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.IX Title "BP_LOAD_GFF 1p"
.TH BP_LOAD_GFF 1p "2020-01-13" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
bp_load_gff.pl \- Load a Bio::DB::GFF database from GFF files.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  % bp_load_gff.pl \-d testdb \-u user \-p pw
\&     \-\-dsn \*(Aqdbi:mysql:database=dmel_r5_1;host=myhost;port=myport\*(Aq
\&        dna1.fa dna2.fa features1.gff features2.gff ...
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.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This script loads a Bio::DB::GFF database with the features contained
in a list of \s-1GFF\s0 files and/or \s-1FASTA\s0 sequence files.  You must use the
exact variant of \s-1GFF\s0 described in Bio::DB::GFF.  Various
command-line options allow you to control which database to load and
whether to allow an existing database to be overwritten.
.PP
This script uses the Bio::DB::GFF interface, and so works with all
database adaptors currently supported by that module (MySQL, Oracle,
PostgreSQL soon).  However, it is slow.  For faster loading, see the
MySQL-specific bp_bulk_load_gff.pl and bp_fast_load_gff.pl scripts.
.SS "\s-1NOTES\s0"
.IX Subsection "NOTES"
If the filename is given as \*(L"\-\*(R" then the input is taken from standard
input. Compressed files (.gz, .Z, .bz2) are automatically
uncompressed.
.PP
\&\s-1FASTA\s0 format files are distinguished from \s-1GFF\s0 files by their filename
extensions.  Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as \s-1FASTA\s0 files.  Everything else is
treated as a \s-1GFF\s0 file.  If you wish to load \-fasta files from \s-1STDIN,\s0
then use the \-f command-line swith with an argument of '\-', as in
.PP
.Vb 1
\&    gunzip my_data.fa.gz | bp_fast_load_gff.pl \-d test \-f \-
.Ve
.PP
On the first load of a database, you will see a number of \*(L"unknown
table\*(R" errors.  This is normal.
.PP
About maxfeature: the default value is 100,000,000 bases.  If you have
features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000, or another
power of 10.
.SH "COMMAND-LINE OPTIONS"
.IX Header "COMMAND-LINE OPTIONS"
Command-line options can be abbreviated to single-letter options.
e.g. \-d instead of \-\-database.
.PP
.Vb 10
\&   \-\-dsn     <dsn>       Data source (default dbi:mysql:test)
\&   \-\-adaptor <adaptor>   Schema adaptor (default dbi::mysqlopt)
\&   \-\-user    <user>      Username for mysql authentication
\&   \-\-pass    <password>  Password for mysql authentication
\&   \-\-fasta   <path>      Fasta file or directory containing fasta files for the DNA
\&   \-\-create              Force creation and initialization of database
\&   \-\-maxfeature          Set the value of the maximum feature size (default 100 Mb; must be a power of 10)
\&   \-\-group               A list of one or more tag names (comma or space separated)
\&                          to be used for grouping in the 9th column.
\&   \-\-upgrade             Upgrade existing database to current schema
\&   \-\-gff3_munge          Activate GFF3 name munging (see Bio::DB::GFF)
\&   \-\-quiet               No progress reports
\&   \-\-summary             Generate summary statistics for drawing coverage histograms.
\&                           This can be run on a previously loaded database or during
\&                           the load.
.Ve
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::GFF, bulk_load_gff.pl, bp_load_gff.pl
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein, lstein@cshl.org
.PP
Copyright (c) 2002 Cold Spring Harbor Laboratory
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.