| blib/lib/Bio/ToolBox/GeneTools.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| condition | 16 | 88 | 18.1 |
| line | l | !l | condition |
|---|---|---|---|
| 1629 | 0 | 0 | scalar @keepers == 0 and scalar @{$results{'NA'};} |
| 0 | 0 | scalar @keepers == 0 and scalar @{$results{'Missing'};} |
| line | !l | l&&!r | l&&r | condition |
|---|---|---|---|---|
| 901 | 9 | 0 | 0 | not @transcripts and @exons |
| 9 | 0 | 0 | not @transcripts || @exons and @other | |
| 981 | 37 | 42 | 5 | $ns == $os and $ne > $oe |
| 42 | 13 | 24 | $ns > $os and $ns < $oe | |
| 55 | 24 | 0 | $ns > $os and $ns < $oe and $ne > $oe | |
| 1254 | 0 | 1 | 0 | @exons and @cdss |
| 1280 | 0 | 0 | 0 | $exon->start > $firstCDS->end and $exon->end < $lastCDS->start |
| 1409 | 0 | 0 | 0 | $feature->primary_tag =~ /gene$/i and not defined $gene |
| 1619 | 0 | 0 | 0 | not @keepers and $tsl > $max |
| 1674 | 0 | 0 | 0 | $basic and $basic eq 'basic' |
| 1709 | 0 | 11 | 2 | $value and $value =~ /$check/i |
| 1757 | 0 | 0 | 0 | $start and $stop |
| line | l | !l | condition |
|---|---|---|---|
| 1405 | 0 | 0 | shift() || undef |
| 1426 | 0 | 0 | $gene->get_tag_values('gene_biotype') || $gene->get_tag_values('biotype') || undef |
| 1431 | 0 | 0 | $feature->get_tag_values('gene_id') || undef |
| 1432 | 0 | 0 | $feature->get_tag_values('gene_name') || undef |
| 1433 | 0 | 0 | $feature->get_tag_values('gene_biotype') || undef |
| 1466 | 0 | 0 | $subf->seq_id || '.' |
| 0 | 0 | $subf->source_tag || '.' | |
| 1579 | 0 | 0 | shift() || 'best' |
| 1599 | 0 | 0 | $tsl ||= 'Missing' |
| 1725 | 0 | 0 | shift() || undef |
| 1728 | 0 | 0 | $transcript->score || 1000 |
| 1791 | 0 | 0 | $keepers->[0] ||= undef |
| line | l | !l&&r | !l&&!r | condition |
|---|---|---|---|---|
| 901 | 9 | 0 | 0 | @transcripts || @exons |
| 1424 | 0 | 0 | 0 | $gene->primary_id || $gene->display_name |
| 1435 | 0 | 0 | 0 | $feature->primary_id || $feature->display_name |
| 1445 | 0 | 0 | 0 | $feature->get_tag_values('transcript_biotype') || $feature->get_tag_values('biotype') |
| 1706 | 0 | 13 | 0 | $t->get_tag_values('transcript_biotype') || $t->get_tag_values('biotype') |
| 1708 | 13 | 0 | 0 | $value ||= $t->primary_tag |
| 1728 | 0 | 0 | 0 | $transcript->display_name || $transcript->primary_id |
| 1746 | 0 | 0 | 0 | $gene->display_name || $gene->primary_id |