BP_SEA...NBLOCKS(1p)

💖 BP_SEA...NBLOCKS(1p) 💖

okay so bestie, welcome to the bp_search2alnblocks page — it lives in the User Contributed Perl Documentation section, manual 1p, and honestly? it's giving glow-up energy for your BLAST output. let's get into it ✨

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🌸 NAME 🌸

bp_search2alnblocks — turn SearchIO parseable reports(s) into a set of aligned blocks 🧚

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✨ SYNOPSIS ✨

bp_search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1.
blast file2.blast ...> out.fas

(yes, the line breaks in that synopsis are exactly what the original says, no cap — don't @ me, I just work here 💅)

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🦋 DESCRIPTION 🦋

This script will parse and filter BLAST (or other formats Bio::SearchIO can parse) output and format the alignment as blocks of alignments based on the HSPs. Note this can only work if the input file parsed contains the necessary. 😭 (yes, that's the whole sentence, it just… ends. iconic behavior, honestly.)

Typically this can be used to turn BLAST output into a FASTA alignment format for input into the QRNA comparative gene finder for RNA genes (E.Rivas). so like, blast → alignment → RNA gene finding pipeline, periodt 👑

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💅 OPTIONS 💅

• --maxevalue — Maximum E-value for an HSP
• --minevalue — Minimum E-value for an HSP
• --minlen — Minimum length of an HSP [default 0]
• --maxid — Maximum Percent Id [default 100] (to help remove sequences which are really close)
• --minid — Minimum Percent Identity for an HSP [default 0]
• -i/--input — An optional input filename (expects input on STDIN by default)
• -o/--output — An optional output filename (exports to STDOUT by default)
• -f/--format — Specify a different Search Alignment format- {fasta, axt, waba, blast, blastxml} are all permitted although the format must have actual alignment sequence for this script to work. See L<Bio::SearchIO> for more information.
• -of/--outformat — Output format for the alignment blocks, anything L<Bio::AlignIO> supports.
• -v/--verbose — Turn on debugging

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👑 AUTHOR - Jason Stajich 👑

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

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bestie reminder 🫶 — if you're feeding it a format, it's gotta have the actual alignment sequence in it, or this whole thing just does not go. vibe check your input first fr fr.

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that's the whole page, we ate and left no crumbs 🍓 this one's running on perl v5.32.1, dated 2021-08-15, straight from the User Contributed Perl Documentation corner of the manual. mwah 💜✨