BP_MASK_BY_SEARCH(1p)

✨ BP_MASK_BY_SEARCH(1p) ✨

okay bestie, gather round, because this is the bp_mask_by_search page from the User Contributed Perl Documentation and it's lowkey a banger 💖

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🌸 NAME 🌸

bp_mask_by_search — mask sequence(s) based on its alignment results

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🎀 SYNOPSIS 🎀

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

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🦋 DESCRIPTION 🦋

So the whole vibe here is: you take the significant alignments of one sequence and you use them to mask another sequence. Periodt. 💅

You gotta hand over two things: the report file, and the entire sequence data that you want to mask. No half-measures, she wants the whole thing.

By default, this tool assumes you did a TBLASTN (or a TFASTY), and it will try and mask the hit sequence — assuming you've provided the sequence file for the hit database. That's the default assumption, okay?

But if you wanna do the reverse and mask the query sequence instead? Just specify the -t/--type query flag and you're golden ✨

⚠️ real talk: this is going to read the whole sequence file into memory, so for large genomes this may fall over. 😭

She's using DB_File to prevent keeping everything in memory — one solution is to split the genome into pieces. But listen closely: do that BEFORE you run the DB search though. You want to use the exact file you BLASTed with as input to this program. iykyk 🧚

Below the double dash (--) options are of the form --format=fasta or --format fasta or you can just say -f fasta. All three, she's flexible like that.

By -f/--format I mean either are acceptable options. The =s or =n or =c specify these arguments expect a 'string'.

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👑 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] — and yes, it literally says "booelean" in the source, we don't gatekeep typos here 💀
• --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

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💜 AUTHOR - Jason Stajich 💜

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

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and that's the whole page, bestie!! 🫶 this one's running on perl v5.32.1 and it was stamped 2021-08-15, so go forth and mask responsibly, mwah 💅💖🌸