Bio::Tools::Seg(3pm)

✨ Bio::Tools::Seg ✨

okay bestie, so this is a page from the User Contributed Perl Documentation collection — it's Bio::Tools::Seg(3pm) and it's about to make your low-complexity-region life so much easier, no cap 💖

🌸 NAME 🌸

Bio::Tools::Seg — literally just here to parse seg output. that's it. that's the whole job. iconic behaviour honestly 🎀

🦋 SYNOPSIS 🦋

use Bio::Tools::Seg;
my $parser = Bio::Tools::Seg->(-file => 'seg.fasta');
while ( my $f = $parser->next_result ) {
  if ($f->score < 1.5) {
    print $f->location->to_FTstring, " is low complexity\n";
  }
}

see how chill that is? you load it, you loop, you vibe check the score, you print. periodt. ✨

💅 DESCRIPTION 💅

so seg is the tool that sniffs out low-complexity regions on a protein sequence. it usually rolls with the WU-BLAST and InterProScan packages — like, it's part of the friend group, iykyk.

here's the thing though, bestie: Bio::Tools::Seg will only parse the fasta output modes of seg. and by that i mean:

• seg -l — low complexity regions only
• seg -h — high complexity regions only
• seg -a — both low and high, the whole buffet 🍓

for every single FASTA-like entry it finds in the input file, it builds a Bio::SeqFeature::Generic. and then… it's on you. it's giving main character responsibility — you're the one who has to filter those features appropriately using the feature's score. the module is not gonna hold your hand on that one. 🙈

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is, like, an integral part of the evolution of this and every other Bioperl module — genuinely the way that the whole ecosystem grows. so 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

🌈 Support

please direct usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

and not to the module maintainer directly, okay? there are so many experienced and reponsive experts on there who will be able to look at your problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible — the more detail the better, bestie, it makes you so much easier to help 💜

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — that's the whole point, tracking. bug reports can be submitted via the web:

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

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👑 AUTHOR - Torsten Seemann 👑

Email — torsten.seemann AT infotech.monash.edu.au

🧚 CONTRIBUTOR - Bala 🧚

Email — savikalpa@fugu-sg.org

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⭐ APPENDIX ⭐

the rest of the documentation goes into the details of each of the object methods. just so you know, internal methods are usually preceded with a _ (that's the secret handshake, iykyk 🤫)

💖 new

Title   : new
Usage   : my $obj = Bio::Tools::Seg->new();
Function: Builds a new Bio::Tools::Seg object
Returns : Bio::Tools::Seg
Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

🔥 next_result

Title   : next_result
Usage   : my $feat = $seg->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args    : none

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and that's the whole page, bestie — you ate it 💅✨ this was Bio::Tools::Seg(3pm) from perl v5.32.1, dated 2021-08-15. go forth and find those low complexity regions, you gorgeous genius 🦋💖🎀