This codebase allows users to search through a bacterial genome to find potential -1 progammed ribosomal frameshifting events. Currently, this can be run locally with small queries (<50 cDNAs). Cloud support is being added soon!
To run this code, you will need working installations of:
- hmmer
- RScape
- python3 and packages: argparse, os, datetime, pandas, shutil, json, RNA (python wrapper for ViennaRNA), localcider, & Bio.Seq (I used Bioconda for this)
Any recent/ stable release should work.
E_coli_small_2021_12_08-21_53_38.report.tsv contains output from searching through small_ecoli.fa, aligning to database bacteria.1236.1.genomic.fna. Intermediate files (including hmmer and RScape/CaCoFold output) are in E_coli_small_2021_12_08-21_53_38. Warning, bacteria.1236.1.genomic.fna is quite large!
Here is the command I used to generate this output. I used all the default parameters:
bash search.sh -o E_coli_small_ -q /path/to/small_ecoli.fa -d /path/to/bacteria.1236.1.genomic.fna -r /path/to/rscape_v1.6.1/bin/R-scape -p /path/to/prf-search