def mafft(fasta_file, output_dir, output_ext, seq_type, cpus, anysymbol):
"""Align sequences."""
in_path = fasta_file
if seq_type == 'aa':
in_path = bio.adjust_aa_seqs(fasta_file, output_dir)
cmd = [
'mafft', '--amino' if seq_type == 'aa' else '--nuc',
'--thread {}'.format(cpus), '--anysymbol' if anysymbol else ''
]
if (bio.fasta_record_count(in_path) >= bio.SEQ_COUNT_CUTOFF
or bio.longest_fasta_seq(in_path) >= bio.SEQ_LEN_CUTOFF):
cmd.append('--auto')
else:
cmd += [
'--genafpair', '--maxiterate {}'.format(MAX_ITERATE),
'--anysymbol' if anysymbol else ''
]
cmd.append(in_path)
cmd = ' '.join(cmd)
aligned = util.file_name(fasta_file, output_ext)
with util.cd(output_dir):
result = subprocess.check_output(cmd, shell=True)
with open(aligned, 'wb') as out_file:
out_file.write(result)
return aligned
def seq_too_long(fasta, seq_type):
"""Warn about really long sequences."""
longest = bio.longest_fasta_seq(fasta)
if bio.seqs_too_long(longest, seq_type):
seq_count = bio.fasta_record_count(fasta)
logging.warning(util.shorten("""{} has {} sequences.
The longest is {} characters.
This is too long and may crash the alignment process.
""".format(fasta, seq_count, longest)))
def fa2tree(args):
"""Build trees from the fasta data."""
for fasta in args.input_files:
logging.info('fa2tree input: {}'.format(fasta))
fasta = abspath(fasta)
if args.bootstrap:
fa2tree_bs(args, fasta)
elif bio.fasta_record_count(fasta) >= bio.SEQ_COUNT_CUTOFF:
fa2tree_big(args, fasta)
else:
fa2tree_default(args, fasta)
def fasta_to_tree(args):
"""Build trees from the fasta data."""
for fasta in util.get_input_files(args.input_dir, args.input_filter):
if args.bootstrap:
fasta_to_tree_bs(args, fasta)
elif bio.fasta_record_count(fasta) >= bio.SEQ_COUNT_CUTOFF:
pass
else:
aligned = mafft(
fasta, args.output_dir, args.seq_type, args.cpus,
args.anysymbol)
cleaned = pxclsq(
aligned, args.output_dir, args.seq_type, args.min_occupancy,
args.min_seq_len)
raxml(
cleaned, args.output_dir, args.seq_type, args.cpus, args.seed)
def too_few_records(fasta):
"""Check if the fasta file is too small to make a good tree."""
if bio.fasta_record_count(fasta) < bio.MIN_SEQ:
logging.warning('"{}" has fewer than {} records, skipping.'.format(
fasta, bio.MIN_SEQ))