comparison codon_usage.py @ 31:3cb2af2435d3 draft

Uploaded

30:e12061ce9601

from pprint import pprint
import argparse as ap
import sys
import os
import pandas as pd
#from BCBio import GFF


def read_input(data = "example.fna", type_ = "fasta"):

    """

    args = vars(parser.parse_args())

    seqs = read_input(data=args['input'], type_=args['type'])
    out = codon_usage(seqs, args['codonTable'])

    with open(args['output'], "w") as outf:
        out["Table"].to_csv(outf, sep="\t", index_label=["AA", "Codon"])

    

31:3cb2af2435d3

from pprint import pprint
import argparse as ap
import sys
import os
import pandas as pd


def read_input(data = "example.fna", type_ = "fasta"):

    """

    args = vars(parser.parse_args())

    seqs = read_input(data=args['input'], type_=args['type'])
    out = codon_usage(seqs, args['codonTable'])

    with open(args['output']+".csv", "w") as outf:
        out["Table"].to_csv(outf, sep="\t", index_label=["AA", "Codon"])