diff --git a/INSTALL b/INSTALL index eebc4ff28..558b5d0f8 100644 --- a/INSTALL +++ b/INSTALL @@ -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 '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', diff --git a/bin/load_genbank.PLS b/bin/load_genbank.PLS index eb8c3b2a7..b53700c61 100644 --- a/bin/load_genbank.PLS +++ b/bin/load_genbank.PLS @@ -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; @@ -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 @@ -67,6 +70,8 @@ L, L, L 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 @@ -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 $options->{method} =~ /^(mRNA|gene)$/;