[med-svn] [Git][med-team/libbio-cluster-perl][master] 3 commits: breaks+replace on bioperl
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Dec 7 11:39:50 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / libbio-cluster-perl
Commits:
3afa5a60 by Michael R. Crusoe at 2019-12-07T11:12:02Z
breaks+replace on bioperl
drop libbio-variation-perl req for now
- - - - -
1be1d34e by Michael R. Crusoe at 2019-12-07T11:32:09Z
drop Bio::Variation::SNP parts
- - - - -
20debcba by Michael R. Crusoe at 2019-12-07T11:35:31Z
update runtime reqs
- - - - -
4 changed files:
- + debian/README.Debian
- debian/control
- + debian/patches/delete-bio-variation-parts
- + debian/patches/series
Changes:
=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,6 @@
+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
=====================================
@@ -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
=====================================
@@ -0,0 +1,199 @@
+Author: Michael R. Crusoe <michael.crusoe at 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
=====================================
@@ -0,0 +1 @@
+delete-bio-variation-parts
View it on GitLab: https://salsa.debian.org/med-team/libbio-cluster-perl/compare/fc14e2d1a365a4b9a576ccc9a1a56da97cbe2611...20debcba1e6f793c5f328d954ae9e7fde1ae196d
--
View it on GitLab: https://salsa.debian.org/med-team/libbio-cluster-perl/compare/fc14e2d1a365a4b9a576ccc9a1a56da97cbe2611...20debcba1e6f793c5f328d954ae9e7fde1ae196d
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