Merge branch 'master' of git://github.com/bioperl/bioperl-live

bioperl · Aug 30, 2012 · f558449 · f558449
2 parents addc1a1 + 5c83c81
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diff --git a/.gitignore b/.gitignore
@@ -17,3 +17,4 @@ t/LocalDB/SeqFeature_*.t
 blib*
 *.bak
 MYMETA.yml
+MYMETA.json
diff --git a/.shipit b/.shipit
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,37 @@
+language: perl
+perl:
+  - "5.16"
+  - "5.14"
+  - "5.12"
+  - "5.10"
+
+env: PERL_CPANM_OPT="--notest --force --skip-satisfied"
+install:
+    #This should solve problem installing Perl's DB_File & GraphViz
+    - "sudo apt-get install libdb-dev graphviz libgd2-xpm-dev libxml2-dev 2>&1 | tail -n 4"
+    #These are recommended or required Perl libraries:
+    - "cpanm GD 2>&1 | tail -n 1"
+    - "cpanm HTML::TableExtract DBI Data::Stag DB_File 2>&1 | tail -n 1"
+    - "cpanm DBD::mysql DBD::Pg DBD::SQLite 2>&1 | tail -n 1"
+    - "cpanm Algorithm::Munkres Array::Compare Convert::Binary::C Error 2>&1 | tail -n 1"
+    - "cpanm Graph SVG SVG::Graph GraphViz 2>&1 | tail -n 1"
+    - "cpanm XML::DOM::XPath XML::Parser XML::Parser::PerlSAX 2>&1 | tail -n 1"
+    - "cpanm XML::SAX XML::SAX::Writer XML::Simple XML::LibXML XML::Twig XML::Writer 2>&1 | tail -n 1"
+    - "cpanm PostScript::TextBlock Set::Scalar Sort::Naturally YAML | tail -n 1"
+    - "cpanm Math::Random SOAP::Lite Spreadsheet::ParseExcel | tail -n 1"
+    - "cpanm Bio::ASN1::EntrezGene | tail -n 1"
+    - "cpanm Bio::Phylo | tail -n 1"
+    #This installs BioPerl itself:
+    - "perl ./Build.PL --accept"
+
+script:
+    - "./Build test"
+
+#TODO - send emails to bioperl-guts-l
+notifications:
+  email: false
+
+# whitelist branches
+branches:
+  only:
+    - master
diff --git a/BUGS b/BUGS
@@ -3,15 +3,15 @@
 Known Bugs
 
 Bugs are tracked at this URL:
-http://bugzilla.bioperl.org/
+https://redmine.open-bio.org/projects/bioperl/
 
 Bioperl 1.6 series
 =============
 
 Though a stable release, some bugs and enhancements remain for this series
 that will be addressed in future point releases. For a full list please see:
 
-http://bugzilla.bioperl.org/
+https://redmine.open-bio.org/projects/bioperl/
 
 Bug     Summary (additional info)
 

diff --git a/Bio/Align/AlignI.pm b/Bio/Align/AlignI.pm
@@ -70,7 +70,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/DNAStatistics.pm b/Bio/Align/DNAStatistics.pm
@@ -313,7 +313,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/PairwiseStatistics.pm b/Bio/Align/PairwiseStatistics.pm
@@ -58,7 +58,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/ProteinStatistics.pm b/Bio/Align/ProteinStatistics.pm
@@ -68,7 +68,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/StatisticsI.pm b/Bio/Align/StatisticsI.pm
@@ -51,7 +51,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/Utilities.pm b/Bio/Align/Utilities.pm
@@ -74,7 +74,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Jason Stajich
 
@@ -101,7 +101,7 @@ require Exporter;
 use base qw(Exporter);
 
 @EXPORT = qw();
-@EXPORT_OK = qw(aa_to_dna_aln bootstrap_replicates cat);
+@EXPORT_OK = qw(aa_to_dna_aln bootstrap_replicates cat bootstrap_replicates_codons);
 %EXPORT_TAGS = (all =>[@EXPORT, @EXPORT_OK]);
 BEGIN {
     use constant CODONSIZE => 3;
@@ -226,6 +226,58 @@ sub bootstrap_replicates {
    return \@alns;
 }
 
