2020-08-10 氨基酸简拼和全拼转换脚本

支持标准输入，标准输出

#!/usr/bin/env python3
'''
About:
    abbre_aa.py is used to manipulate Amino Acids abbreviation and complete spelling.
Example command:
    ./abbre_aa.py  -a 03 -f 1 -d ":" > outfile
'''
import sys
import argparse
import fileinput

amino_acids_13dict = {
'G': 'Gly',
'A': 'Ala',
'V': 'Val',
'L': 'Leu',
'I': 'Ile',
'F': 'Phe',
'W': 'Trp',
'Y': 'Tyr',
'D': 'Asp',
'H': 'His',
'N': 'Asn',
'E': 'Glu',
'K': 'Lys',
'Q': 'Gln',
'M': 'Met',
'R': 'Arg',
'S': 'Ser',
'T': 'Thr',
'C': 'Cys',
'P': 'Pro'
}

amino_acids_30dict = {
'Gly': 'Glycine',
'Ala': 'Alanine',
'Val': 'Valine',
'Leu': 'Leucine',
'Ile': 'Isoleucine',
'Phe': 'Phenylalanine',
'Trp': 'Tryptophan',
'Tyr': 'Tyrosine',
'Asp': 'Aspartate',
'His': 'Histidine',
'Asn': 'Asparagine',
'Glu': 'Glutamate',
'Lys': 'Lysine',
'Gln': 'Glutamine',
'Met': 'Methionine',
'Arg': 'Arginine',
'Ser': 'Serine',
'Thr': 'Threonine',
'Cys': 'Cysteine',
'Pro': 'Proline'
}

amino_acids_10dict = {
'G': 'Glycine',
'A': 'Alanine',
'V': 'Valine',
'L': 'Leucine',
'I': 'Isoleucine',
'F': 'Phenylalanine',
'W': 'Tryptophan',
'Y': 'Tyrosine',
'D': 'Aspartate',
'H': 'Histidine',
'N': 'Asparagine',
'E': 'Glutamate',
'K': 'Lysine',
'Q': 'Glutamine',
'M': 'Methionine',
'R': 'Arginine',
'S': 'Serine',
'T': 'Threonine',
'C': 'Cysteine',
'P': 'Proline'
}

def parse_args():
    '''Parse command-line arguments.
    '''
    parser = argparse.ArgumentParser(
        description=__doc__,
        formatter_class=argparse.RawDescriptionHelpFormatter)

    parser.add_argument('input',
        metavar='',
        type=str,
        help='input filename, amino acid codons should be abbreviated or completed.')

    parser.add_argument('-a', '--action',
        metavar="['01', '03', '10', '13', '30', '31']",
        type=str,
        choices=['01', '03', '10', '13', '30', '31'],
        required=True,
        help='01:complete -> One-letter; 03:complete -> Three-letter; 13:One-letter -> Three-letter ...')
    parser.add_argument('-d', '--delimiter',
        metavar='',
        type=str,
        default='\t',
        help='delimiter of line [default: "\\t"]')
    parser.add_argument('-f', '--field',
        metavar='',
        type=int,
        default=0,
        help='field of amino acid codons [default: entire line]')
    args = parser.parse_args()
    return args

def aa01(string):
    for a,b in amino_acids_10dict.items():
        string = string.replace(b, a)
    return string

def aa10(string):
    for a,b in amino_acids_10dict.items():
        string = string.replace(a, b)
    return string

def aa13(string):
    for a, b in amino_acids_13dict.items():
        string = string.replace(a, b)
    return  string

def aa31(string):
    for a, b in amino_acids_13dict.items():
        string = string.replace(b, a)
    return  string

def aa03(string):
    for a,b in amino_acids_30dict.items():
        string = string.replace(b, a)
    return string

def aa30(string):
    for a,b in amino_acids_30dict.items():
        string = string.replace(a, b)
    return string

if __name__ == '__main__':
    args = parse_args()
    in_fh = fileinput.input(files=args.input)

    for line in in_fh:
        line = line.rstrip('\n')
        if args.field:
            line_lst = line.split(args.delimiter)
            if args.action == '01':
                line_lst[args.field - 1] = aa01(line_lst[args.field - 1])
            elif args.action == '10':
                line_lst[args.field - 1] = aa01(line_lst[args.field - 1])
            elif args.action == '13':
                line_lst[args.field - 1] = aa13(line_lst[args.field - 1])
            elif args.action == '31':
                line_lst[args.field - 1] = aa31(line_lst[args.field - 1])
            elif args.action == '03':
                line_lst[args.field - 1] = aa03(line_lst[args.field - 1])
            elif args.action == '30':
                line_lst[args.field - 1] = aa30(line_lst[args.field - 1])
            else:
                sys.eixt('Error: invalid action.')

            line = args.delimiter.join(line_lst)

        else:
            if args.action == '01':
                line = aa01(line)
            elif args.action == '10':
                line = aa01(line)
            elif args.action == '13':
                line = aa13(line)
            elif args.action == '31':
                line = aa31(line)
            elif args.action == '03':
                line = aa03(line)
            elif args.action == '30':
                line = aa30(line)
            else:
                sys.eixt('Error: invalid action.')

        print(line, file=sys.stdout, flush=True)
    in_fh.close()