BP_SEQPART(1)

💅 bp_seqpart.pl — BP_SEQPART(1), bestie edition

okay so picture this: it's a Perl script, it's got SeqIO energy, and its whole personality is taking your sequence files and splitting them into load-balanced chunks. the manual page is BP_SEQPART(1) and honestly? she ate. ✨

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🌸 NAME 🌸

bp_seqpart.pl — takes one or more sequence files and splits them into a number of load balanced files. literally that's the job. no cap. 🫶

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✨ USAGE ✨

here's the whole thing, exactly as it lives, no edits:

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

  -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

and in group-chat form, one bullet per flag:

• -n — number of files to create through partitioning 👑 (this one's the main character, you gotta have it)
• -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 🍓

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💖 DESCRIPTION 💖

so this is a script wrapping SeqIO that allows partitioning of multiple sequence files into near equal sized parts for later parallel processing. like, it's giving "prep work for your cluster job." 💅

and here's the slay part: even if you have 10 input files, outputting to 10 files will balance the files to contain similar total length of sequence. the balancing is by total sequence length, not by count — which is genuinely the smart way to do it.

⚠️ real talk though: ID's are ignored when deciding on how to balance each sequence. so don't come in here expecting your IDs to influence anything. they do not. 🙈

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🌈 AUTHOR 🌈

Matt Oates — mattoates+support@gmail.com 🫶

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🎀 FEEDBACK 🎀

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules. so like… 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 report them, bestie, they cannot fix what they don't know about 😭

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⭐ EDIT HISTORY ⭐

• 2012-04-03 — Matt Oates — First features added. the origin story. iconic. 👑

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🦋 DEPENDANCY 🦋

(yes, that's how it's spelled in the original, we respect the spelling 💜)

• 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.

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okay that's the whole page 💖 shoutout to perl v5.42.3 and the 2021-02-03 date on this one — that's the version and stamp this gorgeous little manpage shipped with. go partition something and slay, bestie 🌸✨🎀