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)
if(not transcripts): continue
for transcript in transcripts:
transSeq=transcript.loadTranscriptSeq(seq)
writer.addToFasta(">"+transcript.getID(),transSeq,OUT)
reader.close()
OUT.close()
# 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)
fh.close()
print("[done]",file=sys.stderr)
