BP_SEAR...LNBLOCKS(1)

🎀 NAME 🎀

Okay so this is bp_search2alnblocks, and the manual page it lives on is BP_SEAR...LNBLOCKS(1) from the User Contributed Perl Documentation. Its whole job? Turn SearchIO parseable reports(s) into a set of aligned blocks. Slay. 💅

✨ SYNOPSIS ✨

Here's the exact invocation vibe:

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

🦋 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. 😭

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). Iconic. ✨

💖 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 Bio::SearchIO for more information.
• -of, --outformat — Output format for the alignment blocks, anything Bio::AlignIO supports.
• -v, --verbose — Turn on debugging.

👑 AUTHOR - Jason Stajich 👑

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

🌈 Cute little sign-off: this page is from perl v5.42.3, dated 2021-02-03, and its manual is BP_SEAR...LNBLOCKS(1). Bye bestie, go align those blocks! 💖