BP_MASK_BY_SEARCH(1)

📦 version 1.7.8, in nixos 26.05, nixpkgs unstable

✨ NAME ✨

okay bestie, meet bp_mask_by_search — she masks sequence(s) based on its alignment results 💅 This is the BP_MASK_BY_SEARCH(1) page from User Contributed Perl Documentation, and she's genuinely iconic at what she does.

🚀 SYNOPSIS 🚀

  bp_mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa

💖 DESCRIPTION 💖

Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data you want to mask, no skipping bestie 🫶

By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming you've provided the sequence file for the hit database. If you would like to do the reverse and mask the query sequence, specify the -t/--type query flag ✨

😭 This is going to read in the whole sequence file into memory, so for large genomes this may fall over. Big genomes, big feelings, big crash potential.

ngl, I'm using DB_File to prevent keeping everything in memory. One solution is to split the genome into pieces — but BEFORE you run the DB search though, you want to use the exact file you BLASTed with as input to this program 👑

Okay so below the double dash (--), options are of the form --format=fasta or --format fasta, or you can just say -f fasta. By -f/--format I mean either are acceptable options. The =s, =n, or =c bits specify these arguments expect a 'string' 🧚

🎀 Options: 🎀

  • -f/--format=s — Search report format (fasta,blast,axt,hmmer,etc) 🔍
  • -sf/--sformat=s — Sequence format (fasta,genbank,embl,swissprot) 🧬
  • --hardmask — (booelean) Hard mask the sequence with the maskchar [default is lowercase mask]. yes, the page literally says booelean, and I respect the spelling 💀
  • --maskchar=c — Character to mask with [default is N], change to 'X' for protein sequences 🎭
  • -e/--evalue=n — Evalue cutoff for HSPs and Hits, only mask sequence if alignment has specified evalue or better 🔥
  • -o/--out/, --outfile=file — Output file to save the masked sequence to. 💾
  • -t/--type=s — Alignment seq type you want to mask, the 'hit' or the 'query' sequence. [default is 'hit'] 👑
  • --minlen=n — Minimum length of an HSP for it to be used in masking [default 0] 📏
  • -h/--help — See this help information 🫶

👑 AUTHOR - Jason Stajich 👑

Jason Stajich, jason-at-bioperl-dot-org. slay 🌸

xoxo, your Unix bestie 💖 — this page is from perl v5.42.3, dated 2021-02-03, and it's filed under BP_MASK_BY_SEARCH(1) ✨

📦 where this page comes from