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bin/annotate-ali.pl  view on Meta::CPAN

use Tie::IxHash;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(secure_outfile);
use Bio::MUST::Drivers;


# TODO: add support for prebuilt reference database (e.g. nr)

# convert fractional identity threshold to percentage (see Euclid)
$ARGV_identity *= 100.0 if 0 < $ARGV_identity && $ARGV_identity <= 1;

### Building database: $ARGV_ref_file
my $blastdb = Bio::MUST::Drivers::Blast::Database::Temporary->new(
    seqs => $ARGV_ref_file
);

for my $infile (@ARGV_infiles) {

    ### Processing: $infile

bin/annotate-ali.pl  view on Meta::CPAN

    } );

    #### Parsing BLAST report...
    tie my %ann_for,    'Tie::IxHash';
    tie my %hit_id_for, 'Tie::IxHash';
    my $curr_id = q{};

    HIT:
    while ( my $hit = $parser->next_hit ) {
        my ($qid, $hid, $evalue, $identity)
            = map { $hit->$_ } qw(query_id hit_id evalue percent_identity);

        next HIT if $identity < $ARGV_identity;     # skip weak-identity hits

        unless ($ARGV_hit_list) {
            next HIT if $qid eq $curr_id;           # skip non-first hits
            $curr_id = $qid;
        }

        # capture annotation bit in ref seq id using regex
        my ($annotation) = $blastdb->long_id_for($hid) =~ $ARGV_ref_regex;

bin/annotate-ali.pl  view on Meta::CPAN

E-value threshold for annotating a sequence [default: 1e-10].

=for Euclid: float.type: number
    float.default: 1e-10

=item --identity [=] <number>

Identity threshold for annotating a sequence [default: 0]. When specified as a
fraction between 0 and 1 (included), it is first multiplied by 100 to be
interpreted in percentage.

=for Euclid: number.type: number
    number.default: 0

=item --max-hits [=] <number>

Number of hits to return for each query (BLAST -max_target_seqs option)
[default: 10]. Mostly useful in conjunction with the C<--hit-list> option.

=for Euclid: number.type: number