[ensembl-dev] Suggested code changes
Anne Parker
ap5 at sanger.ac.uk
Wed May 15 09:23:39 BST 2013
We should be putting the new interface on our beta site very soon, and the code itself will hopefully go out as part of release 73 at the very latest. We want to get it out there as soon as possible, but it requires thorough testing so that it doesn't cause more headaches than it solves!
Cheers
Anne
On 14 May 2013, at 17:59, "Youens-Clark, Ken" <kclark at cshl.edu> wrote:
> Thanks, Anne. Any idea when? I'm having horrible problems getting Gramene.org's BLAST to work on version 70. I'm also trying with v71 with no luck.
>
> --
>
> Ken Youens-Clark
> Ware Lab/CSHL/USDA-ARS
> kclark at cshl.edu
>
> ________________________________________
> From: dev-bounces at ensembl.org [dev-bounces at ensembl.org] on behalf of Anne Parker [ap5 at sanger.ac.uk]
> Sent: Tuesday, May 14, 2013 9:01 AM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Suggested code changes
>
> Hi Ken
>
> We're going to be releasing a new version of the BLAST interface in the next few months that will make most of the changes below moot :)
>
> Regards
>
> Anne
>
>
> On 14 May 2013, at 16:55, "Youens-Clark, Ken" <kclark at cshl.edu> wrote:
>
>> Below please find suggested minor changes to Perl code that will keep Perl from complaining so much.
>>
>> --
>> Ken Youens-Clark
>> Ware Lab/CSHL/USDA-ARS
>> kclark at cshl.edu
>>
>> Index: common/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
>> ===================================================================
>> RCS file: /cvsroot/ensembl/eg-plugins/common/modules/Bio/EnsEMBL/External/BlastAdaptor.pm,v
>> retrieving revision 1.3
>> diff -r1.3 BlastAdaptor.pm
>> 433,434d432
>> < warn $dbh;
>> < warn $SQL_SEARCH_MULTI_RETRIEVE;
>> 436d433
>> < warn $sth;
>> Index: common/modules/Bio/EnsEMBL/GlyphSet/gsv_transcript.pm
>> ===================================================================
>> RCS file: /cvsroot/ensembl/eg-plugins/common/modules/Bio/EnsEMBL/GlyphSet/gsv_transcript.pm,v
>> retrieving revision 1.6
>> diff -r1.6 gsv_transcript.pm
>> 141,142c141,142
>> < my $start_ex = @l_exons->[0];
>> < my $end_ex = @l_exons->[$#l_exons];
>> ---
>>> my $start_ex = $l_exons[0];
>>> my $end_ex = $l_exons[$#l_exons];
>> 332,333c332,333
>> < my $start_ex = @l_exons->[0];
>> < my $end_ex = @l_exons->[$#l_exons];
>> ---
>>> my $start_ex = $l_exons[0];
>>> my $end_ex = $l_exons[$#l_exons];
>> Index: common/modules/Bio/Search/HSP/EnsemblHSP.pm
>> ===================================================================
>> RCS file: /cvsroot/ensembl/eg-plugins/common/modules/Bio/Search/HSP/EnsemblHSP.pm,v
>> retrieving revision 1.2
>> diff -r1.2 EnsemblHSP.pm
>> 425d424
>> <
>> 430,431d428
>> < $DB::single = 1;
>> <
>> Index: multi/blastview
>> ===================================================================
>> RCS file: /cvsroot/ensembl/ensembl-webcode/perl/multi/blastview,v
>> retrieving revision 1.39
>> diff -r1.39 blastview
>> 2194c2194
>> < foreach my $stat qw( score evalue pvalue identity length ){
>> ---
>>> foreach my $stat ( qw( score evalue pvalue identity length ) ){
>> 2209c2209
>> < foreach my $type qw( subject query ){
>> ---
>>> foreach my $type ( qw( subject query ) ){
>> 2276,2278c2276,2278
>> < foreach my $type qw( query subject genome contig stats ){
>> < foreach my $col qw( name start end orientation
>> < score evalue identity length ){
>> ---
>>> foreach my $type ( qw( query subject genome contig stats ) ){
>>> foreach my $col ( qw( name start end orientation
>>> score evalue identity length ) ){
>> 2388c2388
>> < foreach my $stat qw( score evalue pvalue identity length ){
>> ---
>>> foreach my $stat (qw( score evalue pvalue identity length )){
>> Index: Bio/Tools/Run/Search/WuBlast.pm
>> ===================================================================
>> RCS file: /cvsroot/ensembl/ensembl-webcode/modules/Bio/Tools/Run/Search/WuBlast.pm,v
>> retrieving revision 1.5
>> diff -r1.5 WuBlast.pm
>> 257c257
>> < foreach my $env qw( PATH BLASTMAT BLASTFILTER BLASTDB ){
>> ---
>>> foreach my $env ( qw( PATH BLASTMAT BLASTFILTER BLASTDB ) ){
>> Index: EnsEMBL/Web/Object/Transcript.pm
>> ===================================================================
>> RCS file: /cvsroot/ensembl/ensembl-webcode/modules/EnsEMBL/Web/Object/Transcript.pm,v
>> retrieving revision 1.236.2.1
>> diff -r1.236.2.1 Transcript.pm
>> 1010c1010
>> < foreach my $attrib_code qw(cds_start_NF cds_end_NF mRNA_start_NF mRNA_end_NF) {
>> ---
>>> foreach my $attrib_code ( qw(cds_start_NF cds_end_NF mRNA_start_NF mRNA_end_NF) ) {
>> Index: EnsEMBL/Web/Tools/Registry.pm
>> ===================================================================
>> RCS file: /cvsroot/ensembl/ensembl-webcode/modules/EnsEMBL/Web/Tools/Registry.pm,v
>> retrieving revision 1.19
>> diff -r1.19 Registry.pm
>> 65c65,66
>> < my $is_collection = $self->{'conf'}->{'_storage'}{$species}{'SPP_IN_DB'} > 1 ? 1 : 0;
>> ---
>>> my $val = $self->{'conf'}->{'_storage'}{$species}{'SPP_IN_DB'};
>>> my $is_collection = defined $val && $val > 1 ? 1 : 0;
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
> Anne Parker
> Ensembl Web Production Manager
> http://www.ensembl.org
>
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
Anne Parker
Ensembl Web Production Manager
www.ensembl.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130515/d9a6905f/attachment.html>
More information about the Dev
mailing list