BioPerl

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Bio/Assembly/IO.pm  view on Meta::CPAN

   return 'sam'    if ($arg =~ /\.[bs]am/i);
   return 'bowtie' if ($arg =~ /\.bowtie/i);

}


=head2 _sort

    Title   : _sort
    Usage   : @sorted_values = $ass_io->_sort(@values)
    Function: Sort a list of values naturally if Sort::Naturally is installed
              (nicer), lexically otherwise (not as nice, but safe)
    Returns : array of sorted values
    Args    : array of values to sort

=cut

sub _sort {
    my @arr = @_;
    my @sorted_arr;
    if (eval { require Sort::Naturally }) {
        @sorted_arr = Sort::Naturally::nsort( @arr ); # natural sort (better)
    } else {
        @sorted_arr = sort @arr; # lexical sort (safe)
    }
    return @sorted_arr;
}


sub DESTROY {
    my $self = shift;

Bio/Assembly/IO/ace.pm  view on Meta::CPAN

    }
    return 1;
}


=head2 write_assembly

    Title   : write_assembly
    Usage   : $ass_io->write_assembly($assembly)
    Function: Write the assembly object in ACE compatible format. The contig IDs
              are sorted naturally if the Sort::Naturally module is present, or
              lexically otherwise. Internally, write_assembly use the
              write_contig, write_footer and write_header methods. Use these
              methods if you want more control on the writing process.
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Scaffold object

=cut


=head2 write_contig

Bio/Assembly/IO/tigr.pm  view on Meta::CPAN

   return $singletobj;
}


=head2 write_assembly

    Title   : write_assembly
    Usage   : $asmio->write_assembly($assembly)
    Function: Write the assembly object in TIGR Assembler compatible format. The
              contig IDs are sorted naturally if the Sort::Naturally module is
              present, or lexically otherwise. Internally, write_assembly use
              the write_contig, write_footer and write_header methods. Use these
              methods if you want more control on the writing process.
    Returns : 1 on success, 0 for error
    Args    : A Bio::Assembly::Scaffold object
              1 to write singlets in the assembly file, 0 otherwise

=cut

Build.PL  view on Meta::CPAN

    'LWP::UserAgent' => [
        0,
        'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'
    ],

    'PostScript::TextBlock' => [ 0, 'EPS output/Bio::Tree::Draw::Cladogram' ],

    'Set::Scalar' => [ 0, 'Proper operation/Bio::Tree::Compatible' ],

    'Sort::Naturally' => [
        0,
        'Sort lexically, but sort numeral parts numerically/'
            . 'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'
    ],

    'Spreadsheet::ParseExcel' =>
        [ 0, 'Parsing Excel files/Bio::SeqIO::excel' ],

    'Storable' => [
        2.05,

META.json  view on Meta::CPAN

            "HTML::TableExtract" : "0",
            "HTTP::Request::Common" : "0",
            "IO::Scalar" : "0",
            "Inline::C" : "0.67",
            "LWP::UserAgent" : "0",
            "List::MoreUtils" : "0",
            "PostScript::TextBlock" : "0",
            "SVG" : "2.26",
            "SVG::Graph" : "0.01",
            "Set::Scalar" : "0",
            "Sort::Naturally" : "0",
            "Spreadsheet::ParseExcel" : "0",
            "Storable" : "2.05",
            "Text::ParseWords" : "0",
            "XML::DOM" : "0",
            "XML::DOM::XPath" : "0",
            "XML::LibXML" : "0",
            "XML::Parser" : "0",
            "XML::Parser::PerlSAX" : "0",
            "XML::SAX" : "0.15",
            "XML::SAX::Writer" : "0",

META.yml  view on Meta::CPAN

  HTML::TableExtract: '0'
  HTTP::Request::Common: '0'
  IO::Scalar: '0'
  Inline::C: '0.67'
  LWP::UserAgent: '0'
  List::MoreUtils: '0'
  PostScript::TextBlock: '0'
  SVG: '2.26'
  SVG::Graph: '0.01'
  Set::Scalar: '0'
  Sort::Naturally: '0'
  Spreadsheet::ParseExcel: '0'
  Storable: '2.05'
  Text::ParseWords: '0'
  XML::DOM: '0'
  XML::DOM::XPath: '0'
  XML::LibXML: '0'
  XML::Parser: '0'
  XML::Parser::PerlSAX: '0'
  XML::SAX: '0.15'
  XML::SAX::Writer: '0'