BP_SREFORMAT(1)

📦 version 1.7.8, in nixos 26.05, nixpkgs unstable

💅 BP_SREFORMAT(1) — like, the whole manual bestie

okay so first things first: this is bpsreformat, and it lives in the User Contributed Perl Documentation section of the manual, section 1. That's the vibe. Now let's get into it ✨

🦋 NAME

bpsreformat — convert sequence formats. that's it, that's the whole name, and honestly? iconic.

🌸 DESCRIPTION

okay so this script uses the SeqIO system, which is the thing that lets you convert sequence formats — and it handles both plain sequence data 💫 and multiple sequence alignment data 🎀

now, about the name real quick: it comes from the fact that Sean Eddy's program sreformat (part of the HMMER pkg) already does this exact thing. so yeah, we're not out here inventing words, we're just building on the icon himself 👑

but here's the difference, and it's kind of a big one: Sean's program tries to guess the input formats. our code? nah. currently you have to specify what the input and output formats are, and also whether the data is from a multiple sequence alignment or from straight sequence files. no guessing, no vibes-based parsing, you tell it or it doesn't happen 🫶

Usage:

bpsreformat -if INFORMAT -of OUTFORMAT -i FILENAME -o output.FORMAT

💖 OPTIONS

  • -h, --help — prints this help. the "what does anything do" button 🥺
  • -if, --informat — specify the input format. required, bestie, this program does not guess 💀
  • -of, --outformat — specify the output format. also required. yes both. I know. 🎀
  • -i, --input — specify the input file name. and listen: to pass in data on STDIN, use the minus sign - as the filename 🌀
  • -o, --output — specify the output file name. same deal — to pass data out on STDOUT, use the minus sign - as the filename 🌈
  • --msa — specify that this is multiple sequence alignment data. use this when your data is an alignment and not just loose sequences, iykyk 🧚
  • --special — will pass on special parameters to the AlignIO/SeqIO object — most of these are for Bio::AlignIO objects. it takes a comma separated list of the following:
    • nointerleaved — for phylip, non-interleaved format
    • idlinebreak — for phylip, makes it molphy format
    • percentages — for clustalw, show % id per line
ngl, --special is giving "mystery box of format-specific quirks" but it's literally just those three. comma separated. you got this 💅

🔥 SEE ALSO

nothing listed, bestie — this page is a solo act 👑 (but like, sreformat from HMMER is the spiritual ancestor, if you're curious 🌸)

okay that's the whole page!! this one's from perl v5.42.3, dated 2021-02-03 — so go forth, convert those sequences, and remember: specify your formats, the program is not reading your mind 💖✨🦋

📦 where this page comes from