Made Jason's SequenceDumper check that each format converter

successfully loads before adding that format to the list. Added examples of CDS and translation glyphs to wormbase and yeast example conf files.
tharris · Jul 5, 2002 · 5edb0c9 · 5edb0c9
1 parent e5561df
commit 5edb0c9
Show file tree

Hide file tree

Showing 7 changed files with 227 additions and 58 deletions.
diff --git a/MANIFEST b/MANIFEST
@@ -19,6 +19,7 @@ conf/02.wormbase.conf
 conf/03.fly.conf
 conf/04.human.conf
 conf/05.embl.conf
+conf/enzymes.txt
 conf/plugins/FastaDumper.pm
 conf/plugins/GFFDumper.pm
 conf/plugins/OligoFinder.pm
@@ -69,6 +70,7 @@ htdocs/images/help/upload+edit.gif
 htdocs/images/help/upload+remote.gif
 htdocs/images/help/upload.gif
 lib/Bio/DB/GFF/Aggregator/coding.pm
+lib/Bio/DB/GFF/Aggregator/orf.pm
 lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
 lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
 lib/Bio/Graphics/Browser.pm

diff --git a/Makefile.PL b/Makefile.PL
@@ -26,7 +26,7 @@ foreach (@argv) {
 }
 
 if (-e 'GGB.def' && !%OPTIONS) {
-  print STDERR "You have installed gbrowse before.  Should I use the previous settings to set the file paths? ";
+  print STDERR "You have installed gbrowse before.  Should I use the previous settings to set the file paths (y/n)? ";
   chomp (my $line = <>);
   if ($line =~ /^[yY]/) {
     open F,'GGB.def' or die "GGB.def: $!";

diff --git a/conf/01.yeast.conf b/conf/01.yeast.conf
@@ -3,7 +3,7 @@ description = S. cerevisae (via SGD Nov 2001)
 adaptor     = dbi::mysqlopt
 database    = dbi:mysql:database=yeast;host=localhost
 # fasta_files = 
-aggregators = transcript alignment
+aggregators = transcript alignment orf
 user        =
 passwd      =
 
@@ -55,7 +55,7 @@ footer = <hr>
 	</TR>
 	</table>
 	<hr>
-	<pre>$Id: 01.yeast.conf,v 1.3 2002-06-26 01:57:29 lstein Exp $</pre>
+	<pre>$Id: 01.yeast.conf,v 1.4 2002-07-05 13:53:10 lstein Exp $</pre>
 
 # examples to show in the introduction
 examples = II
@@ -90,6 +90,21 @@ height        = 6
 description   = 1
 key           = ORF
 
+[CDS]
+feature      = coding:sgd
+glyph        = cds
+frame0f      = cadetblue
+frame1f      = blue
+frame2f      = darkblue
+frame0r      = darkred
+frame1r      = red
+frame2r      = crimson
+description  = 0
+height       = 13
+label        = CDS frame
+key          = CDS
+citation     = This track shows CDS reading frames.
+
 [tRNAs]
 feature       = tRNA:sgd
 glyph         = generic
@@ -124,13 +139,37 @@ glyph         = anchored_arrow
 height        = 6
 key           = Long Terminal Repeats
 
-[DNA]
-glyph          = dna
+[TranslationF]
+glyph        = translation
+global feature = 1
+frame0       = cadetblue
+frame1       = blue
+frame2       = darkblue
+height       = 20
+fgcolor      = purple
+strand       = +1
+translation  = 3frame
+key          = 3-frame translation (forward)
+
+[DNA/GC Content]
+glyph        = dna
+global feature = 1
+height       = 40
+do_gc        = 1
+fgcolor      = red
+axis_color   = blue
+
+[TranslationR]
+glyph        = translation
 global feature = 1
-height         = 40
-do_gc          = 1
-fgcolor        = red
-axis_color     = blue
+frame0       = darkred
+frame1       = red
+frame2       = crimson
+height       = 20
+fgcolor      = blue
+strand       = -1
+translation  = 3frame
+key          = 3-frame translation (reverse)
 
 [ncRNA]
 feature       = RNA:sgd rRNA:sgd snRNA:sgd snoRNA:sgd

diff --git a/conf/02.wormbase.conf b/conf/02.wormbase.conf
@@ -4,7 +4,7 @@ adaptor     = dbi::mysqlopt
 database    = dbi:mysql:database=wormbase;host=localhost
 # fasta_files = /var/www/elegans
 fasta_files =
-aggregators = wormbase_gene clone alignment
+aggregators = wormbase_gene clone alignment coding
 user        =
 passwd      =
 
