Bio::Index::EMBL(3pm)

💖 Bio::Index::EMBL 💖

okay bestie, so this is Bio::Index::EMBL — it's part of the User Contributed Perl Documentation collection, and it's the interface for indexing (multiple) EMBL/Swissprot .dat files, aka flat file EMBL/Swissprot format. yes the title of the file literally says Bio::Index::EMBL(3pm) and now you know her name. 🎀

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✨ SYNOPSIS ✨

like, here's the whole vibe — complete code for making an index for several EMBL files:

# Complete code for making an index for several
# EMBL files
use Bio::Index::EMBL;
use strict;

my $Index_File_Name = shift;
my $inx = Bio::Index::EMBL->new(-filename => $Index_File_Name,
                                -write_flag => 'WRITE');
$inx->make_index(@ARGV);

and then printing out several sequences present in the index in Fasta format:

# Print out several sequences present in the index
# in Fasta format
use Bio::Index::EMBL;
use strict;

my $Index_File_Name = shift;
my $inx = Bio::Index::EMBL->new(-filename => $Index_File_Name);
my $out = Bio::SeqIO->new(-format => 'Fasta',-fh => \*STDOUT);

foreach my $id (@ARGV) {
    my $seq = $inx->fetch($id); # Returns Bio::Seq object
    $out->write_seq($seq);
}

# alternatively
my ($id, $acc);
my $seq1 = $inx->get_Seq_by_id($id);
my $seq2 = $inx->get_Seq_by_acc($acc);

it's giving "I have a plan and the plan is indexing" honestly 💅

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🌸 DESCRIPTION 🌸

so, she inherits functions for managing dbm files from Bio::Index::Abstract.pm, and she provides the basic funtionality for indexing EMBL files, and retrieving the sequence from them. (yes "funtionality" — we don't fix typos here, we preserve them like little fossils 🦋). heavily snaffled from James Gilbert and his Fasta system. and ngl there's a note: for best results use strict. periodt.

the keys? they're the identifiers in the ID and AC lines. that's the whole thing. that's the key situation. 🔑

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📬 FEED_BACK 📬

💌 Mailing Lists

user feedback is 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, fr fr 🫶

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

🆘 Support

okay so please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. the reason is that many experienced and reponsive experts will be able look at the problem and quickly address it. and please include a thorough description of the problem with code and data examples if at all possible — like, give them the receipts, 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

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👑 AUTHOR - Ewan Birney 👑

Email - birney@sanger.ac.uk

(iconic. the main character. 💜)

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — so if you see an underscore, mind your business, that's internal energy 😌

🔍 _index_file

Title   : _index_file
Usage   : $index->_index_file( $file_name, $i )
Function: Specialist function to index EMBL format files.
          Is provided with a filename and an integer
          by make_index in its SUPER class.
Example :
Returns :
Args    :

📁 _file_format

Title   : _file_format
Usage   : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns :
Args    :

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heads up bestie: those Example, Returns, and Args fields are genuinely empty in the original. that's not me being lazy, that's canon. 💀

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and that's the whole page, no cap. this lovely little manual ships with perl v5.32.1, dated 2021-08-15, and it lives under the name Bio::Index::EMBL(3pm). mwah, go index something. 🍓✨💖