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

💖 NAME 💖

Bio::DB::SoapEUtilities::GQueryAdaptor — the handle bestie for Entrez SOAP GlobalQuery items 🎀

Like, it's the little adaptor that holds your egquery results and lets you walk through them one by one. Iconic behavior honestly.

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✨ SYNOPSIS ✨

my $fac = Bio::DB::SoapEUtilities->new();
# run a query, returning a GQueryAdaptor
my $queries = $fac->egquery( -term => 'BRCA and human' )->run(-auto_adapt=>1);
# all databases with hits
my @dbs = $queries->found_in_dbs;
# queries by database
my $prot_count = $queries->query_by_db('prot')->count;
# iterate over gquery
while ( my $q = $queries->next_query ) {
   my $db = $q->db;
   my $count = $q->count;
   my $status = $q->status;
}

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🌸 DESCRIPTION 🌸

Okay so this adaptor is literally your iterator (next_query()) plus a bunch of other convenience functions for parsing NCBI Entrez EUtility egquery SOAP results. It's giving "I got you, bestie" energy 🫶

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🦋 SEE ALSO 🦋

• Bio::DB::SoapEUtilities

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is, like, an integral part of the evolution of this and other Bioperl modules — no cap. 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. (Yes, give them the whole story, the code, the data — they'll eat it up 💅)

🐛 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 🙈

🎀 new

Title   : new
Usage   : my $obj = new Bio::DB::SoapEUtilities::GQueryAdaptor();
Function: Builds a new Bio::DB::SoapEUtilities::GQueryAdaptor object
Returns : an instance of Bio::DB::SoapEUtilities::GQueryAdaptor
Args    :

🎀 next_query()

Title   : next_query
Usage   :
Function: return the next global query from the attached Result
Returns :
Args    :

🎀 found_in_dbs()

Title   : found_in_dbs
Usage   :
Function: Return list of db names containing hits for
          the query term
Returns : array of scalar strings
Args    : none

🎀 query_by_db()

Title   : query_by_db
Usage   :
Function: get gquery object by db name
Returns :
Args    : db name (scalar string)

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And that's the whole vibe, bestie! This page is from perl v5.36.0, dated 2023-01-22, and it's the Bio::D...daptor(3pm) page (yes the title got cutely truncated, we don't talk about it 😭). Go parse those queries and slay 💅✨🌈