BioPerl
view release on metacpan - search on metacpan
view release on metacpan or search on metacpan
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__
view all matches for this distributionview release on metacpan - search on metacpan
( run in 4.636 seconds using v1.00-cache-2.02-grep-82fe00e-cpan-d29e8ade9f55 )