[med-svn] r157 - in trunk/packages/perlprimer/trunk: . debian tutorial_files

[Charles Plessy]

Author: charles-guest
Date: 2006-11-08 16:23:58 +0100 (Wed, 08 Nov 2006)
New Revision: 157

Added:
   trunk/packages/perlprimer/trunk/tutorial_files/Thumbs.db
Modified:
   trunk/packages/perlprimer/trunk/Changelog
   trunk/packages/perlprimer/trunk/debian/changelog
   trunk/packages/perlprimer/trunk/debian/control
   trunk/packages/perlprimer/trunk/debian/watch
   trunk/packages/perlprimer/trunk/perlprimer.pl
Log:
New upstream version, fixed watch file.

Modified: trunk/packages/perlprimer/trunk/Changelog
===================================================================
--- trunk/packages/perlprimer/trunk/Changelog	2006-11-08 15:09:39 UTC (rev 156)
+++ trunk/packages/perlprimer/trunk/Changelog	2006-11-08 15:23:58 UTC (rev 157)
@@ -1,3 +1,6 @@
+18/10/06  (PerlPrimer-1.1.14)
+- Ensembl compatibility restored once again (slight change in the searchview output was causing problems)
+
 22/6/06  (PerlPrimer-1.1.13)
 - Ensembl compatibility restored again (back to searchview)
 - Added code to check for the presence of Genomic and mRNA seqs before running spidey (error message that resulted otherwise was confusing to users)

Modified: trunk/packages/perlprimer/trunk/debian/changelog
===================================================================
--- trunk/packages/perlprimer/trunk/debian/changelog	2006-11-08 15:09:39 UTC (rev 156)
+++ trunk/packages/perlprimer/trunk/debian/changelog	2006-11-08 15:23:58 UTC (rev 157)
@@ -1,8 +1,9 @@
-perlprimer (1.1.13-2) unstable; urgency=low
+perlprimer (1.1.14-1) unstable; urgency=medium
 
-  * Debtagged.
+  * New upstream release: Ensembl compatibility restored once again.
+  * Fixed watch file.
 
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Fri,  8 Sep 2006 13:06:15 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Thu,  9 Nov 2006 00:20:56 +0900
 
 perlprimer (1.1.13-1) unstable; urgency=low
 

Modified: trunk/packages/perlprimer/trunk/debian/control
===================================================================
--- trunk/packages/perlprimer/trunk/debian/control	2006-11-08 15:09:39 UTC (rev 156)
+++ trunk/packages/perlprimer/trunk/debian/control	2006-11-08 15:23:58 UTC (rev 157)
@@ -11,7 +11,6 @@
 Depends: ${shlibs:Depends}, ${misc:Depends}, perl-tk, libwww-perl
 Recommends: ncbi-tools-bin
 Suggests: perlprimer-doc
-Tag:
 Description: [Biology] graphical design of primers for PCR
  PerlPrimer is a free, open-source GUI application written in Perl
  that designs primers for standard PCR, bisulphite PCR, real-time PCR
@@ -26,7 +25,6 @@
 Package: perlprimer-doc
 Architecture: all
 Section: doc
-Tag:
 Suggests: perlprimer
 Description: [Biology] tutorial to perlprimer
  An HTML tutorial explaining the use of the user interface and

Modified: trunk/packages/perlprimer/trunk/debian/watch
===================================================================
--- trunk/packages/perlprimer/trunk/debian/watch	2006-11-08 15:09:39 UTC (rev 156)
+++ trunk/packages/perlprimer/trunk/debian/watch	2006-11-08 15:23:58 UTC (rev 157)
@@ -1,8 +1,2 @@
-# Example watch control file for uscan
-# Rename this file to "watch" and then you can run the "uscan" command
-# to check for upstream updates and more.
-# Site		Directory		Pattern			Version	Script
 version=3
-# Uncomment to use Roland's hack for sourceforge based projects - YMMV!
-http://people.debian.org/~lolando/sfdlr.php?project=perlprimer perlprimer-([\d.]*).tar.bz2
-
+http://sf.net/perlprimer/perlprimer-(.*)\.tar\.bz2

Modified: trunk/packages/perlprimer/trunk/perlprimer.pl
===================================================================
--- trunk/packages/perlprimer/trunk/perlprimer.pl	2006-11-08 15:09:39 UTC (rev 156)
+++ trunk/packages/perlprimer/trunk/perlprimer.pl	2006-11-08 15:23:58 UTC (rev 157)
@@ -3,7 +3,7 @@
 # PerlPrimer
 # Designs primers for PCR, Bisulphite PCR, QPCR (Realtime), and Sequencing
 
-# version 1.1.13 (22/6/2006)
+# version 1.1.14 (22/6/2006)
 # Copyright © 2003-2006, Owen Marshall
 
 # This program is free software; you can redistribute it and/or modify
@@ -29,7 +29,7 @@
 
 my ($version, $commandline, $win_exe);
 BEGIN {
-	$version = "1.1.13";
+	$version = "1.1.14";
 	$win_exe = 0;
 	
 	($commandline) = @ARGV;
@@ -372,21 +372,29 @@
 "Homo_sapiens
 Mus_musculus
 -------------------
+Aedes_aegypti
 Anopheles_gambiae
 Apis_mellifera
 Bos_taurus
 Caenorhabditis_elegans
 Canis_familiaris
 Ciona_intestinalis
+Ciona_savignyi
 Danio_rerio
+Dasypus_novemcinctus
 Drosophila_melanogaster
-Fugu_rubripes
+Echinops_telfairi
 Gallus_gallus
+Gasterosteus_aculeatus
+Loxodonta_africana
 Macaca_mulatta
 Monodelphis_domestica
+Oryctolagus_cuniculus
+Oryzias_latipes
 Pan_troglodytes
 Rattus_norvegicus
 Saccharomyces_cerevisiae
+Takifugu_rubripes
 Tetraodon_nigroviridis
 Xenopus_tropicalis");
 
@@ -4722,8 +4730,8 @@
 		
 	# as of 07/2005, we're actually looking for the transcript ID, not the gene ID ...
 	# Here, we scrape both genes and associated transcripts from the server:
-	while (m/Ensembl gene ([\w\d]+) .*?:(.*?)<br \/>(.*?)<br \/>/mg) {
-		my ($gene_id, $transcripts, $name) = ($1, $2, $3);
+	while (m/Ensembl ([\w_].*?) gene ([\w\d]+) .*?:(.*?)<br \/>(.*?)<br \/>/mg) {
+		my ($gene_id, $transcripts, $name) = ($2, $3, $4);
 		$name ||= "$gene_id: no description available";
 		my @enst;
 		while ($transcripts =~ m/(ENS[A-Z]*T\d+)/g) {

Copied: trunk/packages/perlprimer/trunk/tutorial_files/Thumbs.db (from rev 156, trunk/packages/perlprimer/branches/upstream/current/tutorial_files/Thumbs.db)