def concat(newAlignment, f, model):
print f
#inSeq2 = SeqIO.parse(open('concatenated.fas','r'),'fasta')
a = Alignment(f) #make an alignment instance from the file f
a.setmodel(model) #set the model for the alignment
a.populate()
fixFastas(newAlignment, a)
tempAlignment = Alignment('')
writelog(f + ':' + str(a.numchar) + ' ' + model)
for seq in newAlignment.seqs:
flag = 0
for aseq in a.seqs:
if seq.id == aseq.id:
flag = 1
newseq = SeqRecord(seq=seq.seq + aseq.seq, id=seq.id)
tempAlignment.seqs.append(newseq)
tempAlignment.idlist.append(newseq.id)
tempAlignment.numchar = len(tempAlignment.seqs[0].seq)
tempAlignment.numseq = len(tempAlignment.seqs)
#print tempAlignment.numchar
#print tempAlignment.numseq
return tempAlignment