+=head2 bootstrap_replicates_codons
+
+ Title   : bootstrap_replicates_codons
+ Usage   : my $alns = &bootstrap_replicates_codons($aln,100);
+ Function: Generate a pseudo-replicate of the data by randomly
+           sampling, with replacement, the columns from a codon alignment for
+           the non-parametric bootstrap. The alignment is assumed to start on
+		   the first position of a codon.
+ Returns : Arrayref of L<Bio::SimpleAlign> objects
+ Args    : L<Bio::SimpleAlign> object
+           Number of replicates to generate
+
+=cut
+
+sub bootstrap_replicates_codons {
+   my ($aln,$count) = @_;
+   $count ||= 1;
+   my $alen = $aln->length;
+   my $ncodon = int($alen/3);
+   my (@seqs,@nm);
+   $aln->set_displayname_flat(1);
+   for my $s ( $aln->each_seq ) {
+       push @seqs, $s->seq();
+       push @nm, $s->id;
+   }
+   my (@alns,$i);
+   while( $count-- > 0 ) {
+       my @newseqs;
+       for($i =0; $i < $ncodon; $i++ ) {
+			my $index = int(rand($ncodon));
+			my $seqpos = $index * 3;
+			my $c = 0;
+			for ( @seqs ) {
+				$newseqs[$c++] .= substr($_,$seqpos,3);
+			}
+       }
+       my $newaln = Bio::SimpleAlign->new();
+       my $i = 0;
+       for my $s ( @newseqs ) {
+			(my $tmp = $s) =~ s{[$Bio::LocatableSeq::GAP_SYMBOLS]+}{}g;
+			$newaln->add_seq( Bio::LocatableSeq->new
+						(-start         => 1,
+						-end           => length($tmp),
+						-display_id    => $nm[$i++],
+						-seq           => $s));
+       }
+       push @alns, $newaln;
+   }
+   return \@alns;
+}
+
+
 =head2 cat
 
  Title     : cat

diff --git a/Bio/AlignIO.pm b/Bio/AlignIO.pm
@@ -254,7 +254,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Peter Schattner
 
@@ -375,14 +375,29 @@ sub fh {
   return $s;
 }
 
+
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the alignment format
+ Returns : alignment format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 # _initialize is where the heavy stuff will happen when new is called
 
 sub _initialize {
   my($self,@args) = @_;
-  my ($flat,$alphabet) = $self->_rearrange([qw(DISPLAYNAME_FLAT ALPHABET)],
+  my ($flat,$alphabet,$width) = $self->_rearrange([qw(DISPLAYNAME_FLAT ALPHABET WIDTH)],
 				 @args);
   $self->force_displayname_flat($flat) if defined $flat;
   $self->alphabet($alphabet);
+  $self->width($width) if defined $width;
   $self->_initialize_io(@args);
   1;
 }

diff --git a/Bio/AlignIO/Handler/GenericAlignHandler.pm b/Bio/AlignIO/Handler/GenericAlignHandler.pm
@@ -562,7 +562,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Chris Fields
 

diff --git a/Bio/AlignIO/arp.pm b/Bio/AlignIO/arp.pm
@@ -77,7 +77,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS
 

diff --git a/Bio/AlignIO/bl2seq.pm b/Bio/AlignIO/bl2seq.pm
@@ -87,7 +87,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Peter Schattner
 

diff --git a/Bio/AlignIO/clustalw.pm b/Bio/AlignIO/clustalw.pm
@@ -54,7 +54,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS - Peter Schattner
 

diff --git a/Bio/AlignIO/emboss.pm b/Bio/AlignIO/emboss.pm
@@ -59,7 +59,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/AlignIO/fasta.pm b/Bio/AlignIO/fasta.pm
@@ -41,7 +41,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS
 
@@ -227,8 +227,8 @@ sub write_aln {
 
 sub _get_len {
 	my ($self,$seq) = @_;
-	my $chars = $Bio::LocatableSeq::RESIDUE_SYMBOLS;
-	$seq =~ s{[^$chars]+}{}gi;
+	my $chars = $Bio::LocatableSeq::GAP_SYMBOLS.$Bio::LocatableSeq::FRAMESHIFT_SYMBOLS;
+	$seq =~ s{[$chars]+}{}gi;
 	return CORE::length($seq);
 }
 

diff --git a/Bio/AlignIO/largemultifasta.pm b/Bio/AlignIO/largemultifasta.pm
@@ -53,7 +53,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS - Albert Vilella, Heikki Lehvaslaiho
 

diff --git a/Bio/AlignIO/maf.pm b/Bio/AlignIO/maf.pm
@@ -64,7 +64,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS - Allen Day
 

diff --git a/Bio/AlignIO/mase.pm b/Bio/AlignIO/mase.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS - Peter Schattner
 

diff --git a/Bio/AlignIO/mega.pm b/Bio/AlignIO/mega.pm
@@ -59,7 +59,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/AlignIO/meme.pm b/Bio/AlignIO/meme.pm
@@ -59,7 +59,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS - Benjamin Berman
 

diff --git a/Bio/AlignIO/metafasta.pm b/Bio/AlignIO/metafasta.pm
@@ -58,7 +58,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHOR - Heikki Lehvaslaiho
 

diff --git a/Bio/AlignIO/msf.pm b/Bio/AlignIO/msf.pm
@@ -45,7 +45,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS - Peter Schattner
 

diff --git a/Bio/AlignIO/nexml.pm b/Bio/AlignIO/nexml.pm
@@ -38,7 +38,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS
 

diff --git a/Bio/AlignIO/nexus.pm b/Bio/AlignIO/nexus.pm
@@ -49,7 +49,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS - Heikki Lehvaslaiho
 

diff --git a/Bio/AlignIO/pfam.pm b/Bio/AlignIO/pfam.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  http://bugzilla.open-bio.org/
+  https://redmine.open-bio.org/projects/bioperl/
 
 =head1 AUTHORS - Peter Schattner