view release on metacpan or  search on metacpan

bin/prune-outliers.pl  view on Meta::CPAN

        for (my $t = $ARGV_min_ident; $t <= $ARGV_max_ident; $t += 0.1) {

            my @ids
                = grep { ($count_for{$_} / keys %count_for) >= $t }
                  grep {  $count_for{$_} >= $ARGV_min_hits } keys %count_for
            ;

            ### threshold: $t . ' - ' . scalar @ids . ' seqs kept out of ' . scalar keys %count_for

            my $ali = Ali->load($infile);
            $ali->dont_guess if $ARGV_noguessing;

            my $list = IdList->new( ids => \@ids );
            my $new_ali = $list->filtered_ali($ali);

            # create output dirs named after input dir and identity threshold
            my $subdir = dir( $outdir, $t )->relative;
            $subdir->mkpath();

            # store Ali in corresponding dir
            my ($filename) = fileparse($infile);

bin/prune-outliers.pl  view on Meta::CPAN

    n.default: 0.8

=item --min-hits=<n> | --min_hits=<n>

Minimum number of hits in the all-versus-all BLAST searches required for a
sequence to be retained in the output file [default: n.default].

=for Euclid: n.type: num
    n.default: 10

=item --[no]guessing

[Don't] guess whether sequences are aligned or not [default: yes].

=item --version

=item --usage

=item --help

=item --man

Print the usual program information