Bio::Tools::QRNA(3pm)

Bio::Tools::QRNA 💖

okay bestie, so this is a Perl module that lives at Bio::Tools::QRNA(3pm) — it's literally a parser for qrna output, and I'm gonna walk you through every single bit of it, no cap. 🧚

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✨ NAME ✨

Bio::Tools::QRNA — a parser for qrna output. that's it, that's the whole vibe. 🎀

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🌸 SYNOPSIS 🌸

  use Bio::Tools::QRNA;
  my $parser = Bio::Tools::QRNA->new(-file => $qrnaoutput);
  while( my $feature = $parser->next_feature ) {
    # do something here
  }

like… you make a parser, you feed it the file, you loop over features. iconic. 💅

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🦋 DESCRIPTION 🦋

So this parses QRNA output (E.Rivas: http://selab.janelia.org/software.html ftp://selab.janelia.org/pub/software/qrna/). 🫶

heads up bestie: this module is not complete. it still works, but it's giving "work in progress" energy, fr fr.

rn, it packs the info from each QRNA alignment into a single Bio::SeqFeature::Generic object.

Also, not all options for QRNA output have been tested or tried. the ones that HAVE been tested: sliding window output (-w -x) and shuffled output (-b or -B). so if you're using something else… vibe check at your own risk 😭

Peep t/QRNA.t for example usage. 🍓

At some point (future tea ☕) there may be a more complicated feature object which will support this data, rather than forcing most of the information into tag/value pairs in a SeqFeature::Generic. we're manifesting it. ✨

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🌈 extra data mode

Running with -verbose => 1 will store extra data in the feature. the entire unparsed entry for a particular feature gets stored as a string in the tag 'entry', and it's accessible via:

  my ($entry) = $f->each_tag_value('entry');

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👑 the model tea

The winning model for any given alignment test is the name stored in the primary_tag field of the feature. the bit score gets stored in the score field. the logoddpost is available via a tag/value pair. this example code shows how to print out the score and log odds post for each model:

  # assuming you got a feature already
  print "model score logoddspost\n";
  foreach my $model ( qw(OTH COD RNA) ) {
    my ($score)       = $f->get_tag_values("$model\_score");
    my ($logoddspost) = $f->get_tag_values("$model\_logoddspost");
    print "$model $score $logoddspost\n";
  }

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🌸 start/end coordinates

The start and end of the alignment for both the query and hit sequence are available through the Bio::SeqFeature::FeaturePair interface — specifically Bio::SeqFeature::FeaturePair::feature1 and Bio::SeqFeature::FeaturePair::feature2. 🫶

Additionally, if you have run QRNA with an input file which has the location of the alignment stored in the FASTA filename as in (ID/START-END) — which is the default output format from Bio::AlignIO::fasta produced alignment output — this module will re-number start/end for the two sequences so they're in the actual coordinates of the sequence rather than the relative coordinates of the alignment. lowkey so useful.

You may find the bioperl utillity script search2alnblocks useful in creating your input files for QRNA. 💜

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⚠️ words of warning ⚠️

Some other words of warning: QRNA uses a 0 based numbering system for sequence locations, Bioperl uses a 1 based system. You'll notice that locations will be +1 when they are reported in the raw QRNA output. not a bug, just a translation moment. 💀

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💌 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

🫂 Support

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

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts 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. 🙏

🐛 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 - Jason Stajich 👑

Email jason-at-bioperl-dot-org

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🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk, that's the secret-menu underscore). 🤫

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new

• Title: new
• Usage: my $obj = Bio::Tools::QRNA->new();
• Function: Builds a new Bio::Tools::QRNA object
• Returns: an instance of Bio::Tools::QRNA
• Args: -fh/-file filehandle/filename standard input for Bio::Root:IO objects

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next_feature

• Title: next_feature
• Usage: my $feature = $parser->next_feature
• Function: Get the next QRNA feature
• Returns:
• Args:

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PAM_model

• Title: PAM_model
• Usage: $obj->PAM_model($newval)
• Function:
• Example:
• Returns: value of PAM_model (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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RNA_model

• Title: RNA_model
• Usage: $obj->RNA_model($newval)
• Function:
• Example:
• Returns: value of RNA_model (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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seq_file

• Title: seq_file
• Usage: $obj->seq_file($newval)
• Function:
• Example:
• Returns: value of seq_file (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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program_name

• Title: program_name
• Usage: $obj->program_name($newval)
• Function:
• Example:
• Returns: value of program_name (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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program_version

• Title: program_version
• Usage: $obj->program_version($newval)
• Function:
• Example:
• Returns: value of program_version (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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program_date

• Title: program_date
• Usage: $obj->program_date($newval)
• Function:
• Example:
• Returns: value of program_date (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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okay and that's the whole page bestie!! this lil doc came from perl v5.32.1, dated 2021-08-15, and it's filed under Bio::Tools::QRNA(3pm) in the User Contributed Perl Documentation. go parse something cute. 💅✨🦋