Skip to content

Instantly share code, notes, and snippets.

What would you like to do?
make fasta file with one line per taxon name and one line per sequence using AMAS
#! /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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.