Use to append a tab-delimited fasta string to a fasta file

add_taxa_to_fasta.py

#!/usr/bin/env python

""" Usage:
python add_taxa_to_fasta.py input_taxa_file input_fasta_file output_fasta
"""

from sys import argv

from cogent.parse.fasta import MinimalFastaParser

# taxa mapping file expected to be tab separated
input_taxa = open(argv[1], "U")
# labels in fasta (before first whitespace) need to be exact match to ids in taxa mapping file
input_fasta = open(argv[2], "U")
output_fasta = open(argv[3], "w")

ids_taxa = {}
for line in input_taxa:
    if len(line.strip()) == 0:
        continue
    ids_taxa[line.split('\t')[0]] = line.split('\t')[1]


for label,seq in MinimalFastaParser(input_fasta):
    curr_taxa = ids_taxa[label.split()[0]]
    curr_label = "%s\t%s" % (label, curr_taxa)
    output_fasta.write(">%s\n%s\n" % (curr_label, seq))

Thanks Tony! 🥇
EDIT: And so fast, too! 💨