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scripts/biosql/load_seqdatabase.pl  view on Meta::CPAN

        }
        $seqin->sequence_builder->add_object_condition($condition);
    }

    # chain to pipeline if pipelining is requested
    if(@pipemods) {
        $pipemods[0]->source_stream($seqin);
        $seqin = $pipemods[-1];
    }

    # reset entry counter and timer
    $n_entries = 0;
    $time = time();

    # loop over the stream
    while( my $seq = $seqin->$nextobj ) {
        # increment entry counter
        $n_entries++;

        # report progress if enabled
        if (($logchunk > 0) && (($n_entries % $logchunk) == 0)) {

scripts/biosql/terms/add-term-annot.pl  view on Meta::CPAN

    if(! ref($fh)) {
        $fh = gensym;
        my $fspec = $uncompress ? "gunzip -c $file |" : "<$file";
        if(! open($fh, $fspec)) {
            warn "unable to open $file for reading, skipping: $!\n";
            next;
        }
        print STDERR "Loading $file ...\n";
    }

    # reset entry counter and timer
    $n_entries = 0;
    $time = time();

    # loop over the stream
    while (my $line = <$fh>) {
        
        chomp($line);

        if ($line =~ /^##\s*(\w+):\s*(.*)/) {
            # processing instruction line

t/lib/Test/Harness.pm  view on Meta::CPAN

=item C<HARNESS_PERL_SWITCHES>

Its value will be prepended to the switches used to invoke perl on
each test.  For example, setting C<HARNESS_PERL_SWITCHES> to C<-W> will
run all tests with all warnings enabled.

=item C<HARNESS_TIMER>

Setting this to true will make the harness display the number of
milliseconds each test took.  You can also use F<prove>'s C<--timer>
switch.

=item C<HARNESS_VERBOSE>

If true, Test::Harness will output the verbose results of running
its tests.  Setting C<$Test::Harness::verbose> will override this,
or you can use the C<-v> switch in the F<prove> utility.

If true, Test::Harness will output the verbose results of running
its tests.  Setting C<$Test::Harness::verbose> will override this,