BioPerl

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Bio/SeqIO/ace.pm  view on Meta::CPAN

=cut

{
    my %bio_mol_type = (
        'dna'       => 'dna',
        'peptide'   => 'protein',
    );

    sub next_seq {
        my( $self ) = @_;
        local $/ = "";  # Split input on blank lines

        my $fh = $self->_filehandle;
        my( $type, $id );
        while (<$fh>) {
            if (($type, $id) = /^(DNA|Peptide)[\s:]+(.+?)\s*\n/si) {
                s/^.+$//m;  # Remove first line
                s/\s+//g;   # Remove whitespace
                last;
            }
        }

Bio/Tools/FootPrinter.pm  view on Meta::CPAN

 Title   : _parse_predictions
 Usage   : my $r = $footprint->_parse_predictions
 Function: do the parsing 
 Returns : none 
 Args    : none

=cut

sub _parse_predictions {
  my ($self) = @_;
  $/="";
  my ($seq,$second,$third,$name);
  while ($_ = $self->_readline) {
    chomp;
    my @array = split("\n",$_);
    if ($#array == 5) {
      # get rid of header
      shift(@array); shift(@array);
    }
    if($#array == 3){
        if($name){

maintenance/authors.pl  view on Meta::CPAN

feeling too lazy to change the code.

=cut

sub blankline {
    my ($file) = @_;
    return unless ($file =~ /\.PLS$/ or $file =~ /\.p[ml]$/);
    return unless -e $file;

    open my $F, '<', $file or warn "Could not read file '$file': $!\n" && return;
    local $/ = "";
    while (my $line = <$F>) {
        print "$file: +|$1|\n"  if $line =~ /[ \t]\n(=[a-z][^\n]+$)/m and $verbose;
        print "$file: ++|$1|\n" if $line =~ /\w\n(=[a-z][^\n]+$)/m    and $verbose;
        print "$file:|$1|+\n"   if $line =~ /(^=[a-z][^\n]+)\n[\t ]/m;
        #print "$file:|$1|++\n" if /(^=[^\n]+)\n\w/m;
    }
    close $F;
}

__END__

maintenance/authors.pl  view on Meta::CPAN

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

=cut


# find . -name '*.pm' -print | xargs  perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|"  if  /(\s\s^=[^\n]+$)/m ; }'  ;

# find . -name '*.pm' -print | xargs  perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|\n"  if /(^=[^\n]+\n[\t ])/m ; }'  ;

maintenance/pod.pl  view on Meta::CPAN

See: L<perlpodspec>


=cut

sub blankline {
    return unless /\.PLS$/ or /\.p[ml]$/ ;
    return unless -e $_;
    my $file = $_;
    open (F, $_) or warn "can't open file $_: $!" && return;
    local $/="";
    while (<F>) {
        print "$file: +|$1|\n" if /[ \t]\n(=[a-z][^\n]+$)/m and $verbose;
        print "$file: ++|$1|\n" if /\w\n(=[a-z][^\n]+$)/m and $verbose;
        print "$file:|$1|+\n" if /(^=[a-z][^\n]+)\n[\t ]/m;
        #print "$file:|$1|++\n" if /(^=[^\n]+)\n\w/m;
    }
    close F;
}

__END__

maintenance/pod.pl  view on Meta::CPAN

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

=cut


# find . -name '*.pm' -print | xargs  perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|"  if  /(\s\s^=[^\n]+$)/m ; }'  ;

# find . -name '*.pm' -print | xargs  perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|\n"  if /(^=[^\n]+\n[\t ])/m ; }'  ;

scripts/utilities/bp_netinstall.pl  view on Meta::CPAN

  print STDERR "Adding needed PPM repositories. This may take a while....\n";
  for my $name (keys %REPOSITORIES) {
     next if $repository{$name};
     system("ppm rep add $name $REPOSITORIES{$name}");
  }
}

sub find_bioperl_ppm {
  print STDERR "Finding most recent bioperl...";
  open my $S,"ppm search bioperl |" or die "Could not open ppm for listing: $!\n";
  local $/ = ''; # paragraph mode
  my ($blessed_one, $blessed_version);
  my $best = 0;
  while (my $line = <$S>) {
    chomp $line;
    my ($number)     = ($line =~ /^(\d+): bioperl/m);
    my ($version)    = ($line =~ /^\s+Version: (.+)/m);
    my ($repository) = ($line =~ /^\s+Repo: (.+)/m);
    my $multiplier = 10000000;
    my $magnitude  = 0;
    # this dumb thing converts 1.5.1 into a real number