biocantor.io.fasta.fasta

Functions for handling FASTA files. Builds BioCantor sequence objects from various types of FASTA files.

Module Contents

Functions

fasta_to_parents(→ Dict[str, ...)

Parser that converts a FASTA to a dictionary of Parents, with sequence symbols as keys.

collection_to_fasta(collections, fasta_file_handle)

Take an instantiated AnnotationCollection and produce a FASTA file.
biocantor.io.fasta.fasta.fasta_to_parents(fasta_handle: TextIO, alphabet: Optional[inscripta.biocantor.sequence.Alphabet] = Alphabet.NT_EXTENDED_GAPPED) → Dict[str, inscripta.biocantor.parent.Parent]

Parser that converts a FASTA to a dictionary of Parents, with sequence symbols as keys.

Parameters

  • fasta_handle – Open file handle in text mode.

  • alphabet – Alphabet this file is in.

Returns

Dictionary mapping the symbol of the sequence to a Parent object.

biocantor.io.fasta.fasta.collection_to_fasta(collections: Iterable[inscripta.biocantor.gene.AnnotationCollection], fasta_file_handle: TextIO)

Take an instantiated AnnotationCollection and produce a FASTA file.

Parameters

  • collections – Iterable of instantiated AnnotationCollection with attached sequence information.

  • fasta_file_handle – Open file handle to write the FASTA to.

Raises

FastaExportError if there is no sequence attached to any of the collections. –