| Bio/Map/Gene.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| condition | 41 | 94 | 43.6 |
| line | !l | l&&!r | l&&r | condition |
|---|---|---|---|---|
| 163 | 0 | 4 | 6 | $u_name and defined $Bio::Map::Gene::GENES->{$u_name} |
| 351 | 0 | 0 | 320 | $map and $self->in_map($map) |
| 381 | 0 | 0 | 2 | $pos and $pos->isa('Bio::Map::GenePosition') |
| 438 | 0 | 0 | 3 | $int > 0 and $int <= @transcripts |
| 499 | 95 | 0 | 4 | @transcripts == 0 and $value == 0 |
| 617 | 11 | 0 | 9 | @exons == 0 and $exon_num == 1 |
| 755 | 0 | 0 | 0 | $trans_ref and @{$trans_ref;} > 0 |
| 857 | 276 | 4 | 37 | defined $transcript_number and $transcript_number == 0 |
| 909 | 0 | 0 | 110 | $wanted and $wanted > 0 |
| 912 | 0 | 1 | 107 | $index >= 0 and $index <= $#list |
| 921 | 0 | 0 | 6 | $pos and $pos->isa('Bio::Map::GenePosition') |
| 930 | 0 | 0 | 0 | $self->warn('no transcript pos end for pos for gene ' . $self->universal_name . ' and species ' . $pos->map->species . '!') and exit |
| 931 | 0 | 0 | 0 | $self->warn('no pos end for pos for gene ' . $self->universal_name . ' and species ' . $pos->map->species . '!') and exit |
| 947 | 1 | 0 | 0 | ref $thing and $thing->isa('Bio::Map::GeneMap') |
| 951 | 1 | 0 | 0 | $map and $map->isa('Bio::Map::GeneMap') |
| line | l | !l | condition |
|---|---|---|---|
| 536 | 0 | 12 | $transcript_num ||= 0 |
| 541 | 2 | 0 | $thing->map || (return) |
| 592 | 3 | 19 | $value ||= 0 |
| 660 | 1 | 4 | $value ||= 0 |
| 732 | 9 | 0 | $self->universal_name || (return 0) |
| 737 | 0 | 0 | 'Bio::Tools::Run::Ensembl'->get_adaptor($species, 'Slice') || (return 0) |
| 738 | 0 | 0 | 'Bio::Tools::Run::Ensembl'->get_gene_by_name('-species', $species, '-name', $gene_name, '-use_orthologues', 'Homo sapiens', '-use_swiss_lookup', 1, '-use_entrez_lookup', 1) || (return 0) |
| 867 | 41 | 0 | $pos->relative || (next) |
| 945 | 1 | 0 | $self->{$type}{'general'} || '' |
| 948 | 0 | 0 | $self->{$type}{$thing} || '' |
| 964 | 7 | 0 | $map->unique_id || (return) |
| line | l | !l&&r | !l&&!r | condition |
|---|---|---|---|---|
| 383 | 2 | 0 | 0 | $pos->map || $self->throw('Supplied GenePosition has no map') |
| 497 | 9 | 86 | 4 | $value ||= $self->active_transcript($map) |
| 552 | 11 | 1 | 0 | $pos || $self->get_transcript_position($thing, $transcript_num) |
| 733 | 0 | 0 | 9 | $SET_FROM_DB or $self->{'_set_from_db'} |
| 869 | 0 | 41 | 0 | $rel->transcript || $self->active_transcript($map) |
| 923 | 6 | 0 | 0 | $pos->map || $self->throw('Supplied GenePosition has no map') |
| 926 | 2 | 0 | 0 | $self->active_transcript($map) || $self->throw('Asked to be relative to the active transcript, but there is no transcript') |
| 4 | 2 | 0 | $transcript_num ||= $self->active_transcript($map) || $self->throw('Asked to be relative to the active transcript, but there is no transcript') | |
| 929 | 6 | 0 | 0 | $self->get_transcript_position($map, $transcript_num) || $self->throw("Asked to be relative to transcript $transcript_num, but there is no such transcript") |