@@ -48,15 +48,6 @@ fine zoom      = 20%
 overview landmarks = gene:framework
 overview bgcolor = #93CBF4
 
-#header = sub {
-#	use ElegansSubs 'PrintTop','PrintBottom';
-#	PrintTop(undef,undef,undef,
-#	  '-Title'  =>'Genome Browser',
-#	  '-Target' =>'_top',
-#	  '-Class'  =>'search');
-#	'';
-#	}
-
 footer = <hr>
 	<table width="100%">
 	<TR>
@@ -68,22 +59,7 @@ footer = <hr>
 	</TR>
 	</table>
 	<hr>
-	<pre>$Id: 02.wormbase.conf,v 1.3 2002-06-26 01:56:37 lstein Exp $</pre>
-
-#footer = sub {
-#	PrintBottom();
-#	return '
-#	<hr>
-#	<table width="100%">
-#	<TR>
-#	<TD align="LEFT" class="databody">
-#	For the source code for this browser, see the <a href="http://www.gmod.org">
-#	Generic Model Organism Database Project.</a>  For other questions, send
-#	mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.
-#	</TD>
-#	</TR>
-#	</table>';
-#	}
+	<pre>$Id: 02.wormbase.conf,v 1.4 2002-07-05 13:53:10 lstein Exp $</pre>
 
 # examples to show in the introduction
 examples = IV 
@@ -97,7 +73,16 @@ examples = IV
 # "automatic" classes to try when an unqualified identifier is given
 automatic classes = Locus PCR_Product WTP Genbank
 
-# the remainder of the sections configure particular features to show
+# List of remote annotation sources: format is URL/name pairs separated by
+# white space.  Please use quotation marks to prevent internal spaces from
+# being interpreted.
+remote sources = "Lincoln Stein's test 1" http://stein.cshl.org/~lstein/features.txt
+		 "Lincoln Stein's test 2" http://stein.cshl.org/~lstein/features2.gff
+
+
+##################################################################################
+# the remainder of the sections configure particular tracks to show
+##################################################################################
 
 [tRNA]
 feature      = Sequence:tRNAscan-SE-1.11
@@ -128,7 +113,7 @@ glyph        = wormbase_transcript
 bgcolor      = wheat
 fgcolor      = black
 forwardcolor = violet
-reversecolor = turquoise
+reversecolor = indianred
 font2color   = red
 height       = 10
 description  = 1
@@ -137,8 +122,23 @@ citation     = These are gene predictions that have been reviewed by WormBase cu
 	the CDS sections are represented.  For 5' and 3' termini, please examine the paired
 	5' and 3' ESTs, full-length cDNAs, and Worm Transcriptome Project (WTP) gene extents.
 
+[CDS]
+feature      = coding:curated
+glyph        = cds
+frame0f      = cadetblue
+frame1f      = blue
+frame2f      = darkblue
+frame0r      = darkred
+frame1r      = red
+frame2r      = crimson
+description  = 0
+height       = 13
+label        = CDS frame
+key          = CDS
+citation     = This track shows CDS reading frames.
+
 [PG]
-feature      = transcript:NDB_CDS
+feature      = transcript:NDB_CDSl
 glyph        = transcript2
 bgcolor      = white
 curatedexon  = dodgerblue
@@ -432,6 +432,18 @@ key           = Links & Superlinks
 citation      = This track shows the location of contigs created during the assembly
 	of the C. elegans genome.
 
+[TranslationF]
+glyph        = translation
+global feature = 1
+frame0       = cadetblue
+frame1       = blue
+frame2       = darkblue
+height       = 20
+fgcolor      = purple
+strand       = +1
+translation  = 3frame
+key          = 3-frame translation (forward)
+
 [DNA/GC Content]
 glyph        = dna
 global feature = 1
@@ -440,6 +452,18 @@ do_gc        = 1
 fgcolor      = red
 axis_color   = blue
 
+[TranslationR]
+glyph        = translation
+global feature = 1
+frame0       = darkred
+frame1       = red
+frame2       = crimson
+height       = 20
+fgcolor      = blue
+strand       = -1
+translation  = 3frame
+key          = 3-frame translation (reverse)
+
 [overview]
 feature       = gene:framework
 label         = 1

diff --git a/conf/plugins/SequenceDumper.pm b/conf/plugins/SequenceDumper.pm
@@ -1,4 +1,4 @@
-# $Id: SequenceDumper.pm,v 1.2 2002-07-04 21:57:47 lstein Exp $
+# $Id: SequenceDumper.pm,v 1.3 2002-07-05 13:53:10 lstein Exp $
 #
 # BioPerl module for Bio::Graphics::Browser::Plugin::SequenceDumper
 #
@@ -12,7 +12,7 @@
 
