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