# 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)
# print("length="+str(L))
#filename="/home/bmajoros/1000G/assembly/BRCA1-NA19782.fasta";
filename="/Users/bmajoros/python/test/data/subset.fasta"
print(FastaReader.getSize(filename))
[defline,seq]=FastaReader.firstSequence(filename)
print(len(seq))
#filename="/home/bmajoros/1000G/assembly/test.fasta"
filename="/Users/bmajoros/python/test/data/subset.fasta"
hash=FastaReader.readAllAndKeepDefs(filename)
for key in hash.keys():
[defline,seq]=hash[key]
print(defline)
[id,attrs]=FastaReader.parseDefline(defline)
print("id="+id)
for key,value in attrs.items():
print(key+"="+value)
writer=FastaWriter()
writer.writeFasta(">ABCD","ATCGATCGTAGCTAGTCTGCGCGTATCGTCAGTCTCTATCGATCGTACTGCGATCTAGCTAGCTGATCGTAGCTTCTATGACTGCTAGTCATCTAGCTAGCTGATCGTAGCTGCGCGCGATATATTGCATCTATGCTATCATTGCATGCTAGCTCTAGCTAGTCGATGCTATCTTAGCTAC","test1.fasta")
writer.appendToFasta(">XYZ","GATTACA","test1.fasta")
print(Translation.translate(seq))
print("forward:",seq)
print("revcomp: ",Translation.reverseComplement(seq))
