Crate mafft_io 

I/O routines for MAFFT: FASTA, Clustal, PHYLIP, hat2, and localhom formats.

FASTA reading/writing delegates to noodles-fasta. The other formats are MAFFT-specific or simple enough that we implement them directly.

Structs

Hat2Matrix

MAFFT’s hat2 distance matrix format.

IllegalResidue

The first residue seqcheck would reject, in reading order.

Enums

IoError

Functions

apply_case_convention

Apply C MAFFT’s residue-case convention to an already-parsed set: lowercase for DNA/RNA, uppercase for everything else.

compute_clustal_marks

Compute CLUSTAL-format conservation marks per column.

detect_seq_type

Detect whether sequences are DNA/RNA or protein by ATGC frequency.

detect_seq_type_with_limit

find_illegal_residue

Scan set the way C seqcheck does and return the first residue that is not in the alphabet for set.seq_type, or None when every residue is legal. Gap characters (-) are part of both alphabets, so a gapped input passes.

normalize_residues

Apply the FASTA reader’s residue filter to residues that are already in memory, so an in-memory caller ends up with exactly the bytes a FASTA round trip would have produced — and fails exactly where the reader would.

read_fasta

Read a FASTA file from a path into a SequenceSet.

read_fasta_casepreserve

Read a FASTA file preserving case and non-standard residues — used by --anysymbol/--preservecase. Strips only newline, space and carriage return (matching C MAFFT’s readData_pointer_casepreserve → charfilter, io.c:1329-1352); any other character — digits, tabs, punctuation, lowercase — is kept verbatim so the post-alignment restore pass can put the originals back.

read_fasta_from_reader

Read FASTA from any buffered reader.

read_fasta_from_reader_casepreserve

Like read_fasta_from_reader but preserves case and non-standard residues (see read_fasta_casepreserve).

read_hat2

Read a hat2 distance matrix.

read_localhom_table

Read a local homology table (hat3 format).

residues_are_normalized

true when normalize_residues would return raw unchanged, i.e. the residues already look like they came out of the FASTA reader. Lets a caller holding borrowed data skip the copy when nothing needs to change. Residues the reader would reject are not “unchanged”.

residues_follow_case_convention

true when apply_case_convention would leave data unchanged for a set of type seq_type: no uppercase letters for nucleotides, no lowercase letters otherwise.

seqcheck_alphabet

The alphabet seqcheck tests set against — mafft_scoring’s DNA alphabet for nucleotide sets, its protein alphabet otherwise.

write_clustal

Write an alignment in Clustal format.

write_clustal_full

Write an alignment in Clustal format with an optional header comment (e.g. the alignment-mode label FFT-NS-2).

write_fasta

Write a SequenceSet as FASTA to a file path.

write_fasta_to_writer

Write a SequenceSet as FASTA to any writer.

write_fasta_to_writer_with_width

Write FASTA with a custom line width. Pass 0 for unlimited (single line).

write_hat2

Write a hat2 distance matrix.

write_localhom_table

Write a local homology table (hat3 format).

write_phylip

Write an alignment in interleaved PHYLIP format.