BP_SEARCH2TRIBE(1p)

💖 NAME 💖

bp_search2tribe — bestie, this one turns SearchIO parseable report(s) into a TRIBE matrix. That's it, that's the whole vibe. ✨

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🦋 SYNOPSIS 🦋

okay so you run it like this:

Usage:
  bp_search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1
file2 ..

yes the synopsis line really does wrap like that, we don't make the rules 💅

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🌸 DESCRIPTION 🌸

ngl, this script is probably too slow for most people's uses. like, fr fr. 😭

It is better to use something like scripts/searchio/fastam9_to_table, the -m 9 output from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs, and then feed that table into MCL with the mcxdeblast script and the --m9 option. that's the glow-up path, iykyk. ✨

So what does this one actually do? It will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering. main character energy, honestly. 👑

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✨ OPTIONS ✨

the options are, bestie, right here:

• -o filename — the output filename [default STDOUT] 💖
• -f format — search result format (blast, fasta) (ssearch is fasta format). default is blast.
• -w or --weight VALUE — change the default weight for E(0.0) hits to VALUE (default=200 (i.e. 1e-200)) 🔥
• -h — this help menu 🫶

Also — and this part matters — you additionally specify the filenames you want to process on the command-line. If no files are specified then STDIN input is assumed. You specify this by doing:

bp_search2tribe < file1 file2 file3

see? lowkey elegant. 🌈

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🎀 AUTHOR 🎀

Jason Stajich, jason-at-bioperl-dot-org — absolute icon, we stan. 💜

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ok that's the whole page bestie, go cluster something gorgeous 🧚

perl v5.32.1 · 2021-08-15 · BP_SEARCH2TRIBE(1p) — mwah, that's the sign-off, slay 💅✨🍓