1BP_GENBANK2GFF(1)     User Contributed Perl Documentation    BP_GENBANK2GFF(1)
2
3
4

NAME

6       bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files.
7

SYNOPSIS

9         % bp_genbank2gff.pl -d genbank -f localfile.gb
10         % bp_genbank2gff.pl -d genbank --accession AP003256
11         % bp_genbank2gff.pl --accession AP003256 --stdout
12

DESCRIPTION

14       This script loads a Bio::DB::GFF database with the features contained
15       in a either a local genbank file or an accession that is fetched from
16       genbank.  Various command-line options allow you to control which data‐
17       base to load and whether to allow an existing database to be overwrit‐
18       ten.
19
20       The database must already have been created and the current user must
21       have appropriate INSERT and UPDATE privileges.  The --create option
22       will initialize a new database with the appropriate schema, deleting
23       any tables that were already there.
24

COMMAND-LINE OPTIONS

26       Command-line options can be abbreviated to single-letter options.  e.g.
27       -d instead of --database.
28
29          --create                 Force creation and initialization of database
30          --dsn       <dsn>        Data source (default dbi:mysql:test)
31          --user      <user>       Username for mysql authentication
32          --pass      <password>   Password for mysql authentication
33          --proxy     <proxy>      Proxy server to use for remote access
34          --stdout                 direct output to STDOUT
35          --adaptor   <adaptor>    adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle)   --viral                  the genome you are loading is viral (changes tag
36                                        choices)
37          --source    <source>     source field for features ['genbank']
38           EITHER --file           Arguments that follow are Genbank/EMBL file names
39           OR --gb_folder          What follows is a folder full of gb files to process    OR --accession          Arguments that follow are genbank accession numbers
40                                        (not gi!)
41           OR --acc_file           Accession numbers (not gi!) in a file (one per line,                                 no punc.)
42           OR --acc_pipe           Accession numbers (not gi!) from a STDIN pipe (one
43                                        per line)
44

SEE ALSO

46       Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
47

AUTHOR

49       Scott Cain, cain@cshl.org
50
51       Copyright (c) 2003 Cold Spring Harbor Laboratory
52
53       This library is free software; you can redistribute it and/or modify it
54       under the same terms as Perl itself.  See DISCLAIMER.txt for dis‐
55       claimers of warranty.
56
57
58
59perl v5.8.8                       2007-05-07                 BP_GENBANK2GFF(1)