1BP_LOAD_GFF(1) User Contributed Perl Documentation BP_LOAD_GFF(1)
2
6 bp_load_gff.pl - Load a Bio::DB::GFF database from GFF files.
7
9 % bp_load_gff.pl -d testdb -u user -p pw
10 --dsn 'dbi:mysql:database=dmel_r5_1;host=myhost;port=myport'
11 dna1.fa dna2.fa features1.gff features2.gff ...
12
14 This script loads a Bio::DB::GFF database with the features contained
15 in a list of GFF files and/or FASTA sequence files. You must use the
16 exact variant of GFF described in Bio::DB::GFF. Various command-line
17 options allow you to control which database to load and whether to
18 allow an existing database to be overwritten.
19 This script uses the Bio::DB::GFF interface, and so works with all
21 database adaptors currently supported by that module (MySQL, Oracle,
22 PostgreSQL soon). However, it is slow. For faster loading, see the
23 MySQL-specific bp_bulk_load_gff.pl and bp_fast_load_gff.pl scripts.
24 NOTES
26 If the filename is given as "-" then the input is taken from standard
27 input. Compressed files (.gz, .Z, .bz2) are automatically uncompressed.
28 FASTA format files are distinguished from GFF files by their filename
30 extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their
31 uppercase variants are treated as FASTA files. Everything else is
32 treated as a GFF file. If you wish to load -fasta files from STDIN,
33 then use the -f command-line swith with an argument of '-', as in
34 gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -
36 On the first load of a database, you will see a number of "unknown
38 table" errors. This is normal.
39 About maxfeature: the default value is 100,000,000 bases. If you have
41 features that are close to or greater that 100Mb in length, then the
42 value of maxfeature should be increased to 1,000,000,000, or another
43 power of 10.
44
46 Command-line options can be abbreviated to single-letter options. e.g.
47 -d instead of --database.
48 --dsn <dsn> Data source (default dbi:mysql:test)
50 --adaptor <adaptor> Schema adaptor (default dbi::mysqlopt)
51 --user <user> Username for mysql authentication
52 --pass <password> Password for mysql authentication
53 --fasta <path> Fasta file or directory containing fasta files for the DNA
54 --create Force creation and initialization of database
55 --maxfeature Set the value of the maximum feature size (default 100 Mb; must be a power of 10)
56 --group A list of one or more tag names (comma or space separated)
57 to be used for grouping in the 9th column.
58 --upgrade Upgrade existing database to current schema
59 --gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
60 --quiet No progress reports
61
63 Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
64
66 Lincoln Stein, lstein@cshl.org
67 Copyright (c) 2002 Cold Spring Harbor Laboratory
69 This library is free software; you can redistribute it and/or modify it
71 under the same terms as Perl itself. See DISCLAIMER.txt for
72 disclaimers of warranty.
73perl v5.12.0 2010-04-29 BP_LOAD_GFF(1)