[ensembl-dev] Suggested code changes

Youens-Clark, Ken kclark at cshl.edu
Tue May 14 17:59:33 BST 2013


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;
>
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Anne Parker
Ensembl Web Production Manager
http://www.ensembl.org




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