Bio-Graphics

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lib/Bio/Graphics/Feature.pm  view on Meta::CPAN

 Title   : alphabet
 Usage   : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
 Function: Returns the type of sequence being one of
           'dna', 'rna' or 'protein'. This is case sensitive.

           This is not called <type> because this would cause
           upgrade problems from the 0.5 and earlier Seq objects.

 Returns : a string either 'dna','rna','protein'. NB - the object must
           make a call of the type - if there is no type specified it
           has to guess.
 Args    : none
 Status  : Virtual

=head2 desc

 Title   : desc
 Usage   : $seqobj->desc($string) or $seqobj->desc()
 Function: Sets or gets the description of the sequence
 Example :
 Returns : The description

lib/Bio/Graphics/FeatureDir.pm  view on Meta::CPAN

    while (<$fh>) {
	# figure out transitions
	$new_status = /^\#\#gff-version\s+3/i ? 'gff3'
	             :/^\#\#gff/i             ? 'gff2'
	             : /^track/i              ? 'wig'
		     : /^\[(.+)\]/i             ? 'conf'
		     : /^>\w+/i               ? 'fa'
		     : /^reference/i          ? 'ff'
		     : undef;

	unless ($status || $new_status) {  # guess what it is
	    my @tokens = split /\s+/;
	    $new_status = 'gff3' if @tokens >= 9 && $tokens[8] =~ /=/;
	    $new_status = 'ff'   if $tokens[2] =~ /\d+(\.\.|-)\d+/;
	}

	

	if ($new_status) {
	    # this will create a new conf file for each section
	    if ($new_status eq 'conf') {

lib/Bio/Graphics/Glyph/image.pm  view on Meta::CPAN

  }
  my $gd      =   $format eq 'image/png'  ? GD::Image->newFromPngData($image,1)
                : $format eq 'image/jpeg' ? GD::Image->newFromJpegData($image,1)
		: $format eq 'image/gif'  ? GD::Image->newFromGifData($image)
		: $format eq 'image/gd'   ? GD::Image->newFromGdData($image)
		: $format eq 'image/gd2'  ? GD::Image->newFromGd2Data($image)
		: $self->throw("This module cannot handle images of type $format");
  return $gd;
}

sub _guess_format {
  my $self = shift;
  my $path = shift;
  return 'image/png'   if $path =~ /\.png$/i;
  return 'image/jpeg'  if $path =~ /\.jpe?g$/i;
  return 'image/gif'   if $path =~ /\.gif(87)?$/i;
  return 'image/gd'    if $path =~ /\.gd$/i;
  return 'image/gd2'   if $path =~ /\.gd2$/i;
  my ($extension) = $path =~ /\.(\w+)$/;  #cop-out
  return $extension;
}

lib/Bio/Graphics/Glyph/image.pm  view on Meta::CPAN

    my $ua = LWP::UserAgent->new(env_proxy => 1);
    my $response = $ua->get($path);
    if ($response->is_success) {
      return ($response->content_type,$response->content);
    } else {
      $self->throw($response->status_line);
    }


  } else {
    my $content_type = $self->_guess_format($path);
    open F,$path or $self->throw("Can't open $path: $!");
    binmode F;
    my $data;
    $data .= $_ while read(F,$_,1024);
    close F;
    return ($content_type,$data);
  }
}

sub pad_left {

lib/Bio/Graphics/Glyph/processed_transcript.pm  view on Meta::CPAN

package Bio::Graphics::Glyph::processed_transcript;

use strict;
use base qw(Bio::Graphics::Glyph::transcript2);
use constant DEFAULT_UTR_COLOR => '#D0D0D0';

sub new {
  my $class = shift;
  my $self = $class->SUPER::new(@_);
  $self->guess_options if !defined $self->option('implied_utrs') 
    && !defined $self->option('adjust_exons');
  $self;
}

