[med-svn] r155 - in trunk/packages/perlprimer/branches/upstream/current: . tutorial_files

[Charles Plessy]

Author: charles-guest
Date: 2006-11-08 16:09:22 +0100 (Wed, 08 Nov 2006)
New Revision: 155

Added:
   trunk/packages/perlprimer/branches/upstream/current/tutorial_files/Thumbs.db
Modified:
   trunk/packages/perlprimer/branches/upstream/current/Changelog
   trunk/packages/perlprimer/branches/upstream/current/perlprimer.pl
Log:
Load /tmp/tmp.qDXEw7/perlprimer-1.1.14 into
trunk/packages/perlprimer/branches/upstream/current.


Modified: trunk/packages/perlprimer/branches/upstream/current/Changelog
===================================================================
--- trunk/packages/perlprimer/branches/upstream/current/Changelog	2006-10-28 09:31:41 UTC (rev 154)
+++ trunk/packages/perlprimer/branches/upstream/current/Changelog	2006-11-08 15:09:22 UTC (rev 155)
@@ -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/branches/upstream/current/perlprimer.pl
===================================================================
--- trunk/packages/perlprimer/branches/upstream/current/perlprimer.pl	2006-10-28 09:31:41 UTC (rev 154)
+++ trunk/packages/perlprimer/branches/upstream/current/perlprimer.pl	2006-11-08 15:09:22 UTC (rev 155)
@@ -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");
 
@@ -4714,8 +4722,8 @@
 		
 	# 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) {


Property changes on: trunk/packages/perlprimer/branches/upstream/current/perlprimer.pl
___________________________________________________________________
Name: svn:executable
   - 
   + *

Added: trunk/packages/perlprimer/branches/upstream/current/tutorial_files/Thumbs.db
===================================================================
(Binary files differ)


Property changes on: trunk/packages/perlprimer/branches/upstream/current/tutorial_files/Thumbs.db
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream