comparison tools/align_back_trans/align_back_trans.py @ 1:ec202446408a draft

Uploaded v0.0.4, fixed an error message.

0:0c24e4e2177d

from Bio import SeqIO
from Bio import AlignIO
from Bio.Data.CodonTable import ambiguous_generic_by_id

if "-v" in sys.argv or "--version" in sys.argv:
    print "v0.0.3"
    sys.exit(0)

def stop_err(msg, error_level=1):
    """Print error message to stdout and quit with given error level."""
    sys.stderr.write("%s\n" % msg)

def check_trans(identifier, nuc, prot, table):
    """Returns nucleotide sequence if works (can remove trailing stop)"""
    if len(nuc) % 3:
        stop_err("Nucleotide sequence for %s is length %i (not a multiple of three)"
                 % (identifier, nuc))

    p = str(prot).upper().replace("*", "X")
    t = str(nuc.translate(table)).upper().replace("*", "X")
    if len(t) == len(p) + 1:
        if str(nuc)[-3:].upper() in ambiguous_generic_by_id[table].stop_codons:

1:ec202446408a

from Bio import SeqIO
from Bio import AlignIO
from Bio.Data.CodonTable import ambiguous_generic_by_id

if "-v" in sys.argv or "--version" in sys.argv:
    print "v0.0.4"
    sys.exit(0)

def stop_err(msg, error_level=1):
    """Print error message to stdout and quit with given error level."""
    sys.stderr.write("%s\n" % msg)

def check_trans(identifier, nuc, prot, table):
    """Returns nucleotide sequence if works (can remove trailing stop)"""
    if len(nuc) % 3:
        stop_err("Nucleotide sequence for %s is length %i (not a multiple of three)"
                 % (identifier, len(nuc)))

    p = str(prot).upper().replace("*", "X")
    t = str(nuc.translate(table)).upper().replace("*", "X")
    if len(t) == len(p) + 1:
        if str(nuc)[-3:].upper() in ambiguous_generic_by_id[table].stop_codons: