def filter_alignment_positions(aligned_sequences_file: AlignedDNAFASTAFormat,
maximum_gap_frequency: str,
maximum_position_entropy: str) -> \
AlignedDNAFASTAFormat:
aligned_sequences_fh = aligned_sequences_file.open()
fasta_file = AlignedDNAFASTAFormat()
skbio.write(filter_positions(aligned_sequences_fh, maximum_gap_frequency,
maximum_position_entropy),
into=str(fasta_file),
format='fasta')
return fasta_file
def extract_fungi(
aligned_silva_file: AlignedDNAFASTAFormat,
accession_file: SilvaAccessionFormat,
taxonomy_file: SilvaTaxonomyFormat,
) -> AlignedDNAFASTAFormat:
aligned_silva_fh = aligned_silva_file.open()
accession_fh = accession_file.open()
taxonomy_fh = taxonomy_file.open()
fasta_file = AlignedDNAFASTAFormat()
skbio.write(fungi_from_fasta(aligned_silva_fh, accession_fh,
taxonomy_fh), into=str(fasta_file), format='fasta')
# TODO this code is a good example of pithy return for plugins
# TODO redo other functions in the same way by instantiating a
return fasta_file
def _trim_all_sequences(aligned_sequences: AlignedDNAFASTAFormat,
trim_positions: dict) -> AlignedDNAFASTAFormat:
"""
Trim all sequences within given alignment based on provided positions.
Arguments:
aligned_sequences (AlignedDNAFASTAFormat): original, aligned sequences
trim_positions (dict): dictionary containing positions for trimming
Returns:
result (AlignedDNAFASTAFormat): trimmed aligned sequences
"""
result = AlignedDNAFASTAFormat()
with result.open() as out_fasta:
for seq in aligned_sequences.view(AlignedDNAIterator):
seq_trimmed = _trim_sequence(seq, trim_positions["start"],
trim_positions["end"])
seq_trimmed.write(out_fasta)
return result
