BP_HMMER_TO_TABLE(1p)

💖 BP_HMMER_TO_TABLE — the manual, but make it make sense 💖

okay so bestie, welcome to bp_hmmer_to_table (that's the 1p page from the User Contributed Perl Documentation section, iykyk). It does one (1) iconic thing: it takes your HMMER output and turns it into a tidy little table. no cap. 🦋

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✨ NAME ✨

bp_hmmer_to_table — turn HMMER output into tabular format 💅

like. that's it. that's the job. and it eats.

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🌸 SYNOPSIS 🌸

bp_hmmer_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...

yes you can throw MULTIPLE input files at it, she's flexible 💖

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🎀 DESCRIPTION 🎀

🫶 Command line options

• -e/--evalue evalue — filter by evalue. you set the bar, she respects it.
• -b/--bitscore bitscore — filter by bitscore. same energy, different number.
• --header — boolean flag to print column header. flip it on and you get labels, flip it off and you get pure vibes (and columns you have to remember).
• -o/--out — optional outputfile to write data. if you don't hand her one, she'll write to STDOUT instead. no pressure either way.
• -h/--help — show this documentation. hi bestie 👋

🧚 the tea on this script

Not technically a SearchIO script, because she doesn't use any Bioperl components — but she's useful and fast. fr fr. and the output? tabular output. 🌈

👑 the columns, in order, as promised

• query sequence/domain (these are flip-flopped for hmmsearch / hmmpfam)
• query start
• query end
• domain/sequence name or PFAM accession
• hit start
• hit end
• score
• e-value
• domain/sequence name (these are flip-flopped for hmmsearch / hmmpfam)

bestie take note: columns 1 and 9 are the flip-floppy ones when you're on hmmsearch or hmmpfam. the manpage says it twice for a reason. do not come for me, come for the flip-flop. 💀

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⭐ AUTHOR — Jason Stajich ⭐

Jason Stajich — jason_at_bioperl-dot-org 💜

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and that's the whole page, periodt. this little legend shipped as part of perl v5.30.0, dated 2019-10-29, in the BP_HMMER_TO_TABLE(1p) era of the User Contributed Perl Documentation. go make some tables, main character 🎀✨🔥