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bcgsc / btllib

Bioinformatics Technology Lab common code library
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Seq Reader FAA Module #64

Closed jwcodee closed 1 year ago

jwcodee commented 1 year ago

To enable future development with amino acids using seq_reader, I have added the FAA modules based on the FA modules already part of btllib.

vlad0x00 commented 1 year ago

The FASTA file format is used for both nucleotide and amino acid sequences (https://en.wikipedia.org/wiki/FASTA_format). My suggestion would be using the FASTA module/format for both. Might be confusing otherwise.

Ideal solution would probably be to use the FASTA format/module for both nucleotides and amino acid sequences, but add a check like is_nucleotide_seq() and is_amino_acid_seq() to SeqReader. The implementation would probably look at the first N chars (e.g. 2048) to determine that.

jwcodee commented 1 year ago

New version found in #88.