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bin/tag-loc-ids.pl  view on Meta::CPAN

    my %new_id_for;
    my $org = join "_", (split "_", $infile)[0,1];

    my $report_file = file($infile);
    my $report = Table->new( file => $report_file );

    HIT:
    # loop through first hits for each query
    while (my $hit = $report->next_query) {

        # consider only hits over percent_id threshold
        next HIT if $hit->percent_identity < $ARGV_percent_id;

        # strict check of length unless percent_id filter only
        unless ($ARGV_pid_only) {
            next HIT
                unless ( $hit->query_end - $hit->query_start )
                    == (   $hit->hit_end -   $hit->hit_start )
            ;
        }

        my $seq_id = SeqId->new( full_id => $hit->hit_id );
        my $query_id = $hit->query_id;
           $query_id =~ s/_/ /xms;

bin/tag-loc-ids.pl  view on Meta::CPAN

=over

=item --in[-strip]=<str>

Substring(s) to strip from infile basenames before attempting to derive other
infile (e.g., IDM files) and outfile names [default: none].

=for Euclid: str.type: string
    repeatable

=item --percent-id=<n>

Min percentage identity to consider a hit.

=for Euclid: n.type: n
    n.default: 99

=item --fasta[-suffix]=<suffix>

Suffix to append to infile basenames for deriving outfile names [default:
none]. When not specified, outfile names are taken from infiles but original
infiles are preserved by being appended a .bak suffix.