MutCount and multi line fasta

[lecorguille]

It seems that MutCount only allow one-line fasta: S01a_codons_counting.py#L743-L750

    # read sequences
    sequences_for_counts = {}
    sequences_for_resampling = {}
    with open(args.sequences_file, "r") as file:
        for line1,line2 in itertools.izip_longest(*[file]*2):
            species = line1.strip(">\r\n")
            sequence = line2.strip("\r\n")
            if species in list_species:                
                sequences_for_counts[species] = sequence
            if species in list_species_boot:
                sequences_for_resampling[species] = sequence

@casteljade uploaded her own fasta where the sequence themself are on several lines.