Python SeqGroup.iter_entries Examples

Example #1

File: msa.py Project: epruesse/ARB

def merge_alignment(aln1, aln2, fout, numsites):
    seqs1 = SeqGroup(aln1)
    seqs2 = SeqGroup(aln2)
    if len(seqs1) == 0 or len(seqs2) == 0:
        print("No sequences aligned! ")
        sys.exit()
    with open(fout, "w") as fo:
        for seq in seqs1.iter_entries():
            if len(seq[1].strip()) == numsites:
                fo.write(">" + seq[0] + "\n" + seq[1] + "\n")
            else:
                print("Error in alignment ....")
                sys.exit()
        for seq in seqs2.iter_entries():
            if len(seq[1].strip()) == numsites:
                fo.write(">" + seq[0] + "\n" + seq[1] + "\n")
            else:
                print("Error in alignment ....")
                sys.exit()

Example #2

File: msa.py Project: amkozlov/sativa

def merge_alignment(aln1, aln2, fout, numsites):
    seqs1 = SeqGroup(aln1)
    seqs2 = SeqGroup(aln2)
    if len(seqs1) == 0 or len(seqs2) == 0:
        print("No sequences aligned! ")
        sys.exit()
    with open(fout, "w") as fo:
        for seq in seqs1.iter_entries():
            if len(seq[1].strip()) == numsites:
                fo.write(">" + seq[0] + "\n" + seq[1] + "\n")
            else:
                print("Error in alignment ....")
                sys.exit()
        for seq in seqs2.iter_entries():
            if len(seq[1].strip()) == numsites:
                fo.write(">" + seq[0] + "\n" + seq[1] + "\n")
            else:
                print("Error in alignment ....")
                sys.exit()