sub guess_options {
  my $self = shift;
  my ($exons,$utrs,$cds);
  foreach ($self->parts) {
    $exons++ if $_->feature->type =~ /exon/i;
    $utrs++  if $_->feature->type =~ /utr$/i;
    $cds++   if $_->feature->type =~ /^cds/i;
    $self->configure(implied_utrs=>1) if $exons && $cds && !$utrs;
    $self->configure(adjust_exons=>1) if $exons && $utrs;
  }
}

lib/Bio/Graphics/Glyph/trace.pm  view on Meta::CPAN

        return \%scf;
    }
    else{
        my %scf;
        tie %scf, 'Bio::SCF', $trace_file;
        $self->{'max_trace'} = 1600;
        return \%scf;
    }
}

sub _guess_format {
    my $self = shift;
    my $path = shift;

    my $modded_path = $path;
    $self->{'gzipped'} = ($modded_path =~ s/\.gz\s*$// );
    if ($modded_path =~ /\.scf/){
        $self->{'content_type'} = 'Bio::SCF';
    }
    elsif ($modded_path =~ /\.ab1/){
        $self->{'content_type'} = 'ABI';

lib/Bio/Graphics/Glyph/trace.pm  view on Meta::CPAN

    return unless $basename;
    return $basename if $basename =~ m!^\w+:/!;    # looks like a URL
    return $basename if $basename =~ m!^/!;        # looks like an abs path
    return "$dirname/$basename";
}

sub trace_data {
    my $self = shift;
    my $path = $self->trace_path;
    $self->_guess_format($path);

    if ( $path =~ m!^\w+:/! ) {                    # looks like a URL
        require LWP::UserAgent;
        my $ua       = LWP::UserAgent->new;
        my $response = $ua->get($path);
        if ( $response->is_success ) {

            # In the future, make extensible to ABI format
            my $data      = $response->content;
            my $signature = md5_hex($data);

scripts/contig_draw.pl  view on Meta::CPAN

Options:
 -i/--input        The input filename, otherwise input is assumed from STDIN
 -o/--output       The output filename, this is optional, if you do not
                   provide the output filename the script will create a file
                   using the name of the query sequence and will process
                   all the sequences in the file.  If an output filename
                   IS provided the script will only display an image for the 
                   first one.
 -f/--format       The SearchIO format parser to use, if not provided
                   SearchIO will guess based on the file extension.
 -l/--labels       Display the hit sequence name as a label in the overview.
                   For lots of sequences this will make the image very long
                   so by default it is turned off.

=head1 AUTHOR Jason Stajich

Jason Stajich, jason[-at-]open-bio[-dot-]org.

=cut

scripts/render_msa.pl  view on Meta::CPAN

use Bio::Tools::GuessSeqFormat;
use Getopt::Long;

my ($inputfile,$debug);

GetOptions(
	   'i|input|inputfile:s' => \$inputfile,
           'debug' => \$debug,
          );

my $guessed_format = new Bio::Tools::GuessSeqFormat
    (-file=>"$inputfile"
    )->guess;

my $aio = Bio::AlignIO->new(-file   => $inputfile,
                            -format => $guessed_format) or die "parse failed";

my $aln = $aio->next_aln() or die "no alignment";

my $panel = Bio::Graphics::Panel->new(
    -image_class => 'SVG',
    -length    => $aln->length,
    -width     => 800,
    -pad_left  => 150,
    -pad_right => 10,
);

scripts/search_overview.pl  view on Meta::CPAN

Options:
 -i/--input        The input filename, otherwise input is assumed from STDIN
 -o/--output       The output filename, this is optional, if you do not
                   provide the output filename the script will create a file
                   using the name of the query sequence and will process
                   all the sequences in the file.  If an output filename
                   IS provided the script will only display an image for the 
                   first one.
 -f/--format       The SearchIO format parser to use, if not provided
                   SearchIO will guess based on the file extension.
 -l/--labels       Display the hit sequence name as a label in the overview.
                   For lots of sequences this will make the image very long
                   so by default it is turned off.

=head1 AUTHOR Jason Stajich

Jason Stajich, jason[-at-]open-bio[-dot-]org.

=cut