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debian/README.Debian 0 → 100644
View file @ 20debcba
Due to Bio::Variation[1] being split from the Bio-Perl distribution, but not yet
released on its own, part of this package have been disabled:
Bio::ClusterIO::dbsnp's next_cluster & start_document
[1] https://github.com/bioperl/Bio-Variation
debian/control
View file @ 20debcba
......@@ -6,9 +6,9 @@ Priority: optional
Build-Depends: debhelper-compat (= 12)
Build-Depends-Indep: perl,
libbio-perl-perl,
libbio-variation-perl,
libxml-sax-perl,
libtest-most-perl
# libbio-variation-perl,
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/libbio-cluster-perl
Vcs-Git: https://salsa.debian.org/med-team/libbio-cluster-perl.git
......@@ -17,7 +17,10 @@ Homepage: https://metacpan.org/release/Bio-Cluster
Package: libbio-cluster-perl
Architecture: all
Depends: ${misc:Depends},
${perl:Depends}
${perl:Depends},
libbio-perl-perl
Breaks: libbio-perl-perl (<= 1.7.2)
Replaces: libbio-perl-perl (<= 1.7.2)
Description: BioPerl cluster modules
The ClusterIO module works with the ClusterIO format module to read various
cluster formats such as NCBI UniGene.
......
debian/patches/delete-bio-variation-parts 0 → 100644
View file @ 20debcba
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: Bio::Variation::SNP is unmaintained and no longer released
So remove references to it
--- libbio-cluster-perl.orig/lib/Bio/ClusterIO/dbsnp.pm
+++ libbio-cluster-perl/lib/Bio/ClusterIO/dbsnp.pm
@@ -65,7 +65,6 @@
$Bio::ClusterIO::dbsnp::VERSION = '1.7.3';
use strict;
use Bio::Root::Root;
-use Bio::Variation::SNP;
use XML::SAX;
use Data::Dumper;
use IO::File;
@@ -167,108 +166,8 @@
$DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
}
-=head2 next_cluster
-
- Title : next_cluster
- Usage : $dbsnp = $stream->next_cluster()
- Function: returns the next refSNP in the stream
- Returns : Bio::Variation::SNP object representing composite refSNP
- and its component subSNP(s).
- Args : NONE
-
-=cut
-
-###
-#Adapted from Jason's blastxml.pm
-###
-
-# you shouldn't have to preparse this; the XML is well-formed and refers
-# accurately to a remote DTD/schema
-
-sub next_cluster {
- my $self = shift;
- my $data = '';
- my($tfh);
-
- if( $self->use_tempfile ) {
- $tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
- $tfh->autoflush(1);
- }
-
- my $start = 1;
- while( defined( $_ = $self->_readline ) ){
- #skip to beginning of refSNP entry
- if($_ !~ m{<Rs[^>]*>} && $start){
- next;
- } elsif($_ =~ m{<Rs[^>]*>} && $start){
- $start = 0;
- }
-
- #slurp up the data
- if( defined $tfh ) {
- print $tfh $_;
- } else {
- $data .= $_;
- }
-
- #and stop at the end of the refSNP entry
- last if $_ =~ m{</Rs>};
- }
-
- #if we didn't find a start tag
- return if $start;
-
- my %parser_args;
- if( defined $tfh ) {
- seek($tfh,0,0);
- %parser_args = ('Source' => { 'ByteStream' => $tfh },
- 'Handler' => $self);
- } else {
- %parser_args = ('Source' => { 'String' => $data },
- 'Handler' => $self);
- }
-
- my $starttime;
- my $result;
-
- if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; }
-
- eval {
- $result = $self->{'_xmlparser'}->parse(%parser_args);
- };
-
- if( $@ ) {
- $self->warn("error in parsing a report:\n $@");
- $result = undef;
- }
-
- if( $DEBUG ) {
- $self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime)));
- }
-
- return $self->refsnp;
-}
-
=head2 SAX methods
-=cut
-
-=head2 start_document
-
- Title : start_document
- Usage : $parser->start_document;
- Function: SAX method to indicate starting to parse a new document.
- Creates a Bio::Variation::SNP
- Returns : none
- Args : none
-
-=cut
-
-sub start_document{
- my ($self) = @_;
- $self->{refsnp} = Bio::Variation::SNP->new;
-}
-
sub refsnp {
return shift->{refsnp};
}
--- libbio-cluster-perl.orig/META.json
+++ libbio-cluster-perl/META.json
@@ -46,7 +46,6 @@
"Bio::Root::RootI" : "0",
"Bio::Seq::SeqFactory" : "0",
"Bio::Species" : "0",
- "Bio::Variation::SNP" : "0",
"Data::Dumper" : "0",
"IO::File" : "0",
"Time::HiRes" : "0",
--- libbio-cluster-perl.orig/META.yml
+++ libbio-cluster-perl/META.yml
@@ -39,7 +39,6 @@
Bio::Root::RootI: '0'
Bio::Seq::SeqFactory: '0'
Bio::Species: '0'
- Bio::Variation::SNP: '0'
Data::Dumper: '0'
IO::File: '0'
Time::HiRes: '0'
--- libbio-cluster-perl.orig/Makefile.PL
+++ libbio-cluster-perl/Makefile.PL
@@ -30,7 +30,6 @@
"Bio::Root::RootI" => 0,
"Bio::Seq::SeqFactory" => 0,
"Bio::Species" => 0,
- "Bio::Variation::SNP" => 0,
"Data::Dumper" => 0,
"IO::File" => 0,
"Time::HiRes" => 0,
@@ -69,7 +68,6 @@
"Bio::Root::Test" => 0,
"Bio::Seq::SeqFactory" => 0,
"Bio::Species" => 0,
- "Bio::Variation::SNP" => 0,
"Data::Dumper" => 0,
"File::Spec" => 0,
"IO::File" => 0,
--- libbio-cluster-perl.orig/t/ClusterIO.t
+++ libbio-cluster-perl/t/ClusterIO.t
@@ -7,7 +7,7 @@
use lib '.';
use Bio::Root::Test;
- test_begin(-tests => 12,
+ test_begin(-tests => 4,
-requires_module => 'Time::HiRes');
use_ok('Bio::ClusterIO');
@@ -22,16 +22,16 @@
'-format' => 'dbsnp',
'-file' => test_input_file('LittleChrY.dbsnp.xml'));
- $result = $clusterio->next_cluster;
- ok($result);
- is($result->observed, 'C/T');
- is($result->type, 'notwithdrawn');
- ok($result->seq_5);
- ok($result->seq_3);
- my @ss = $result->each_subsnp;
- is scalar @ss, 5;
- is($ss[0]->handle, 'CGAP-GAI');
- is($ss[1]->handle, 'LEE');
+ # $result = $clusterio->next_cluster;
+ # ok($result);
+ # is($result->observed, 'C/T');
+ # is($result->type, 'notwithdrawn');
+ # ok($result->seq_5);
+ # ok($result->seq_3);
+ # my @ss = $result->each_subsnp;
+ # is scalar @ss, 5;
+ # is($ss[0]->handle, 'CGAP-GAI');
+ # is($ss[1]->handle, 'LEE');
# don't know if these were ever meant to work... cjf 3/7/07
#is($result->heterozygous, 0.208738461136818);
debian/patches/series 0 → 100644
View file @ 20debcba
delete-bio-variation-parts