Bio::DB::DBFetch(3pm)

💖 Bio::DB::DBFetch 💖

okay bestie, welcome to the manual page for Bio::DB::DBFetch — that's a Perl module, 3pm manual, and it's literally the whole vibe for pulling database entries down using the dbfetch script. no cap. 🦋

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✨ NAME ✨

Bio::DB::DBFetch — Database object for retrieving using the dbfetch script 💅

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🌸 SYNOPSIS 🌸

  #do not use this module directly

that's it. that's the whole synopsis. it's giving "don't touch, this is not for you" energy 🙈

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💜 DESCRIPTION 💜

So here's the tea: this module lets you dynamically retrieve entries from databases using the dbfetch script over at EBI, which lives at http://www.ebi.ac.uk/cgi-bin/dbfetch. 🌐

To keep changes transparent (iconic behaviour honestly), the host type and the location got separated out. Right now the host type is only ebi, and the location defaults to ebi too. Why tho? Because later on, more servers in different geographical locations can get added. forward thinking. main character planning. 👑

This is a superclass — it gets called by instantiable subclasses that pass in the correct parameters. so like, it's the blueprint, not the building. fr fr. 🏗️

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🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. So like, send your comments and suggestions — preferably to one of the Bioperl mailing lists. Your participation is so 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. 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, not just "it broke" 💀)

🐛 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 - Heikki Lehvaslaiho 👑

Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-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, that underscore means "hands off bestie"). 🙅‍♀️

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🧚 Routines from Bio::DB::WebDBSeqI 🧚

⭐ get_request

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

⭐ postprocess_data

Title   : postprocess_data
Usage   : $self->postprocess_data ( 'type' => 'string',
                                    'location' => \$datastr);
Function: process downloaded data before loading into a Bio::SeqIO
Returns : void
Args    : hash with two keys - 'type' can be 'string' or 'file'
                             - 'location' either file location or string
                                          reference containing data

⭐ 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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🦋 Bio::DB::DBFetch specific routines 🦋

💫 get_Stream_by_id

Title   : get_Stream_by_id
Usage   : $seq = $db->get_Stream_by_id($ref);
Function: Retrieves Seq objects from the server 'en masse', rather than one
          at a time.  For large numbers of sequences, this is far superior
          than get_Stream_by_[id/acc]().
Example :
Returns : a Bio::SeqIO stream object
Args    : $ref : either an array reference, a filename, or a filehandle
          from which to get the list of unique ids/accession numbers.

NOTE: for backward compatibility, this method is also called get_Stream_by_batch.

💫 get_Seq_by_version

Title   : get_Seq_by_version
Usage   : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args    : version number (as a string)
Throws  : "version does not exist" exception

💫 request_format

Title   : request_format
Usage   : my ($req_format, $ioformat) = $self->request_format;
          $self->request_format("genbank");
          $self->request_format("fasta");
Function: Get/Set sequence format retrieval. The get-form will normally not
          be used outside of this and derived modules.
Returns : Array of two strings, the first representing the format for
          retrieval, and the second specifying the corresponding SeqIO format.
Args    : $format = sequence format

💫 servertype

Title   : servertype
Usage   : my $servertype = $self->servertype
           $self->servertype($servertype);
Function: Get/Set server type
Returns : string
Args    : server type string [optional]

💫 hostlocation

Title   : hostlocation
Usage   : my $location = $self->hostlocation()
         $self->hostlocation($location)
Function: Set/Get Hostlocation
Returns : string representing hostlocation
Args    : string specifying hostlocation [optional]

💫 location_url

Title   : location
Usage   : my $url = $self->location_url()
Function: Get host url
Returns : string representing url
Args    : none

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🌟 Bio::DB::DBFetch routines 🌟

These methods allow subclasses to pass parameters. sharing is caring fr. 🤝

🎀 hosts

Title   : hosts
Usage   :
Function: get/set for host hash
Returns :
Args    : optional hash

🎀 formatmap

Title   : formatmap
Usage   :
Function: get/set for format hash
Returns :
Args    : optional hash

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and that's the whole page, bestie! 🎉 this one shipped as perl v5.32.1, dated 2021-08-15, and it's part of the User Contributed Perl Documentation collection — so go forth, fetch those databases, and slay. 💅✨🎀🦋💖