1BP_INDEX(1)           User Contributed Perl Documentation          BP_INDEX(1)
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NAME

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

9       bp_index.pl index_name file1 file2 etc.
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DESCRIPTION

12       bp_index.pl builds a bioperl index for the sequence files given in the
13       argument list, under the index name. For example
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15          bp_index.pl nrdb /data/nrdb/nrdb.fasta
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17       would build an index called 'nrdb' as the index name for the file
18       nrdb.fasta, and
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20          bp_index.pl -fmt EMBL swiss /data/swiss/*.dat
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22       would build an index called swiss for all the files in /data/swiss
23       which end in .dat which are in EMBL format.
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25       The indexes are built using the Bio/Index/* modules, in particular,
26       Bio::Index::EMBL and the Bio::Index::Fasta modules. Any script which
27       uses these modules can use the index. A good example script is bp_fetch
28       which fetches sequences and pipes them to STDOUT, for example
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30          bp_fetch swiss:ROA1_HUMAN
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32       gets the ROA1_HUMAN sequence from the swiss index and writes it as
33       fasta format on STDOUT.
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OPTIONS

36         -fmt  <format>   - Fasta (default), swiss or EMBL
37         -dir  <dir>      - directory where the index files are found
38                            (overrides BIOPERL_INDEX environment variable)
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40       Options for expert use
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42         -type <db_type>  - DBM_file type.
43                            (overrides BIOPERL_INDEX_TYPE environment variable)
44         -v               - report every index addition (debugging)
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ENVIRONMENT

47       bp_index and bp_fetch coordinate where the databases lie using the
48       enviroment variable BIOPERL_INDEX. This can be overridden using the
49       -dir option. There is no default value, so you must use the -dir option
50       or set BIOPERL_INDEX.
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52       The DB type is coordinated with BIOPERL_INDEX_TYPE which if it is not
53       there, defaults to whatever the bioperl modules have installed, which
54       itself defaults to SDBM_File.
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USING IT YOURSELF

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

63       bp_index is just a wrapper around James Gilbert's excellent Index mod‐
64       ules found in bioperl
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FEEDBACK

67       Mailing Lists
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69       User feedback is an integral part of the evolution of this and other
70       Bioperl modules. Send your comments and suggestions preferably to the
71       Bioperl mailing list.  Your participation is much appreciated.
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73         bioperl-l@bioperl.org                  - General discussion
74         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
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76       Reporting Bugs
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78       Report bugs to the Bioperl bug tracking system to help us keep track of
79       the bugs and their resolution. Bug reports can be submitted via the
80       web:
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82         http://bugzilla.open-bio.org/
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AUTHOR - Ewan Birney

85       Ewan Birney <birney@ebi.ac.uk>
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89perl v5.8.8                       2007-05-07                       BP_INDEX(1)