modules/
rpbp_preparegenome

Description

Build the per-ORF reference files that Rp-Bp's downstream scoring needs, starting from a genome FASTA and an annotation GTF. Enumerates every candidate open reading frame (ORF) in the annotation (annotated CDSs plus alternative start codons within transcript exons), records their genomic and per-exon coordinates, and labels them with the transcript and gene they belong to.

Invokes Rp-Bp's get_orfs Python function directly, chaining the upstream helpers gtf-to-bed12, extract-bed-sequences, extract-orf-coordinates, split-bed12-blocks and label-orfs. Bypasses Rp-Bp's prepare-rpbp-genome umbrella script, which would also build bowtie2 (rRNA filtering) and STAR (alignment) indices - neither is consumed by the Rp-Bp tools wrapped here, since alignment is supplied externally as a BAM.

A minimal chrName.txt (one contig name per line) is seeded from the FASTA headers because gtf-to-bed12 reads it via --chr-name-file to control output sort order.

Note: emits the *.annotated.bed.gz filenames produced by get_orfs directly, rather than the *.bed.gz-renamed forms that the upstream umbrella prepare-rpbp-genome script produces. The downstream module outputs and consumers in this module set reference these names explicitly, so the two are functionally equivalent.