 =head1 NAME
 
-Bio::Graphics::Browser::Plugin::SequenceDumper - A plugin for dumping 
+Bio::Graphics::Browser::Plugin::SequenceDumper - A plugin for dumping sequences in various formats
 
 =head1 SYNOPSIS
 
@@ -50,7 +50,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Graphics::Browser::Plugin::SequenceDumper;
-# $Id: SequenceDumper.pm,v 1.2 2002-07-04 21:57:47 lstein Exp $
+# $Id: SequenceDumper.pm,v 1.3 2002-07-05 13:53:10 lstein Exp $
 # Sequence Dumper plugin
 
 use strict;
@@ -59,18 +59,32 @@ use Bio::SeqIO;
 use Bio::Seq;
 use CGI qw(:standard *pre);
 
-use vars '$VERSION','@ISA', '%LABELS', '@ORDER';
-
-%LABELS = ( 'fasta'   => 'Fasta',
-	    'genbank' => 'Genbank',
-	    'embl'    => 'EMBL',
-	    'game'    => 'GAME (XML)',
-	    'bsml'    => 'BSML (XML)',
-	    'gcg'     => 'GCG',
-	    'raw'     => 'Raw sequence'
-	    );
+use vars qw($VERSION @ISA);
+use constant DEBUG => 0;
+
+             # module        label           is xml?
+my @FORMATS = ( 'fasta'   => ['Fasta',        undef],
+		'genbank' => ['Genbank',      undef],
+		'embl'    => ['EMBL',         undef],
+		'gcg'     => ['GCG',          undef],
+		'raw'     => ['Raw sequence', undef],
+		'game'    => ['GAME (XML)',   'xml'],
+		'bsml'    => ['BSML (XML)',   'xml'],
+	      );
+
+# initialize @ORDER using the even-numbered elements of the array
+# and grepping for those that load successfully (some of the
+# modules depend on optional XML modules).
+my @ORDER = grep {
+  my $module = "Bio::SeqIO::$_";
+  warn "trying to load $module\n" if DEBUG;
+  eval "require $module; 1";
+}
+  map { $FORMATS[2*$_] } (0..@FORMATS/2-1);
 
-@ORDER = qw(fasta genbank embl gcg raw game bsml);
+# initialize %FORMATS and %LABELS from @FORMATS
+my %FORMATS = @FORMATS;
+my %LABELS  = map { $_ => $FORMATS{$_}[0] } keys %FORMATS;
 
 $VERSION = '0.11';
 
@@ -93,10 +107,10 @@ sub dump {
   my %markuptype;
   my $out = new Bio::SeqIO(-format => $config->{'fileformat'});
   if ($config->{'format'} eq 'html') {
-    if ($config->{'fileformat'} =~ /^game|bsml$/i) {
+    if ($FORMATS{$config->{'fileformat'}}[1]) {  # is xml
       print header('text/xml');
       $out->write_seq($segment);
-    }  else {
+    } else {
       print header('text/html');
       print start_html($segment),h1($segment), start_pre;
       $out->write_seq($segment);
@@ -105,8 +119,8 @@ sub dump {
     }
   } else { 
     print header('text/plain');
-    $out->write_seq($segment);      
-  }  
+    $out->write_seq($segment);
+  }
   undef $out;
 }
 
@@ -145,7 +159,7 @@ sub configure_form {
   push @choices, TR({-class => 'searchtitle'}, 
 			th({-align=>'RIGHT',-width=>'25%'},"Sequence File Format",
 			   td(popup_menu('-name'   => "$objtype.fileformat",
-					 '-values' =>  \@ORDER, 
+					 '-values' => \@ORDER,
 					 '-labels' => \%LABELS,
 					 '-default'=> $current_config->{'fileformat'} ))));
   my $html= table(@choices);

diff --git a/lib/Bio/DB/GFF/Aggregator/coding.pm b/lib/Bio/DB/GFF/Aggregator/coding.pm
@@ -88,7 +88,8 @@ None reported.
 
 =head1 SEE ALSO
 
-L<Bio::DB::GFF>, L<Bio::DB::GFF::Aggregator>, L<Bio::Graphics::Glyph::cds>
+L<Bio::DB::GFF>, L<Bio::DB::GFF::orf>,
+L<Bio::DB::GFF::Aggregator>, L<Bio::Graphics::Glyph::cds>,
 
 =head1 AUTHOR