Branch Coverage

blib/lib/Bio/ToolBox/GeneTools.pm
Criterion Covered Total %
branch 122 362 33.7


line true false branch
608 0 102 unless ref($transcript) =~ /seqfeature/i
616 682 690 if ($type =~ /exon/i) { }
690 0 elsif ($type =~ /cds|utr|untranslated/i) { }
0 0 elsif ($type =~ /rna|transcript/i) { }
630 102 0 if (@exons) { }
0 0 elsif (@cdss) { }
0 0 elsif (@transcripts) { }
651 0 0 if (defined $list[$i + 1])
652 0 0 if ($list[$i + 1]->start - $list[$i]->end <= 1)
669 0 0 unless $Bio::ToolBox::GeneTools::a->[1] <=> $Bio::ToolBox::GeneTools::b->[1]
678 102 0 wantarray ? :
685 1 14 if $k eq 'common'
686 1 13 if $k eq 'uncommon'
689 1 0 if (@alts)
695 1 0 wantarray ? :
700 1 0 wantarray ? :
705 1 0 wantarray ? :
717 0 42 unless ref($transcript) =~ /seqfeature/i
722 0 42 unless @exons
723 0 42 if scalar @exons == 1
729 42 0 if ($transcript->strand >= 0) { }
767 0 0 if (@introns)
769 0 0 unless $Bio::ToolBox::GeneTools::a->[1] <=> $Bio::ToolBox::GeneTools::b->[1]
776 42 0 wantarray ? :
783 1 14 if $k eq 'common'
784 1 13 if $k eq 'uncommon'
787 1 0 if (@alts)
793 1 0 wantarray ? :
798 1 0 wantarray ? :
803 1 0 wantarray ? :
814 0 6 unless @_
815 6 0 if (scalar @_ == 1) { }
0 0 elsif (scalar @_ > 1) { }
817 0 6 unless ref($_[0]) =~ /seqfeature/i
832 0 6 unless @transcripts
835 0 6 if (scalar @transcripts == 1)
838 0 0 $do_exon ? :
846 39 39 $do_exon ? :
860 81 84 if (scalar @names == 1) { }
0 84 elsif (scalar @names == $trx_number) { }
883 0 9 unless $gene
884 0 9 unless ref($gene) =~ /seqfeature/i
885 0 9 if $gene->primary_tag =~ /rna|transcript/i
890 106 0 if ($subf->primary_tag =~ /rna|transcript|\bprocessed/i) { }
0 0 elsif ($subf->primary_tag =~ /^(?:cds|exon|\w+codon)$/i) { }
901 0 9 if (not @transcripts and @exons) { }
0 18 elsif (not @transcripts || @exons and @other) { }
922 0 217 unless $Bio::ToolBox::GeneTools::a->[1] <=> $Bio::ToolBox::GeneTools::b->[1]
925 9 0 wantarray ? :
931 0 1 unless @_
933 0 1 if (scalar @_ == 1) { }
1 0 elsif (scalar @_ > 1) { }
936 0 0 unless @transcripts
937 0 0 if scalar @transcripts == 1
951 0 1 unless (@exons)
957 0 1 unless @exons
961 0 324 unless $Bio::ToolBox::GeneTools::a->[1] <=> $Bio::ToolBox::GeneTools::b->[1]
981 5 79 if ($ns == $os and $ne > $oe) { }
0 79 elsif ($ns > $os and $ns < $oe and $ne > $oe) { }
13 66 elsif ($ns > $oe) { }
1017 0 4 unless ref($transcript) =~ /seqfeature/i
1018 0 4 if ($transcript->primary_tag =~ /gene$/i)
1040 0 3 unless $transcript
1041 0 3 unless ref($transcript) =~ /seqfeature/i
1042 0 3 if ($transcript->primary_tag =~ /gene$/i)
1050 1 2 if $transcript->primary_tag =~ /mrna/i
1051 0 2 if $transcript->source =~ /protein.?coding/i
1052 0 2 if ($transcript->has_tag('transcript_biotype')) { }
2 0 elsif ($transcript->has_tag('biotype')) { }
0 0 elsif ($transcript->has_tag('gene_biotype')) { }
1055 0 0 $biotype =~ /protein.?coding/i ? :
1060 0 2 $biotype =~ /protein.?coding/i ? :
1067 0 0 if $biotype =~ /protein.?coding/i
1071 0 0 if $_->primary_tag eq 'CDS'
1078 0 13 unless $transcript
1079 0 13 unless ref($transcript) =~ /seqfeature/i
1082 43 127 if $subfeat->primary_tag eq 'CDS'
1084 6 7 unless @cds
1089 1 6 wantarray ? :
1094 0 4 unless ref($transcript) =~ /seqfeature/i
1096 2 2 unless $cds
1097 2 0 if ($transcript->strand >= 0) { }
1103 0 0 if ($codon) { }
1104 0 0 $codon->start < $cds->[0]->start ? :
1115 0 4 unless ref($transcript) =~ /seqfeature/i
1117 2 2 unless $cds
1118 2 0 if ($transcript->strand >= 0) { }
1120 2 0 if ($codon) { }
1121 0 2 $codon->end > $cds->[-1]->end ? :
1134 0 4 unless ref($transcript) =~ /seqfeature/i
1137 40 13 unless $subf->primary_tag eq 'CDS'
1145 0 0 unless ref($transcript) =~ /seqfeature/i
1150 0 0 if $subfeat->primary_tag =~ /start.?codon/i
1152 0 0 if $start_codon
1156 0 0 unless $cdss
1157 0 0 if ($transcript->strand >= 0) { }
1186 0 2 unless ref($transcript) =~ /seqfeature/i
1191 0 37 if $subfeat->primary_tag =~ /stop.?codon/i
1193 0 2 if $stop_codon
1199 0 2 unless $cdss
1200 2 0 if ($transcript->strand >= 0) { }
1229 0 13 unless ref($transcript) =~ /seqfeature/i
1238 104 120 if ($type =~ /exon/i) { }
78 42 elsif ($type =~ /cds/i) { }
42 0 elsif ($type =~ /utr|untranslated/i) { }
0 0 elsif ($type =~ /rna|transcript/i) { }
1254 12 1 if (@utrs) { }
0 1 elsif (@transcripts) { }
0 1 elsif (@exons and @cdss) { }
1280 0 0 if ($exon->end < $firstCDS->start) { }
0 0 elsif ($exon->overlaps($firstCDS)) { }
0 0 elsif ($exon->start > $firstCDS->end and $exon->end < $lastCDS->start) { }
0 0 elsif ($exon->overlaps($lastCDS)) { }
0 0 elsif ($exon->start > $lastCDS->end) { }
1283 0 0 $transcript->strand >= 0 ? :
1291 0 0 unless $pieces
1293 0 0 $transcript->strand >= 0 ? :
1307 0 0 unless $pieces
1309 0 0 $transcript->strand >= 0 ? :
1319 0 0 $transcript->strand >= 0 ? :
1336 2 10 wantarray ? :
1341 0 2 unless ref($transcript) =~ /seqfeature/i
1352 0 4 unless ref($transcript) =~ /seqfeature/i
1356 0 4 unless scalar @$utrs
1359 2 2 wantarray ? :
1364 0 4 unless ref($transcript) =~ /seqfeature/i
1368 0 4 unless scalar @$utrs
1371 2 2 wantarray ? :
1406 0 0 unless ref($feature) =~ /seqfeature/i
1409 0 0 if ($feature->primary_tag =~ /gene$/i and not defined $gene)
1419 0 0 unless @exons
1423 0 0 if ($gene) { }
1442 0 0 if ($gene_biotype)
1447 0 0 if ($biotype)
1451 0 0 if ($tsl)
1463 0 0 unless $Bio::ToolBox::GeneTools::a->[1] <=> $Bio::ToolBox::GeneTools::b->[1]
1466 0 0 defined $subf->score ? :
0 0 $subf->strand < 0 ? :
0 0 defined $subf->phase ? :
1485 0 0 unless ref($feature) =~ /seqfeature/i
1489 0 0 if ($feature->primary_tag =~ /gene$/i) { }
0 0 elsif ($feature->primary_tag =~ /rna|transcript/i) { }
1493 0 0 if $ucsc
1499 0 0 if $ucsc
1527 0 0 unless ref($feature) =~ /seqfeature/i
1531 0 0 if ($feature->primary_tag =~ /gene$/i) { }
0 0 elsif ($feature->primary_tag =~ /rna|transcript/i) { }
1535 0 0 if $ucsc
1541 0 0 if $ucsc
1578 0 0 unless $gene
1584 0 0 if (ref($gene) =~ /seqfeature/i) { }
0 0 elsif (ref $gene eq 'ARRAY') { }
1593 0 0 unless @transcripts
1605 0 0 if ($min_tsl eq 'best') { }
0 0 elsif ($min_tsl =~ /^best(\d)$/) { }
0 0 elsif ($min_tsl =~ /^\d$/) { }
0 0 elsif ($min_tsl eq 'NA') { }
1608 0 0 if (scalar @{$results{$tsl};})
1618 0 0 if (scalar @{$results{$tsl};})
1619 0 0 if ($tsl <= $max) { }
0 0 elsif (not @keepers and $tsl > $max) { }
1629 0 0 if (scalar @keepers == 0 and scalar @{$results{'NA'};}) { }
0 0 elsif (scalar @keepers == 0 and scalar @{$results{'Missing'};}) { }
1647 0 0 unless @keepers
1655 0 0 unless $gene
1659 0 0 if (ref($gene) =~ /seqfeature/i) { }
0 0 elsif (ref $gene eq 'ARRAY') { }
1668 0 0 unless @transcripts
1674 0 0 if ($basic and $basic eq 'basic')
1686 0 1 unless $gene
1688 0 1 unless $check
1692 1 0 if (ref($gene) =~ /seqfeature/i) { }
0 0 elsif (ref $gene eq 'ARRAY') { }
1701 0 1 unless @transcripts
1709 2 11 if ($value and $value =~ /$check/i)
1728 0 0 $transcript->strand < 0 ? :
1744 0 0 if ($gene) { }
1754 0 0 if (is_coding($transcript)) { }
1757 0 0 if ($start and $stop) { }
1787 1 0 if (ref($gene) =~ /seqfeature/i) { }
1789 0 1 if ($gene->primary_tag =~ /transcript|rna/i)