BP_SEQCUT(1p)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💅 bp_seqcut(1p) — ok bestie, let's cut some sequences

so this is a page from the User Contributed Perl Documentation section of the manual, and it's literally called bp_seqcut.pl. it cuts FASTA sequences with a given range. that's the whole vibe. periodt. 🎀

✨ NAME ✨

bp_seqcut.pl — cut FASTA sequences with a given range 🦋

✨ USAGE ✨

bp_seqcut.pl [options -h,-s,-e,-f,-w] <FILES>...
bp_seqcut.pl [options -h,-f,-w] s-e <FILES>...

and here's what all those little flags mean, bestie, one by one:

  • -h — this help message. she's the "pls explain" button 💖
  • -s — which residue to start cutting on
  • -e — which residue to finish cutting on
  • -f — format of the files, defaults to FASTA but you can specify anything supported by SeqIO from BioPerl
  • -w — hard wrap width, this might not be supported depending on which format you are using 🙈

✨ DESCRIPTION ✨

okay so picture this: it's a script to cut FASTA sequences with a given range, like fastacut -s 1 -e 10 *.fasta or fastacut 1-10 *.fasta. no cap.

and honestly? it's just a convenience wrapper around the Bio::SeqIO module. that's it. that's the whole personality. 🫶

but it's useful if you wish to trim out a section of an alignment to build a profile of a specific region of sequence. lowkey iconic behaviour honestly.

✨ AUTHOR ✨

Matt Oates — Matt.Oates@bristol.ac.uk 👑

✨ FEEDBACK ✨

Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, your input matters. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated. fr fr 💜

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. bug reports can be submitted via email or the web:

https://github.com/bioperl/bioperl-live/issues

like please actually report them, bestie, we can't fix what we don't know about 😭

✨ EDIT HISTORY ✨

2010-11-22 — Matt Oates First features added. a whole era began ✨

✨ DEPENDENCY ✨

  • Getopt::Long — Used to parse command line options.
  • Pod::Usage — Used for usage and help output.
  • Bio::SeqIO — Used to cut up sequences and parse FASTA.

the whole girlband right there 💅

reminder bestie: -w (hard wrap width) might not be supported depending on which format you are using — so don't come for me if it ghosts you.

and that's the page!! 🌈 this little gem comes to you from perl v5.32.1, dated 2021-08-15, in the BP_SEQCUT(1p) manual. go forth and cut, queen. 🎀💖✨

📦 where this page comes from