CLI API

[emiliorighi]

The idea behind the CLI is to act as a fast wrapper around user provided fastas and gff/gtf files.

• User provide a fasta file path (.fa/.gz, .fasta/.gz) and a a list of gff/gtf file paths -> fetch fasta headers and seqids (1st column from gff/gtf files) -> fetch aliases -> map aliases -> overwrite seqids of gff/gtf files -> output new gff/gtf files path/overwrite existing if specified from the user
• User provide URL of the fasta and/or related gff/gtf files -> download fasta->stream gff/gtf and replace seqids with correct alias on the fly
• How to handle not found aliases?

[Max25R]

• Single-file path: done in v1. alias-mapper convert <file> --to <convention> covers GFF/GTF/FASTA with source convention and assembly auto-detected.
• Multi-file align flow (fasta + gff/gtf paths, all aligned to one convention): v2 work, not started. This is the main remaining CLI feature.
• URL input / streaming: further out, no work yet.
• Not-found alias handling: v1 does warn-and-pass-through. Reasonable default; --strict / --skip-unknown flags could be added if needed.