Bio::I...GenBank(3pm)

✨ NAME ✨

Bio::Index::GenBank — bestie, it's the Interface for indexing one or more GenBank files (i.e. flat file GenBank format). 💖

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🌸 SYNOPSIS 🌸

# Complete code for making an index for one or more GenBank files
use strict;
use Bio::Index::GenBank;

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

# Print out sequences present in the index in gcg format
use Bio::Index::GenBank;
use Bio::SeqIO;
use strict;

my $Index_File_Name = shift;
my $inx = Bio::Index::GenBank->new(-filename => $Index_File_Name);
my $seqio = Bio::SeqIO->new(-format => 'gcg');
foreach my $id (@ARGV) {
    my $seq = $inx->fetch($id); # Returns Bio::Seq object
    $seqio->write_seq($seq);
}

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

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🦋 DESCRIPTION 🦋

Okay so here's the tea ☕ — by default, the index that gets created uses the LOCUS, ACCESSION, and VERSION identifiers as keys. It inherits all the dbm-file-management functions from Bio::Index::Abstract.pm, and it hands you the basic functionality for indexing GenBank files and pulling the sequence back out of them. For best results, use strict — no cap, it's just good manners. 💅

You can also set or customize the unique key used to retrieve stuff by writing your own function and calling the id_parser() method. Like, for example:

$inx->id_parser(\&get_id);
# make the index
$inx->make_index($file_name);

# here is where the retrieval key is specified
sub get_id {
   my $line = shift;
   $line =~ /clone="(\S+)"/;
   $1;
}

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💌 FEED_BACK 💌

🎀 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. So many experienced and responsive experts will be able to 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. 🙏

🐛 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 - Ewan Birney 👑

Email — birney@ebi.ac.uk ✨

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _.

🧚 _index_file

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

🧚 id_parser

• Title — id_parser
• Usage — $index->id_parser( CODE )
• Function — Stores or returns the code used by record_id to parse the ID for record from a string. Returns \&default_id_parser (see below) if not set. An entry will be added to the index for each string in the list returned.
• Example — $index->id_parser( \&my_id_parser )
• Returns — reference to CODE if called without arguments
• Args — CODE

🧚 default_id_parser

• Title — default_id_parser
• Usage — $id = default_id_parser($line)
• Function — The default parser for GenBank.pm
• Returns — Array of specified ids
• Args — a line string

🧚 _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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And that's the whole page, bestie! 💜 This lil' slice of docs was served up by perl v5.32.1, dated 2021-08-15, and it lives under the User Contributed Perl Documentation banner. Slay, go index something. 🌈👑