dammit_gff3_to_trinity_names.py

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"""Function: Take in a dammit gff3, dammit fasta, dammit namemap.
Output gff3 and fasta with trinity names.
by Dr. Tessa Pierce
"""
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import sys
import os
import argparse
import screed

def dammit_to_trin(dammit_fasta,dammit_namemap,outdir,dammit_gff3, outFasta, outGFF):
    with open(dammit_namemap, 'r') as f:
        dammit2trin = {y:x.split(' ')[0] for x,y in split_more(f)}
    with open(outFasta, 'w') as outF:
        with screed.open(dammit_fasta) as seqs:
            for read in seqs:
                dammit_name, rest = read.name.split(' ', 1)
                trinName = dammit2trin[dammit_name][1:]
                full_name = trinName + ' ' + 'dammit=' +  dammit_name + ' ' + rest
                outF.write('>' + full_name + '\n' + read.sequence + '\n')
    with open(outGFF, 'w') as outG:
        with open(dammit_gff3, 'r') as gff:
             next(gff)
             for line in gff:
                 dammit_name, rest_gff_line = line.split('\t', 1)
                 trinName = dammit2trin[dammit_name][1:]
                 outG.write(trinName + '\t' + rest_gff_line)

#really quite unnecessary generator to "simplify" reading namemap into dict
def split_more(file_object):
    for line in file_object:
        yield line.strip().rsplit(',', 1)



if __name__ == '__main__':
    """Function: Take in a list of trinity gene names, a dammit namemap,
and a dammit fasta file. Output fasta of matching dammit contigs.
"""
    psr = argparse.ArgumentParser()
    psr.add_argument('dammit_fasta')
    psr.add_argument('--dammit_namemap')
    psr.add_argument('--dammit_gff3')
    psr.add_argument('-o', '--outdir', default=os.getcwd())
    psr.add_argument('--outFasta')
    psr.add_argument('--outGFF')
    args = psr.parse_args()
    dammit_to_trin(args.dammit_fasta,args.dammit_namemap,args.outdir,args.dammit_gff3, args.outFasta, args.outGFF)