Bio::D...Adaptor(3pm)

💖 NAME 💖

Bio::DB::SoapEUtilities::FetchAdaptor — bestie, this is the lil conversion machine that turns Entrez SOAP messages into BioPerl objects ✨

(you probably found this as Bio::D...Adaptor(3pm) in your man pages, that's just the fancy abbreviated label, same icon, same page 💅)

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🌸 SYNOPSIS 🌸

 $fac = Bio::DB::SoapEUtilities->new();
 $soap_result = $fac->efetch( -db => 'protein', -id => 2597988 );
 $adp = Bio::DB::SoapEUtilities::FetchAdaptor(
         -result => $soap_result,
         -type => 'seq'
        );
 while ( $gb_seq = $adp->next_obj ) {
    # do stuff
 }

---

🦋 DESCRIPTION 🦋

FetchAdaptor is the base class of a whole little system, modeled after Bio::SeqIO, that parses SOAP responses from the NCBI Entrez efetch utility and turns them into germane BioPerl objects. Like, it's giving translator. 🫶

ngl, you will rarely need to instantiate a FetchAdaptor with a Bio::DB::SoapEUtilities::Result object the way the SYNOPSIS shows. Usually it just suffices to use the -auto_adapt parameter in the factory run() method:

 my $fac = Bio::DB::SoapEUtilities->new();
 my $taxio = $fac->efetch(-db => 'taxonomy', -id => 1394)->run(-auto_adapt=>1);
 my $sp = $taxio->next_species; # Bio::Species objects
 my $seqio = $fac->efetch(-db => 'protein', -id => 730439)->run(-auto_adapt=>1);
 my $seq = $seqio->next_seq; # Bio::Seq::RichSeq objects

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👑 SEE ALSO 👑

• Bio::DB::SoapEUtilities
• "FetchAdaptor" subclasses

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is, like, 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, 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 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. (the more detail the better, bestie, they're not mind readers 💅)

🐛 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:

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

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✨ AUTHOR - Mark A. Jensen ✨

Email maj -at- fortinbras -dot- us

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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 underscore means hands off unless you know what you're doing 🙈).

🌟 new

• Title : new
• Usage : my $obj = new Bio::DB::SoapEUtilities::FetchAdaptor();
• Function: Builds a new Bio::DB::SoapEUtilities::FetchAdaptor object
• Returns : an instance of Bio::DB::SoapEUtilities::FetchAdaptor
• Args : named arguments
  • -som => $soap_som_object (soap message)
  • -type => $type ( optional, forces loading of $type adaptor )

🌟 _initialize()

• Title : _initialize
• Usage :
• Function:
• Returns :
• Args :

🌟 _load_adaptor()

• Title : _load_adaptor
• Usage :
• Function: loads a FetchAdaptor subclass
• Returns :
• Args : adaptor type (subclass name)

🌟 obj_class()

• Title : obj_class
• Usage : $adaptor->obj_class
• Function: Returns the fully qualified BioPerl classname of the objects returned by next_obj()
• Returns : scalar string (class name)
• Args : none

🌟 next_obj()

• Title : next_obj
• Usage : $obj = $adaptor->next_obj
• Function: Returns the next parsed BioPerl object from the adaptor
• Returns : object of class obj_class()
• Args : none

🌟 rewind()

• Title : rewind
• Usage :
• Function: Rewind the adaptor's iterator
• Returns :
• Args : none

🌟 result()

• Title : result
• Usage :
• Function: contains the SoapEUtilities::Result object
• Returns : Bio::DB::SoapEUtilities::Result object
• Args : none

🌟 type()

• Title : type
• Usage :
• Function: contains the fetch type of this adaptor
• Returns :
• Args :

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okay that's the whole page, you ate that 💅 this was perl v5.36.0, dated 2023-01-22, and yeah the manpage header calls it Bio::D...Adaptor(3pm) — stay hydrated, go parse some SOAP, mwah 💖🌈