combine_fasta_files.py

import anvio.utils as utils
fasta_suffix = '.fna'
output_file = 'merged_fasta.fna'
samples_list = 'samples.txt'
output_fasta_dictionary = {}
with open(samples_list,'r') as s:
        for sample in s:
                sample=sample.strip()
                sample_fasta = "".join([sample,fasta_suffix])
                print(sample)
                print(sample_fasta)
                fasta_dic = utils.get_FASTA_file_as_dictionary(sample_fasta)
                for contig_name in fasta_dic:
                        new_contig_name = sample + '_' + contig_name
                        output_fasta_dictionary[new_contig_name] = fasta_dic[contig_name]

utils.store_dict_as_FASTA_file(output_fasta_dictionary, output_file)