BioPerl

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Bio/DB/GFF.pm  view on Meta::CPAN

  my $self              = shift;
  my $file_or_directory = shift || '.';
  my $verbose           = shift;

  local $self->{__verbose__} = $verbose;
  return $self->do_load_gff($file_or_directory) if ref($file_or_directory) 
                                                   && tied *$file_or_directory;

  my $tied_stdin = tied(*STDIN);
  open my $SAVEIN, "<&STDIN" unless $tied_stdin;
  local @ARGV = $self->setup_argv($file_or_directory,'gff','gff3') or return;  # to play tricks with reader
  my $result = $self->do_load_gff('ARGV');
  open STDIN, '<', $SAVEIN unless $tied_stdin;  # restore STDIN
  return $result;
}

*load = \&load_gff;

=head2 load_gff_file

 Title   : load_gff_file

Bio/DB/GFF.pm  view on Meta::CPAN

  my $self              = shift;
  my $file_or_directory = shift || '.';
  my $verbose           = shift;

  local $self->{__verbose__} = $verbose;
  return $self->load_sequence($file_or_directory) if ref($file_or_directory)
                                                     && tied *$file_or_directory;

  my $tied = tied(*STDIN);
  open my $SAVEIN, "<&STDIN" unless $tied;
  local @ARGV = $self->setup_argv($file_or_directory,'fa','dna','fasta') or return;  # to play tricks with reader
  my $result = $self->load_sequence('ARGV');
  open STDIN, '<', $SAVEIN unless $tied;  # restore STDIN
  return $result;
}


=head2 load_fasta_file

 Title   : load_fasta_file
 Usage   : $db->load_fasta_file($file [,$verbose]);

maintenance/check_NAME.pl  view on Meta::CPAN

    
    my $fname = $_;
    my $pm = $File::Find::name;
    $pm =~ s{.*?/(?=Bio/)}{};  # remove up to first slash before Bio/
    $pm =~ s{\.pm$}{};         # remove .pm suffix
    $pm =~ s{/}{::}g;          # convert / to ::
    
    print STDERR "# $File::Find::name\n" if $verbose;
    
    # slurp in the file
    my $text = do { local( @ARGV, $/ ) = $fname ; <> } ;

    # check if the NAME section has the _full_ module name in it
    if ($text !~ m/^=head1\s+NAME.*?^$pm/xms) {
      print "$pm\n";
      $num_found++;
    }
}


=head1 OPTIONS

maintenance/check_URLs.pl  view on Meta::CPAN

#

sub find_modules {
    # only want files with .pm
    return unless m/\.pm$/;
    return unless -f $_;
    
    my $fname = $_;
    
    # slurp in the file
    my $text = do { local( @ARGV, $/ ) = $fname ; <> } ;
    
    # keep track of URLs
    while ($text =~ m/$RE{URI}{HTTP}{-keep}/g) {
        my $url = $1 or next;
        # remove Perl code if URL was embedded in string and other stuff
        $url =~ s/\s*[.,;'")]*\s*$//;
        check_url($url, $File::Find::name);
    }    
}

scripts/Bio-DB-GFF/bp_genbank2gff.pl  view on Meta::CPAN

			   @dsn,
			   @auth,
			   -preferred_tags => \%preferred_tags,
			   -source=> $SOURCE || 'Genbank')
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";

if ($CREATE) {
  $db->initialize(1);
}

die "you must specify either an accession to retrieve from\nembl or a local file containing data in embl format\n" if (($FILE || $ACC) && !scalar(@ARGV));

if ($ACC) {
  while ($_ = shift) {
    status(loading => $_);
    my $result = $db->load_from_embl(/^NC_/?'refseq':'embl' => $_);
    status(done    => $result);
  }
  exit 1;
}