BP_SEQCUT(1)

📦 version 1.7.8, in nixos 26.05, nixpkgs unstable

💖 BP_SEQCUT(1) 💖

okay bestie, this is the whole manual for bp_seqcut.pl, and it is literally here to cut FASTA sequences with a given range. no cap, it's giving “tiny tool, very useful” energy 🎀

✨ 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>...

the flags are giving:

  • -h — this help message 🫶
  • -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 🌸

bestie, this is a script to cut FASTA sequences with a given range: fastacut -s 1 -e 10 *.fasta or fastacut 1-10 *.fasta. it's literally just a convenience wrapper around the Bio::SeqIO module. lowkey useful if you wish to trim out a section of an alignment to build a profile of a specific region of sequence ✨

👑 AUTHOR 👑

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

💌 FEEDBACK 💌

user feedback is an integral part of the evolution of this and other Bioperl modules. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated 🫶

📬 Mailing Lists 📬

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

🕰️ EDIT HISTORY 🕰️

  • 2010-11-22 — Matt Oates First features added. 👑

🧚 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.

xoxo, your Unix bestie 💖 — this iconic page is perl v5.42.3, dated 2021-02-03, and it's literally BP_SEQCUT(1) 💅✨

📦 where this page comes from