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

💖 Bio::Tools::Run::Promoterwise 💖

okay bestie, so this whole page is about Bio::Tools::Run::Promoterwise, a lil wrapper module living in the User Contributed Perl Documentation, and it exists for one glorious reason: aligning two sequences using promoterwise. it's giving very niche, very powerful. let's get into it 🫶

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✨ NAME ✨

Bio::Tools::Run::Promoterwise — wrapper for aligning two sequences using promoterwise. that's the whole vibe. two sequences, one alignment, slay.

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🌸 SYNOPSIS 🌸

here's the tea, literally the whole usage in one go:

# Build a Promoterwise alignment factory
my @params = ('-s'=>1,'-query_start'=>10,'-dymem'=>1);
my  $factory = Bio::Tools::Run::Promoterwise->new(@params);

my (@fp)= $factory->run($seq1,$seq2);

# each feature pair is a group of hsps
foreach my $fp(@fp){
  print "Hit Length: ".$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 = $fp->feature2->sub_SeqFeature;
  for ($i..$#first_hsp){
    print $first_hsp[$i]->seq." ".$second_hsp[$i]->seq."\n";
  }
}
print "end: ". $fp->feature2->start."\t".$fp->feature2->end."\n";

#Available parameters include:
#( S T U V QUERY_START QUERY_END TARGET_START
#TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT
#LHREJECT LHMAX DYMEM KBYTE DYCACHE)
#For an explanation of these parameters, please see documentation
#from the Wise package.

so the ✨available parameters✨ you can pass in are:

S T U V QUERY_START QUERY_END TARGET_START TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT LHREJECT LHMAX DYMEM KBYTE DYCACHE

(no bestie, LHREJECT really is listed twice, i'm not being chaotic, that's just how it's written 💀)

and if you wanna know what any of those actually do? please see the documentation from the Wise package. i'm not gatekeeping, it's just not in here. iykyk.

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🦋 DESCRIPTION 🦋

okay so Promoterwise is an alignment algorithm with main character energy: it relaxes the constraint that local alignments have to be co-linear. that's the whole twist. otherwise? it's serving a similar model to DBA, which was designed for promoter sequence alignments by Ewan Birney.

it's part of the wise2 package, which lives at:

http://www.sanger.ac.uk/software/wise2

no cap, that's the source. go look. 💅

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💌 FEEDBACK 💌

🌈 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — fr fr, it's the glow-up arc. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated. 🥹

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫶 Support

okay important, listen: please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. why? because there are many experienced and responsive experts on there who'll be able look at the problem and quickly address it. so many. the way that this works is genuinely iconic.

and pls, if at all possible, include a thorough description of the problem with code and data examples. give them the full lore, not just the cliff notes. 💖

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

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👑 AUTHOR - Shawn Hoon 👑

Email: shawnh@fugu-sg.org

periodt. that's the author. 🎀

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — so if you see that underscore, mind your business and don't call it directly, bestie. 🙈

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⭐ program_name

• Title: program_name
• Usage: $factory>program_name()
• Function: holds the program name
• Returns: string
• Args: None

---

⭐ program_dir

• Title: program_dir
• Usage: $factory->program_dir(@params)
• Function: returns the program directory, obtained from ENV variable.
• Returns: string
• Args:

---

⭐ version

• Title: version
• Usage: exit if $prog->version() < 1.8
• Function: Determine the version number of the program
• Example:
• Returns: float or undef
• Args: none

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⭐ run

• Title: run
• Usage: 2 sequence objects

@fp = $factory->run($seq1, $seq2);

• Function: run
• Returns: An array of <Bio::SeqFeature::FeaturePair>
• Args: Name of a file containing a set of 2 fasta sequences or else 2 Bio::Seq objects.

⚠️ it throws an exception if argument is not either a string (eg a filename) or 2 Bio::Seq objects. and if the arguments are strings, it throws an exception if the file corresponding to the string name can not be found. so like... give it something real. 💀

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⭐ _run

• Title: _run
• Usage: Internal function, not to be called directly
• Function: makes actual system call to a promoterwise program
• Example:
• Returns: L<Bio::SeqFeature::FeaturePair>
• Args: Name of a files containing 2 sequences in the order of peptide and genomic

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⭐ _setparams

• Title: _setparams
• Usage: Internal function, not to be called directly
• Function: creates a string of params to be used in the command string
• Example:
• Returns: string of params
• Args:

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⭐ _query_pep_seq

• Title: _query_pep_seq
• Usage: Internal function, not to be called directly
• Function: get/set for the query sequence
• Example:
• Returns:
• Args:

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⭐ _subject_dna_seq

• Title: _subject_dna_seq
• Usage: Internal function, not to be called directly
• Function: get/set for the subject sequence
• Example:
• Returns:
• Args:

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and that's the whole page, bestie!! 🌸 this lil doc was brought to you by perl v5.36.0, dated 2023-01-22, and it's the Bio::T...terwise(3pm) page (yes the name is truncated in the header, we don't know why, we don't ask 🔥). go align something cute. mwah 💅💖