Christopher Fields > BioPerl > bp_index.pl

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NAME ^

bp_index.pl - indexes files for use by bp_fetch.pl

SYNOPSIS ^

bp_index.pl index_name file1 file2 etc.

DESCRIPTION ^

bp_index.pl builds a bioperl index for the sequence files given in the argument list, under the index name. For example

   bp_index.pl nrdb /data/nrdb/nrdb.fasta

would build an index called 'nrdb' as the index name for the file nrdb.fasta, and

   bp_index.pl -fmt EMBL swiss /data/swiss/*.dat

would build an index called swiss for all the files in /data/swiss which end in .dat which are in EMBL format.

The indexes are built using the Bio/Index/* modules, in particular, Bio::Index::EMBL and the Bio::Index::Fasta modules. Any script which uses these modules can use the index. A good example script is bp_fetch which fetches sequences and pipes them to STDOUT, for example

   bp_fetch swiss:ROA1_HUMAN

gets the ROA1_HUMAN sequence from the swiss index and writes it as fasta format on STDOUT.

OPTIONS ^

  -fmt  <format>   - Fasta (default), swiss or EMBL
  -dir  <dir>      - directory where the index files are found
                     (overrides BIOPERL_INDEX environment variable)

Options for expert use

  -type <db_type>  - DBM_file type. 
                     (overrides BIOPERL_INDEX_TYPE environment variable)
  -v               - report every index addition (debugging)

ENVIRONMENT ^

bp_index and bp_fetch coordinate where the databases lie using the enviroment variable BIOPERL_INDEX. This can be overridden using the -dir option. There is no default value, so you must use the -dir option or set BIOPERL_INDEX.

The DB type is coordinated with BIOPERL_INDEX_TYPE which if it is not there, defaults to whatever the bioperl modules have installed, which itself defaults to SDBM_File.

USING IT YOURSELF ^

bp_index.pl is a script that drives the Index modules. If you want to use this script heavily in your work, if it is Perl based, it is almost certainly better to look at the code in this script and copy it across (probably you will be more likely to want to use the bp_fetch code).

EXTENDING IT ^

bp_index is just a wrapper around James Gilbert's excellent Index modules found in bioperl

FEEDBACK ^

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

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

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney ^

Ewan Birney <birney@ebi.ac.uk>

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