Bio::T...erwise(3pm)

✨ NAME ✨

Bio::Tools::Promoterwise — a parser for Promoterwise tab format output 💖 (yes bestie, the manual page is Bio::T...erwise(3pm), and it's filed under User Contributed Perl Documentation, iykyk)

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🌸 SYNOPSIS 🌸

use Bio::Tools::Promoterwise;

my $pw = Bio::Tools::Promoterwise->new(-file=>"out",
                                       -query1_seq=>$seq1,
                                       -query2_seq=>$seq2);
while (my $fp = $pw->next_result){
  print "Hit Length: ".$fp->feature1->length."\n";
  print "Hit Start: ".$fp->feature1->start."\n";
  print "Hit End: ".$fp->feature1->end."\n";
  print "Hsps: \n";
  my @first_hsp = $fp->feature1->sub_SeqFeature;
  my @second_hsp = $fp->feature2->sub_SeqFeature;
  foreach my $i (0..$#first_hsp){
    print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ".
          $second_hsp[$i]->start. " ".$second_hsp[$i]->end."\n";
  }
}

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🦋 DESCRIPTION 🦋

okay so Promoteriwise is an alignment algorithm that relaxes the constraint that local alignments have to be co-linear. the way it just... lets them be free?? iconic. otherwise it gives you a similar model to DBA, which is designed for promoter sequence alignments 🧬

Promoterwise is written by Ewan Birney. it is part of the wise2 package available at <ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/> — go get it bestie, no cap 🫶

This module is the parser for the Promoterwise output in tab format. that's literally its whole job and it does it flawlessly 💅

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💌 FEEDBACK 💌

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. 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

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. there are so many experienced and reponsive experts who will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible — help them help you bestie 🙏

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 the web:

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

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👑 AUTHOR - Shawn Hoon 👑

Email shawnh@fugu-sg.org

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💖 APPENDIX 💖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (you know, the secret ones 🤫).

new

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

next_result

• Title: next_result
• Usage: my $r = $rpt_masker->next_result
• Function: Get the next result set from parser data
• Returns: an L<Bio::SeqFeature::FeaturePair>
• Args: none

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and that's the whole page bestie, every single option, every default, nothing skipped 💀✨ go parse some promoters, you got this 🌈

perl v5.32.1 · 2021-08-15 · Bio::T...erwise(3pm) — mwah, thanks for reading, ily, slay 🎀🦋💜