Bio::DB::GenPept(3pm)

💖 Bio::DB::GenPept 💖

okay bestie, welcome to Bio::DB::GenPept — the little Perl module that's your database object interface to GenPept. yes, that's the whole vibe. let's get into it 🧬✨

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✨ SYNOPSIS ✨

$gb = Bio::DB::GenPept->new();

$seq = $gb->get_Seq_by_id('195055'); # Unique ID

# or ...

$seq = $gb->get_Seq_by_acc('P09651.5'); # Accession Number

my $seqio = $gb->get_Stream_by_id(['195055', 'P09651.5']);
while( my $seq = $seqio->next_seq ) {
        print "seq is is ", $seq->display_id, "\n";
}

(yes the double "is is" is in there, we don't fix it, we respect it 🫶)

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🌸 DESCRIPTION 🌸

so like, this module lets you dynamically retrieve Sequence objects (aka Bio::Seq) from the GenPept database at NCBI, via an Entrez query. lowkey iconic.

⚠️ WARNING: please do NOT spam the Entrez web server with multiple requests, bestie. NCBI literally offers Batch Entrez for exactly this purpose. Batch Entrez support will likely be supported in a future version of DB::GenPept. so like... patience, babe.

Currently the only return format supported by NCBI Entrez for GenPept database is GenPept format, so any format specification passed to GenPept will be ignored — still be forced to GenPept format (which is just GenBank format). no cap, that's just how it is 💅

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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 one of the Bioperl mailing lists. 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. help us help you bestie 🙈

🐛 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:

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

go off, tell us what's broken, we wanna know 💀✨

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👑 AUTHOR - Aaron Mackey, Jason Stajich 👑

Email amackey@virginia.edu Email jason@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 _ (iykyk).

🦋 get_params 🦋

Title   : get_params
Usage   : my %params = $self->get_params($mode)
Function: Returns key,value pairs to be passed to NCBI database
          for either 'batch' or 'single' sequence retrieval method
Returns : a key,value pair hash
Args    : 'single' or 'batch' mode for retrieval

🦋 default_format 🦋

Title   : default_format
Usage   : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args    : none

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🌈 Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI 🌈

⭐ get_Seq_by_id ⭐

Title   : get_Seq_by_id
Usage   : $seq = $db->get_Seq_by_id('P09651.5')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object
Args    : the id (as a string) of a sequence
Throws  : "id does not exist" exception

💀 heads up: this one throws an "id does not exist" exception. dramatic but fair.

⭐ get_Seq_by_acc ⭐

Title   : get_Seq_by_acc
Usage   : $seq = $db->get_Seq_by_acc('AAC73346');
Function: Gets a Seq objects by accession number
Returns : Bio::Seq object
Args    : accession number to retrieve by

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🧚 Routines implemented by Bio::DB::NCBIHelper 🧚

💜 get_request 💜

Title   : get_request
Usage   : my $url = $self->get_request
Function: HTTP::Request
Returns :
Args    : %qualifiers = a hash of qualifiers (ids, format, etc)

(Returns is literally blank in the original. we leave it blank. we are not the ones to fill that void 💅)

💜 get_Stream_by_id 💜

Title   : get_Stream_by_id
Usage   : $stream = $db->get_Stream_by_id( [$uid1, $uid2] );
Function: Gets a series of Seq objects by unique identifiers
Returns : a Bio::SeqIO stream object
Args    : $ref : a reference to an array of unique identifiers for
                 the desired sequence entries

💜 get_Stream_by_acc (2) 💜

Title   : get_Stream_by_acc
Usage   : $seq = $db->get_Stream_by_acc($acc);
Function: Gets a series of Seq objects by accession numbers
Returns : a Bio::SeqIO stream object
Args    : $ref : a reference to an array of accession numbers for
                 the desired sequence entries
Note    : For GenBank, this just calls the same code for get_Stream_by_id()

💜 get_Stream_by_query 💜

Title   : get_Stream_by_query
Usage   : $seq = $db->get_Stream_by_query('ROA1_HUMAN');
Function: Gets a series of Seq objects by unique display_id
Returns : a Bio::SeqIO stream object
Args    : $ref : display_id to query by

💜 request_format 💜

Title   : request_format
Usage   : my $format = $self->request_format;
          $self->request_format($format);
Function: Get/Set sequence format retrieval
Returns : string representing format
Args    : $format = sequence format

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and that's the whole page, bestie 🎀✨

Bio::DB::GenPept is part of the User Contributed Perl Documentation, running on perl v5.36.0 and dated 2023-12-17. slay, go fetch some sequences, and remember: do not spam Entrez 💖🦋