def printSequences(novelteseqs,outfasta):
fw=FastaWriter(outfasta,100)
idset=set([])
for n,s in novelteseqs.items():
if n in idset:
raise ValueError("Already present"+n)
fw.write(n,s)
fw.close()
def printSequences(novelrefseqs, oldteseqs, novelteseqs, outfasta):
fw = FastaWriter(outfasta, 60)
idset = set([])
for n, s in novelrefseqs.items():
if n in idset:
raise ValueError("Alreade present" + n)
fw.write(n, s)
for n, s in oldteseqs.items():
if n in idset:
raise ValueError("Alreade present" + n)
fw.write(n, s)
for n, s in novelteseqs.items():
if n in idset:
raise ValueError("Alreade present" + n)
fw.write(n, s)
fw.close()
def printSequences(seq,outfasta): fw=FastaWriter(outfasta,60) for n,s in seq.items(): fw.write(n,s) fw.close()
def printSequences(seq, outfasta):
fw = FastaWriter(outfasta, 60)
for n, s in seq.items():
fw.write(n, s)
fw.close()
crap,chasis=SequenceUtility.load_chasis(args.ref_fasta)
else:
print "No chasis file found; Will use chasis from the population definition file"
chasis=pgdr.get_chasis()
if chasis=="":
raise Exception("No chasis was provided, neither in a fastq file nor in the population genome definition file")
print "Will proceed with chasis having a size of {0} nt".format(len(chasis))
counter=1
fw=FastaWriter(args.output,60)
print "Start writing population genome"
for tmp in tedeftuples:
# translate into sequences
seqtup=[(t[0],sc.getTESequence(t[1])) for t in tmp]
seq_with_te=SeqInserter.insertSequences(chasis,seqtup)
# TODO seqinserter must check if position is smaller than sequence length
fw.write("hg"+str(counter),seq_with_te)
counter+=1
print "Done; Wrote {0} genomes to file {1}".format(counter-1,args.output)
fw.close()