Bio::DB::EMBL(3pm)

💖 Bio::DB::EMBL 💖

okay bestie, so this is Bio::DB::EMBL — the database object interface for EMBL entry retrieval ✨ it lives in the Bio::DB::EMBL(3pm) part of the Perl manual (User Contributed Perl Documentation, no big deal 💅).

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🌸 SYNOPSIS 🌸

like, here's the whole vibe in code, fr fr:

  use Bio::DB::EMBL;

  $embl = Bio::DB::EMBL->new();

  # remember that EMBL_ID does not equal GenBank_ID!
  $seq = $embl->get_Seq_by_id('HSFOS'); # EMBL ID
  print "cloneid is ", $seq->id, "\n";

  # or changeing to accession number and Fasta format ...
  $embl->request_format('fasta');
  $seq = $embl->get_Seq_by_acc('J02231'); # EMBL ACC
  print "cloneid is ", $seq->id, "\n";

  # especially when using versions, you better be prepared
  # in not getting what what want
  eval {
      $seq = $embl->get_Seq_by_version('J02231.1'); # EMBL VERSION
  };
  print "cloneid is ", $seq->id, "\n" unless $@;

  # or ... best when downloading very large files, prevents
  # keeping all of the file in memory

  # also don't want features, just sequence so let's save bandwidth
  # and request Fasta sequence
  $embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' ,
                            -format => 'fasta');
  my $seqio = $embl->get_Stream_by_id(['AC013798', 'AC021953'] );
  while( my $clone =  $seqio->next_seq ) {
        print "cloneid is ", $clone->id, "\n";
  }

heads up bestie 🚨 EMBL_ID does not equal GenBank_ID!! do not mix them up, i am begging 🙈

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✨ DESCRIPTION ✨

so what does it actually do 👀 it lets you dynamically retrieve sequence objects, Bio::Seq, straight out of the EMBL database, using the dbfetch script over at EBI:

<http://www.ebi.ac.uk/Tools/dbfetch/dbfetch>

the way it keeps things transparent is iconic honestly 💅 — it splits out host type (currently only ebi) from location (defaults to ebi). why? so that later on, more servers in different geographical locations can just get added in. future-proofing, we love to see it 🫶

also the functionality of this module is inherited from Bio::DB::DBFetch, which itself implements Bio::DB::WebDBSeqI. so it's giving family tree 🌳

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🎀 FEEDBACK 🎀

💌 Mailing Lists

user feedback is, like, an integral part of the evolution of this and other Bioperl modules 💖 so send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, no cap.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫂 Support

okay so if you have usage questions or support issues, please direct them to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly 🙏 because there are so many experienced and reponsive experts who'll be able to look at the problem and quickly address it. and bestie, please include a thorough description of the problem with code and data examples if at all possible — it helps so much 😭

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of 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 goes into detail on each of the object methods 💅 internal methods are usually preceded with a _

🦋 new

Title   : new
Usage   : $gb = Bio::DB::GenBank->new(@options)
Function: Creates a new genbank handle
Returns : New genbank handle
Args    : -delay   number of seconds to delay between fetches (3s)

NOTE: there are other options that are used internally 👀 (iykyk)

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and that's the whole page, bestie 💖 this was Bio::DB::EMBL(3pm) from perl v5.32.1, dated 2021-02-23 🌸 go forth and fetch those sequences, you absolute main character 👑✨💅