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

💖 NAME 💖

Bio::Index::Swissprot — the interface for indexing one (or a whole little squad) of Swissprot files. 🧚✨

---

✨ SYNOPSIS ✨

okay bestie, first up: making an index for one or more Swissprot files:

# Make an index for one or more Swissprot files:

  use Bio::Index::Swissprot;
  use strict;

  my $index_file_name = shift;
  my $inx = Bio::Index::Swissprot->new(
      -filename => $index_file_name,
      -write_flag => 1);
  $inx->make_index(@ARGV);

# Print out several sequences present in the index in Genbank
# format:

  use Bio::Index::Swissprot;
  use Bio::SeqIO;
  use strict;

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

  foreach my $id (@ARGV) {
      my $seq = $inx->fetch($id); # Returns a 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);

---

🌸 DESCRIPTION 🌸

so, by default the index it builds uses the AC and ID identifiers as keys. no cap. 💅

This module inherits all the dbm-file-managing functions from Bio::Index::Abstract.pm, and it gives you the basic functionality for indexing Swissprot files and pulling Sequence objects back out of them. For best results, use strict. fr fr.

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
   $inx->make_index($index_file_name);

   # here is where the retrieval key is specified
   sub get_id {
      my $line = shift;
      $line =~ /^KW\s+([A-Z]+)/i;
      $1;
   }

---

📬 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. 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.

🐛 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

---

👑 AUTHOR - Ewan Birney 👑

Also lorenz@ist.org, bosborne at alum.mit.edu

---

🎀 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: Specialist function to index Swissprot 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 : ref 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 Swissprot.pm. Returns $1 from applying the regexp /^ID\s*(\S+)/ or /^AC\s+([A-Z0-9]+)/ to the current line.
• Returns : ID string
• 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 :

---

perl v5.32.1 · 2021-08-15 — that's the vibe check for this page, bestie, go index some proteins and slay 💅✨🫶