make fasta file with one line per taxon name and one line per sequence using AMAS

non-interleave-fasta.py

#! /usr/bin/env python3

from amas import AMAS
from glob import glob

# glob all fasta files into a list
in_fs = glob('*.fasta')

# get a list of alignments in
meta_aln = AMAS.MetaAlignment(in_files=in_fs, data_type="dna",in_format="fasta", cores=1)

# extract {taxon : seq} dictionaries
aln_dicts = meta_aln.get_parsed_alignments()


# for each alignment in the list of dicts (here only one)
for index, alignment in enumerate(aln_dicts):

    # open file for writing
    fn = 'non-interleaved{}.fas'.format(index + 1)
    out_f = open(fn, "w")

    # for each taxon name and sequence
    for taxon, sequence in alignment.items():
        # write on separate lines:
        # taxon name and sequence
        out_f.write('>{}\n{}\n'.format(taxon, sequence))

    # close file
    out_f.close()