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

Conflicts: Bio/Tools/Protparam.pm
bioperl · Sep 21, 2011 · 9b3cbb3 · 9b3cbb3
2 parents 644673c + ecbb594
commit 9b3cbb3
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Showing 37 changed files with 996 additions and 636 deletions.
diff --git a/Bio/AlignIO.pm b/Bio/AlignIO.pm
@@ -375,6 +375,20 @@ 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 {

diff --git a/Bio/Assembly/IO.pm b/Bio/Assembly/IO.pm
@@ -141,6 +141,19 @@ sub new {
 }
 
 
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the assembly format
+ Returns : assembly format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 # _initialize is chained for all SeqIO classes
 sub _initialize {
     my($self, @args) = @_;

diff --git a/Bio/Assembly/IO/ace.pm b/Bio/Assembly/IO/ace.pm
@@ -814,25 +814,15 @@ sub write_footer {
 =head2 variant
 
  Title   : variant
- Usage   : $format  = $obj->variant();
+ Usage   : $variant = $ass_io->variant();
  Function: Get and set method for the assembly variant. This is important since
            not all assemblers respect the reference ACE format.
  Returns : string
  Args    : string: 'consed' (default) or '454'
 
 =cut
 
-sub variant {
-    my ($self, $enc) = @_;
-    if (defined $enc) {
-        $enc = lc $enc;
-        if (not exists $variant{$enc}) {
-            $self->throw('Not a valid ACE variant format');
-        }
-        $self->{variant} = $enc;
-    }
-    return $self->{variant};
-}
+# variant() method inherited from Bio::Root::IO
 
 
 =head2 _write_read

diff --git a/Bio/ClusterIO.pm b/Bio/ClusterIO.pm
@@ -186,6 +186,18 @@ sub new {
     }
 }
 
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the cluster format
+ Returns : cluster format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
 
 # _initialize is chained for all ClusterIO classes
 

diff --git a/Bio/DB/CUTG.pm b/Bio/DB/CUTG.pm
@@ -46,6 +46,11 @@ reference variable.
 I intend at a later date to allow retrieval of multiple codon tables
 e.g., from a wildcard search.
 
+Examples URLs:
+
+L<http://www.kazusa.or.jp/codon/cgi-bin/spsearch.cgi?species=Pan+troglodytes&c=s>
+L<http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=37011&aa=1&style=GCG>
+
 =head1 SEE ALSO
 
 L<Bio::Tools::CodonTable>, 
@@ -57,7 +62,6 @@ L<Bio::CodonUsage::IO>
 
 =head2 Mailing Lists
 
-
 User feedback is an integral part of the evolution of this and other
 Bioperl modules. Send your comments and suggestions preferably to one
 of the Bioperl mailing lists.  Your participation is much appreciated.

diff --git a/Bio/DB/Fasta.pm b/Bio/DB/Fasta.pm
@@ -60,7 +60,7 @@ sequences without bringing the entire sequence into memory.
 When you initialize the module, you point it at a single fasta file or
 a directory of multiple such files.  The first time it is run, the
 module generates an index of the contents of the file or directory
-using the AnyDBM module (Berkeley DB* preferred, followed by GDBM_File,
+using the AnyDBM_File module (BerkeleyDB preferred, followed by GDBM_File,
 NDBM_File, and SDBM_File).  Thereafter it uses the index file to find
 the file and offset for any requested sequence.  If one of the source
 fasta files is updated, the module reindexes just that one file.  (You

diff --git a/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/Bio/DB/SeqFeature/Store/DBI/mysql.pm
@@ -566,7 +566,7 @@ sub _finish_bulk_update {
     my $fh = $self->dump_filehandle($table);
     my $path = $self->dump_path($table);
     $fh->close;
-    print STDERR "$path\n";
+    #print STDERR "$path\n";
 
     $dbh->do("LOAD DATA LOCAL INFILE '$path' REPLACE INTO TABLE $table FIELDS OPTIONALLY ENCLOSED BY '\\''") 
       or $self->throw($dbh->errstr);

diff --git a/Bio/FeatureIO.pm b/Bio/FeatureIO.pm
@@ -342,6 +342,19 @@ sub fh {
   return $s;
 }
 
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the feature format
+ Returns : feature format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 # _initialize is chained for all FeatureIO classes
 
 sub _initialize {

diff --git a/Bio/MapIO.pm b/Bio/MapIO.pm
@@ -120,6 +120,20 @@ sub new {
 
 }
 
+
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the map format
+ Returns : map format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 =head2 Bio::Factory::MapFactoryI methods
 
 =cut

diff --git a/Bio/Matrix/IO.pm b/Bio/Matrix/IO.pm
@@ -19,7 +19,7 @@ Bio::Matrix::IO - A factory for Matrix parsing
 
   use Bio::Matrix::IO;
   my $parser = Bio::Matrix::IO->new(-format => 'scoring',
-                                   -file   => 'BLOSUMN50');
+                                    -file   => 'BLOSUMN50');
 
   my $matrix = $parser->next_matrix;
 
