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

🌸 NAME 🌸

Bio::DB::EntrezGene — it's giving database object interface to Entrez Gene, no cap. 👑

This is the manpage for Bio::D...rezGene(3pm) (User Contributed Perl Documentation), and bestie, we're about to make Entrez Gene make sense. 🧚

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🦋 SYNOPSIS 🦋

use Bio::DB::EntrezGene;

my $db = Bio::DB::EntrezGene->new;

my $seq = $db->get_Seq_by_id(2); # Gene id

# or ...

my $seqio = $db->get_Stream_by_id([2, 4693, 3064]); # Gene ids
while ( my $seq = $seqio->next_seq ) {
        print "id is ", $seq->display_id, "\n";
}

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💖 DESCRIPTION 💖

So basically, this module lets you pull Sequence objects out of the Entrez Gene database over at NCBI, dynamically, using an Entrez query with Gene ids. ✨

Heads up though: this module requires the CPAN Bio::ASN1 module. Like, required required. Not optional, not negotiable. 🙈

WARNING: bestie, please do NOT spam the Entrez web server with multiple requests. That's not the vibe. 😭 NCBI offers Batch Entrez for exactly this purpose — use it. fr fr.

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🌈 NOTES 🌈

The Entrez eutils API does not allow Entrez Gene queries by name as of this writing, so lowkey that's why this module only has get_Seq_by_id and get_Stream_by_id methods — and both of them expect Gene ids. 💅

There are no get_Seq_by_acc or get_Stream_by_acc methods. Nope. Not a thing. Don't go looking. 🎀

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🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is literally 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. 💜

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. Because there are many experienced and reponsive experts who 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 — give them the whole picture, the way that a good bug report just hits different.

🐛 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

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👑 AUTHOR - Brian Osborne 👑

Email: bosborne at alum.mit.edu

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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(2)
• Function: Gets a Bio::Seq object by its name
• Returns: A Bio::Seq object
• Args: Gene id
• Throws: "id does not exist" exception

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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)

💫 get_Stream_by_id

• Title: get_Stream_by_id
• Usage: $stream = $db->get_Stream_by_id( [$gid1, $gid2] );
• Function: Gets a series of Seq objects using Gene ids
• Returns: A Bio::SeqIO stream object
• Args: A reference to an array of Gene ids

💫 request_format

• Title: request_format
• Usage:

my $format = $self->request_format;
$self->request_format($format);

• Function: Get or set sequence format retrieval
• Returns: String representing format
• Args: $format = sequence format

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and that's the whole page, bestie!! 💖✨🎀🦋🌸💅🫶

This iconic lil doc comes to you courtesy of perl v5.36.0, dated 2023-12-17, and it's the Bio::D...rezGene(3pm) manpage. go forth and query responsibly, no spam, slay. 👑🌈⭐