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load_genbank.pl is now a copy of the bioperl equivalent; brought in b…
…ecause of demand for this script and slow release schedule of bioperl 1.3
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lstein committed Jul 28, 2003
1 parent a393e76 commit f04603c
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Showing 3 changed files with 16 additions and 10 deletions.
15 changes: 9 additions & 6 deletions INSTALL
Expand Up @@ -291,11 +291,11 @@ distributed separately and can be downloaded from:

Load the file with this command:

bp_load_gff.pl -d yeast -fasta yeast.fasta.gz </dev/null
load_gff.pl -d yeast -fasta yeast.fasta.gz </dev/null

(or, if you are on a windows system:

bp_load_gff.pl -d yeast -fasta yeast.fasta.gz
load_gff.pl -d yeast -fasta yeast.fasta.gz

and hit ^Z when the script pauses.)

Expand Down Expand Up @@ -333,10 +333,13 @@ scripts/Bio-DB-GFF directory if you didn't install them directly.

They are:

bp_process_gadfly.pl For FlyBase D. melanogaster flat files
bp_process_ncbi_human.pl For human annotations from NCBI
bp_process_sgd.pl For SGD S. cerevisiae flat files
bp_process_wormbase.pl For WormBase C. elegans flat files
process_gadfly.pl For FlyBase D. melanogaster flat files
process_ncbi_human.pl For human annotations from NCBI
process_sgd.pl For SGD S. cerevisiae flat files
process_wormbase.pl For WormBase C. elegans flat files

In Bioperl 1.3, these scripts are named bp_process_gadfly.pl, and so
forth.

Run the script with the -h option to get some data-specific help:

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1 change: 1 addition & 0 deletions Makefile.PL
Expand Up @@ -126,6 +126,7 @@ WriteMakefile(
'bin/process_wormbase.PLS' => 'bin/process_wormbase.pl',
'bin/process_ncbi_human.PLS' => 'bin/process_ncbi_human.pl',
'bin/ucsc_genes2gff.PLS' => 'bin/ucsc_genes2gff.pl',
'bin/load_genbank.PLS' => 'bin/load_genbank.pl',
'install_util/gbrowse_ppm_install.PLS' => 'install_util/gbrowse_ppm_install.pl',
'cgi-bin/gbrowse.PLS' => 'cgi-bin/gbrowse',
'cgi-bin/gbrowse_syn.PLS' => 'cgi-bin/gbrowse_syn',
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10 changes: 6 additions & 4 deletions bin/load_genbank.PLS
Expand Up @@ -19,7 +19,7 @@ $Config{startperl}
# In the following, perl variables are not expanded during extraction.

print OUT <<'!NO!SUBS!';
# $Id: load_genbank.PLS,v 1.3 2003-07-17 18:47:57 scottcain Exp $
# $Id: load_genbank.PLS,v 1.4 2003-07-28 17:06:12 lstein Exp $
use strict;
use Bio::DB::GFF;
use Getopt::Long;
Expand All @@ -33,6 +33,9 @@ load_genbank.pl - Load a Bio::DB::GFF database from GENBANK files.
% load_genbank.pl -d genbank -f localfile.gb
% load_genbank.pl -d genbank -a AP003256
NOTE: The script bp_genbank2gff.pl in the BioPerl distribution is the
same as this script.
=head1 DESCRIPTION
This script loads a Bio::DB::GFF database with the features contained
Expand Down Expand Up @@ -67,6 +70,8 @@ L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
Scott Cain, cain@cshl.org
Lincoln Stein, lstein@cshl.org
Copyright (c) 2003 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
Expand Down Expand Up @@ -96,9 +101,6 @@ sub new {
sub load_gff_line {
my ($self,$options) = @_;
# synthesize GFF3-compatible line
$options->{score} = '.' unless $options->{score};
my @attributes;
if (my $parent = $options->{gname}) {
push @attributes,"Parent=".escape($parent) unless $options->{method} =~ /^(mRNA|gene)$/;
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