@@ -159,6 +159,19 @@ sub fh {
 }
 
 
+=head2 format
+
+ Title   : format
+ Usage   : $format = $obj->format()
+ Function: Get the matrix format
+ Returns : matrix format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 =head2 next_matrix
 
  Title   : next_matrix

diff --git a/Bio/OntologyIO.pm b/Bio/OntologyIO.pm
@@ -111,7 +111,7 @@ my %format_driver_map = (
                          "interpro"    => "InterProParser",
                          "interprosax" => "Handlers::InterPro_BioSQL_Handler",
                          "evoc"        => "simplehierarchy",
-                         "obo"        => "obo"
+                         "obo"         => "obo"
                          );
 
 =head2 new
@@ -185,6 +185,20 @@ sub new {
 
 }
 
+
+=head2 format
+
+ Title   : format
+ Usage   : $format = $parser->format()
+ Function: Get the ontology format
+ Returns : ontology format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 sub _initialize {
     my($self, @args) = @_;
 

diff --git a/Bio/PopGen/IO.pm b/Bio/PopGen/IO.pm
@@ -16,10 +16,10 @@
 Bio::PopGen::IO - Input individual,marker,allele information
 
 =head1 SYNOPSIS
-
+ 
   use Bio::PopGen::IO;
   my $io = Bio::PopGen::IO->new(-format => 'csv',
-                               -file   => 'data.csv');
+                                -file   => 'data.csv');
 
   # Some IO might support reading in a population at a time
 
@@ -126,6 +126,20 @@ sub new {
   }
 }
 
+
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the PopGen format
+ Returns : PopGen format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 # _initialize is chained for all PopGen::IO classes
 
 sub _initialize {

diff --git a/Bio/Restriction/IO.pm b/Bio/Restriction/IO.pm
@@ -160,6 +160,19 @@ sub new {
 }
 
 
+=head2 format
+
+ Title   : format
+ Usage   : $format = $stream->format()
+ Function: Get the restriction format
+ Returns : restriction format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 sub _load_format_module {
   my ($class, $format) = @_;
   my $module = "Bio::Restriction::IO::" . $format;

diff --git a/Bio/Root/IO.pm b/Bio/Root/IO.pm
@@ -374,6 +374,7 @@ sub _initialize_io {
     return 1;
 }
 
+
 =head2 _fh
 
  Title   : _fh
@@ -393,6 +394,7 @@ sub _fh {
     return $obj->{'_filehandle'};
 }
 
+
 =head2 mode
 
  Title   : mode
@@ -441,6 +443,7 @@ sub mode {
     return $obj->{'_mode'};
 }
 
+
 =head2 file
 
  Title   : file
@@ -460,6 +463,60 @@ sub file {
     return $obj->{'_file'};
 }
 
+
+=head2 format
+
+ Title   : format
+ Usage   : $self->format($newval)
+ Function: Get the format of a Bio::Root::IO sequence file or filehandle. Every
+           object inheriting Bio::Root::IO is guaranteed to have a format.
+ Returns : format of the file or filehandle, e.g. fasta, fastq, genbank, embl.
+ Args    : none
+
+=cut
+
+sub format {
+    my ($self) = @_;
+    my $format = (split '::', ref($self))[-1];
+    return $format;
+}
+
+
+=head2 variant
+
+ Title   : format
+ Usage   : $self->format($newval)
+ Function: Get the variant of a Bio::Root::IO sequence file or filehandle.
+           The format variant depends on the specific format used. Note that not
+           all formats have variants
+ Returns : variant of the file or filehandle, e.g. sanger, solexa or illumina for
+           the fastq format, or undef for formats that do not have variants.
+ Args    : none
+ Note    : The Bio::Root::IO-implementing modules that require access to variants
+           need to define a global hash that has the allowed variants as its keys.
+
+=cut
+
+sub variant {
+    my ($self, $variant) = @_;
+    if (defined $variant) {
+        $variant = lc $variant;
+        my $var_name = '%'.ref($self).'::variant';
+        my %ok_variants = eval $var_name; # e.g. %Bio::Assembly::IO::ace::variant
+        if (scalar keys %ok_variants == 0) {
+            $self->throw('Cannot check for validity of variant because global '.
+                "variant $var_name is not set or is empty\n");
+        }
+        if (not exists $ok_variants{$variant}) {
+            $self->throw($variant.' is not a valid variant of the '.$self->format.
+                ' format');
+        }
+        $self->{variant} = $variant;
+    }
+    return $self->{variant};
+}
+
+
 =head2 _print
 
  Title   : _print

diff --git a/Bio/SearchIO.pm b/Bio/SearchIO.pm
@@ -288,6 +288,20 @@ sub fh {
   return $s;
 }
 
+
+=head2 format
+
+ Title   : format
+ Usage   : $format = $obj->format()
+ Function: Get the search format
+ Returns : search format
+ Args    : none
+
+=cut
+
+# format() method inherited from Bio::Root::IO
+
+
 =head2 attach_EventHandler
 
  Title   : attach_EventHandler