" reader=GffTranscriptReader() #transcripts=reader.loadGFF(filename) #for transcript in transcripts: #print(transcript.getID()) #gff=transcript.toGff() #print(gff) #genes=reader.loadGenes(filename) #for gene in genes: # print("gene",gene.getID()) # n=gene.getNumTranscripts() # for i in range(n): # transcript=gene.getIthTranscript(i) # transID=transcript.getID() # print("\t"+transID+"\t"+str(transcript.getBegin())+"\t" # +str(transcript.getEnd()))
readCounts={}
with open(readCountsFile,"rt") as IN:
while(True):
line=IN.readline()
if(line==""): break
if(rex.find("TOTAL MAPPED READS:\s*(\d+)",line)):
totalMappedReads=rex[1]
else:
fields=line.split()
(gene,count)=fields
readCounts[gene]=count
# Read GFF file to find annotated sites to exclude
gff={}
exclude={}
reader=GffTranscriptReader()
transcripts=reader.loadGFF(gffFile)
for transcript in transcripts:
if(transcript.getID()[0:3]=="ALT"): continue
if(rex.find("(\S+)_\d",transcript.getID())): gff[rex[1]]=transcript
substrate=transcript.getSubstrate()
exclusions=exclude.get(substrate,None)
if(exclusions is None): exclusions=exclude[substrate]={}
exons=transcript.getRawExons()
exons.sort(key=lambda exon:exon.begin)
numExons=len(exons)
for i in range(numExons-1):
key=str(exons[i].getEnd())+"-"+str(exons[i+1].getBegin())
exclusions[key]=True
# Read broken-sites file
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".
import sys
from FastaReader import FastaReader
from FastaWriter import FastaWriter
from GffTranscriptReader import GffTranscriptReader
if(len(sys.argv)!=4):
exit(sys.argv[0]+" <in.fasta> <in.gff> <out.fasta>")
(fastaFile,gffFile,outFile)=sys.argv[1:]
reader=GffTranscriptReader()
transcripts=reader.loadGFF(gffFile)
keep=set()
for transcript in transcripts:
if(transcript.getID()[:3]!="ALT"): continue
keep.add(transcript.getSubstrate())
reader=FastaReader(fastaFile)
writer=FastaWriter()
fh=open(outFile,"wt")
while(True):
(defline,seq)=reader.nextSequence()
if(not defline): break
(id,attr)=FastaReader.parseDefline(defline)
if(id not in keep): continue
writer.addToFasta(defline,seq,fh)
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".
import sys
from FastaReader import FastaReader
from FastaWriter import FastaWriter
from GffTranscriptReader import GffTranscriptReader
from Rex import Rex
rex=Rex()
# Process command line
if(len(sys.argv)!=4): exit(sys.argv[0]+" <in.fasta> <in.gff> <out.fasta>")
(fastaFile,gffFile,outFile)=sys.argv[1:]
# Read GFF
reader=GffTranscriptReader()
hash=reader.hashBySubstrate(gffFile)
# Open output file
OUT=open(outFile,"wt")
writer=FastaWriter()
# Process each substrate in the FASTA file
reader=FastaReader(fastaFile)
while(True):
[defline,seq]=reader.nextSequence()
if(not defline): break
if(not rex.find("^\s*>\s*(\S+)",defline)):
exit("Can't parse defline: "+defline)
id=rex[1]
transcripts=hash.get(id,None)
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 GffTranscriptReader import GffTranscriptReader
#filename="/home/bmajoros/1000G/assembly/local-genes.gff"
#filename="/home/bmajoros/1000G/assembly/tmp.gff"
#filename="test/data/tmp.gff"
#filename="test/data/local-genes.gff"
filename = "/home/bmajoros/ensembl/protein-coding.gff"
reader = GffTranscriptReader()
genes = reader.loadGenes(filename)
for gene in genes:
exons = gene.getMergedExons()
unmerged = 0
for transcript in gene.transcripts:
unmerged += len(transcript.getRawExons())
print(unmerged, "exons merged to", len(exons))
#for i in range(len(exons)):
# print("MERGED TO:",exons[i].begin,exons[i].end)
# print()
#transcripts=reader.loadGFF(filename)
#for transcript in transcripts:
#print(transcript.getID())
#gff=transcript.toGff()