BP_SEQPART(1p)

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

💖 bp_seqpart.pl — the manual, but make it make sense 💖

okay bestie, so this is a page from the User Contributed Perl Documentation situation, and it's all about bp_seqpart.pl — a whole lil script that takes one or more sequence files and splits them into a bunch of load-balanced files. no cap. it's giving "divide and conquer but make it fair" 🎀

✨ NAME ✨

bp_seqpart.pl — takes one or more sequence files and splits them into a number of load balanced files. literally that's the whole personality 🦋

🌸 USAGE 🌸

bp_seqpart.pl -n <NUM_PARTS> [-h, -p <PREFIX>, -f <FORMAT>, -o <OUT_DIR>] <FILES...>

and here's the tea on every single flag, no skipping:

  • -n — number of files to create through partitioning
  • -h — this help message
  • -p — prefix for all FASTA file names output, files are of the form <outdir>/<prefix>#.<format>
  • -f — format of the files, defaults to FASTA but you can specify anything supported by SeqIO from BioPerl
  • -o — output directory where to dump the split sequence files

🫶 DESCRIPTION 🫶

so basically this is a script wrapping SeqIO that lets you partition multiple sequence files into near equal sized parts for later parallel processing. 🧚

and here's the part that's actually iconic: even if you have 10 input files, outputting to 10 files will balance the files to contain similar total length of sequence. ID's are ignored when deciding on how to balance each sequence. periodt. 💅

👑 AUTHOR 👑

Matt Oates - mattoates+support@gmail.com

💌 FEEDBACK 💌

Mailing Lists

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. 🥺🫶

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 ⭐

2012-04-03 - Matt Oates      First features added.

🌈 DEPENDANCY 🌈

(yes it's spelled like that, we keep it 💀) — Getopt::Long is used to parse command line options. Pod::Usage is used for usage and help output. Bio::SeqIO is used to cut up sequences and parse FASTA.

💀 heads up: the DEPENDANCY heading above is exactly as it appears in the original, typos and all, because we do not edit the lore. 🙈

okay that's the whole page bestie, you're so welcome, go balance some sequences 🌸✨ — this was written against perl v5.32.1, dated 2021-08-15, mwah 💅💖

📦 where this page comes from