BP_SEARCH2TRIBE(1)

🦋 bp_search2tribe — turning SearchIO reports into a TRIBE matrix, bestie 💅

okay so this is the manual for bp_search2tribe, a Perl script for the bioperl crew ✨ (iykyk) — and the whole vibe is "turn your search output into something MCL can actually chew on".

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✨ NAME ✨

bp_search2tribe — Turn SearchIO parseable reports(s) into TRIBE matrix 🧚

no cap, that's literally the whole job.

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🌸 SYNOPSIS 🌸

Usage:

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

yes bestie, those files go on separate-ish lines in the original and we're keeping it exactly like that 🫶

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💖 DESCRIPTION 💖

okay so real talk first, and I'm gonna be honest with you because that's what besties do: this script is probably too slow for most people's uses. 😭 like, not me being dramatic — that's straight from the source.

it's better to use something like scripts/searchio/fastam9_to_table, or -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 route 🔥

but if you're here for what this script does: it will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering 👑

the options are:

• -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

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

main character energy fr fr 🌈

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👑 AUTHOR 👑

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

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💜 the cute sign-off 💜

this page is living its best life as part of perl v5.42.3, dated 2021-02-03 — and yes, that's the footer, we're mentioning it here instead of copying it because ✨ formatting ✨. mwah 💋 periodt.