# 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)
if(not transcripts): continue
