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

💖 Bio::Tools::Est2Genome 💖

okay bestie, gather round, because we're about to talk about a Perl module from the User Contributed Perl Documentation corner of the world, and it's genuinely a little legend. it's called Bio::Tools::Est2Genome and yes it's giving ✨ niche bioinformatics icon ✨

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🌸 NAME 🌸

Bio::Tools::Est2Genome — it parses est2genome output and turns it into cute lil' Bio::SeqFeature::Generic objects. that's the whole job. slay.

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✨ SYNOPSIS ✨

use Bio::Tools::Est2Genome;

my $featureiter = Bio::Tools::Est2Genome->new(-file => 'output.est2genome');

# This is going to be fixed to use the SeqAnalysisI next_feature
# Method eventually when we have the objects to put the data in
# properly
while( my $f = $featureiter->parse_next_gene ) {
 # process Bio::SeqFeature::Generic objects here
}

like, that's it. that's the vibe. loop until it stops giving. 💅

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🧚 DESCRIPTION 🧚

okay so this module is a parser for "est2genome" [EMBOSS] alignments — specifically est/cdna sequence aligned to genomic DNA. and ngl? this is generally accepted as the best program for predicting splice sites based on est/dnas (as far as the author knows, and we're keeping it real here).

as for right now? this module currently does not try to pull out the ungapped alignments (Segment)… but it might in the future. main character growth arc pending. 🦋

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, and honestly? your comments and suggestions are wanted. send them 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 or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. many experienced and responsive experts will be able look at the problem and quickly address it. and if you're gonna ask, please include a thorough description of the problem with code and data examples if at all possible. give them the whole story, bestie, not just the vibes.

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so everyone can keep track of the bugs and their resolution. bug reports can be submitted at the web:

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

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👑 AUTHOR - Jason Stajich 👑

Email jason-at-bioperl.org

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _.

💜 new

Title   : new
Usage   : my $obj = Bio::Tools::Est2Genome->new();
Function: Builds a new Bio::Tools::Est2Genome object
Returns : an instance of Bio::Tools::Est2Genome
Args    : -file => 'output.est2genome' or
          -fh   => \*EST2GENOMEOUTPUT
          -genomefirst => 1  # genome was the first input (not standard)

note that -genomefirst => 1 means the genome was the first input, which is not standard. iykyk. 🙈

💜 analysis_method

Usage     : $sim4->analysis_method();
Purpose   : Inherited method. Overridden to ensure that the name matches
            /est2genome/i.
Returns   : String
Argument  : n/a

it's an inherited method, but it's overridden so that the name matches /est2genome/i. returns a String. argument is n/a, so like, don't even try.

💜 parse_next_gene

Title   : parse_next_gene
Usage   : @gene = $est2genome_result->parse_next_gene;
          foreach $exon (@exons) {
              # do something
          }

Function: Parses the next alignments of the est2genome result file and
          returns the found exons as an array of
          Bio::SeqFeature::SimilarityPair objects. Call
          this method repeatedly until an empty array is returned to get the
          results for all alignments.

          The $exon->seq_id() attribute will be set to the identifier of the
          respective sequence for both sequences.
          The length is accessible via the seqlength()
          attribute of $exon->query() and
          $exon->est_hit().
Returns : An array (or array reference) of Bio::SeqFeature::SimilarityPair and Bio::SeqFeature::Generic objects
          or Bio::SeqFeature::Gene::GeneStructure
Args    : flag(1/0) indicating to return Bio::SeqFeature::Gene::GeneStructure or Bio::SeqFeature::SimilarityPair
          defaults to 0

the tea ☕: it parses the next alignments out of the est2genome result file and hands you the found exons as an array of Bio::SeqFeature::SimilarityPair objects. keep calling this method over and over until you get an empty array back — that's your signal that you've collected the results for all alignments. 🏁

the $exon->seq_id() attribute gets set to the identifier of the respective sequence for both sequences. and the length? accessible via the seqlength() attribute of $exon->query() and $exon->est_hit(). obsessed.

returns an array (or array reference) of Bio::SeqFeature::SimilarityPair and Bio::SeqFeature::Generic objects, or a Bio::SeqFeature::Gene::GeneStructure. the arg is a flag (1/0) indicating whether to return Bio::SeqFeature::Gene::GeneStructure or Bio::SeqFeature::SimilarityPair, and it defaults to 0.

💜 next_feature

Title   : next_feature
Usage   : $seqfeature = $obj->next_feature();
Function: Returns the next feature available in the analysis result, or
          undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
          more features.
Args    : none

hands you the next feature available in the analysis result, or undef if there are no more features. Example : is empty, so like, no example, no notes. returns a Bio::SeqFeatureI implementing object, or undef if there are no more features. args: none. periodt. 💅

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and that's the whole page, bestie. go parse some alignments. 🌸

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this icon of a manual page is perl v5.32.1, dated 2021-08-15, and it lives under Bio::T...Genome(3pm) — mwah, no notes. 💖