Condition Coverage

blib/lib/Bio/ToolBox/parser/ucsc.pm
Criterion Covered Total %
condition 71 193 36.7


and 3 conditions

line !l l&&!r l&&r condition
584 0 2 5 $filename =~ /ensgene/i and $self->source eq "UCSC"
2 0 0 $filename =~ /xenorefgene/i and $self->source eq "UCSC"
2 0 0 $filename =~ /refgene/i and $self->source eq "UCSC"
2 0 0 $filename =~ /refseq/i and $self->source eq "UCSC"
2 0 0 $filename =~ /knowngene/i and $self->source eq "UCSC"
894 2 0 0 $chrom and $start
2 0 0 $chrom and $start and $end
896 0 0 0 $g->strand == $strand and not $g->start > $end || $g->end < $start
1418 120 27 26 $t and $t =~ /protein.coding/i
120 12 15 $t and $t =~ /rna|transcript/i
1512 243 0 0 exists $self->{'spid'} and defined $self->{'spid'}
1517 243 0 0 exists $self->{'spdid'} and defined $self->{'spdid'}
1522 243 0 0 exists $self->{'protacc'} and defined $self->{'protacc'}
1552 229 89 277 $ucsc->share and $gene
1626 64 12 0 $self->exonStarts->[$i] < $self->cdsStart and $self->exonEnds->[$i] > $self->cdsEnd
64 9 3 $self->exonStarts->[$i] < $self->cdsStart and $self->exonEnds->[$i] < $self->cdsStart
64 0 9 $self->exonStarts->[$i] < $self->cdsStart and $self->exonEnds->[$i] >= $self->cdsStart
0 14 50 $self->exonStarts->[$i] >= $self->cdsStart and $self->exonEnds->[$i] <= $self->cdsEnd
7 0 7 $self->exonStarts->[$i] <= $self->cdsEnd and $self->exonEnds->[$i] > $self->cdsEnd
0 0 7 $self->exonStarts->[$i] > $self->cdsEnd and $self->exonEnds->[$i] > $self->cdsEnd
1722 0 0 26 $ucsc->share and $gene
1814 64 12 0 $self->exonStarts->[$j] < $self->cdsStart and $self->exonEnds->[$j] > $self->cdsEnd
64 9 3 $self->exonStarts->[$j] < $self->cdsStart and $self->exonEnds->[$j] < $self->cdsStart
64 0 9 $self->exonStarts->[$j] < $self->cdsStart and $self->exonEnds->[$j] >= $self->cdsStart
0 14 50 $self->exonStarts->[$j] >= $self->cdsStart and $self->exonEnds->[$j] <= $self->cdsEnd
7 0 7 $self->exonStarts->[$j] <= $self->cdsEnd and $self->exonEnds->[$j] > $self->cdsEnd
0 0 7 $self->exonStarts->[$j] > $self->cdsEnd and $self->exonEnds->[$j] > $self->cdsEnd
1931 0 0 0 $ucsc->share and $gene
1975 0 0 0 $ucsc->share and $gene
2037 0 0 48 $g->strand == $self->strand and not $g->start > $self->txEnd || $g->end < $self->txStart
2061 2932 5123 229 $subfeature->primary_tag eq $type and $subfeature->start == $start
8055 66 163 $subfeature->primary_tag eq $type and $subfeature->start == $start and $subfeature->end == $stop

or 2 conditions

line l !l condition
865 0 0 $opt{'name'} || $opt{'display_name'} || undef
866 0 0 $opt{'id'} || $opt{'primary_id'} || undef
867 0 0 $opt{'chrom'} || $opt{'seq_id'} || undef
868 0 0 $opt{'start'} || undef
869 0 0 $opt{'stop'} || $opt{'end'} || undef
870 0 0 $opt{'strand'} || 0
1014 87 0 $linedata[12] || undef
1015 51 0 $ucsc->{'ensembldata'}{$linedata[1]}[0] || $linedata[12] || undef
1017 0 87 $ucsc->{'refseqsum'}{$linedata[1]}[1] || undef
1018 0 87 $ucsc->{'refseqstat'}{$linedata[1]}[0] || undef
1019 0 87 $ucsc->{'refseqsum'}{$linedata[1]}[0] || undef
1056 0 0 $linedata[11] || undef
1057 0 0 $ucsc->{'ensembldata'}{$linedata[0]}[0] || $linedata[11] || undef
1059 0 0 $ucsc->{'refseqsum'}{$linedata[0]}[1] || undef
1060 0 0 $ucsc->{'refseqstat'}{$linedata[0]}[0] || undef
1061 0 0 $ucsc->{'refseqsum'}{$linedata[0]}[0] || undef
1098 0 0 $ucsc->{'kgxref'}{$linedata[0]}[6] || undef
1099 0 0 $ucsc->{'kgxref'}{$linedata[0]}[4] || undef
1100 0 0 $ucsc->{'refseqstat'}{$self{'refseq'}}[0] || undef
1101 0 0 $ucsc->{'refseqsum'}{$self{'refseq'}}[0] || undef
1102 0 0 $ucsc->{'kgxref'}{$linedata[0]}[1] || undef
1103 0 0 $ucsc->{'kgxref'}{$linedata[0]}[2] || undef
1104 0 0 $ucsc->{'kgxref'}{$linedata[0]}[5] || undef
1122 0 0 $ucsc->{'ensembldata'}{$linedata[1]}[0] || $linedata[0] || undef
1135 0 0 $ucsc->{'refseqsum'}{$linedata[1]}[1] || undef
1136 0 0 $ucsc->{'refseqstat'}{$linedata[1]}[0] || undef
1137 0 0 $ucsc->{'refseqsum'}{$linedata[1]}[0] || undef
1170 0 86 $ucsc->{'refseqsum'}{$linedata[0]}[1] || undef
1171 0 86 $ucsc->{'refseqstat'}{$linedata[0]}[0] || undef
1172 0 86 $ucsc->{'refseqsum'}{$linedata[0]}[0] || undef
1204 53 120 $ucsc->{'ensembldata'}{$self{'name'}}[1] || undef
1417 53 120 $$ensembldata{$self->name}[1] || undef

or 3 conditions

line l !l&&r !l&&!r condition
401 3 0 0 exists $options{'file'} or $options{'table'}
402 3 0 0 $options{'file'} ||= $options{'table'}
570 7 0 0 $ncol == 16 or $ncol == 15
7 0 0 $ncol == 16 or $ncol == 15 or $ncol == 12
0 0 0 $ncol == 16 or $ncol == 15 or $ncol == 12 or $ncol == 11
0 0 0 $ncol == 16 or $ncol == 15 or $ncol == 12 or $ncol == 11 or $ncol == 10
760 27 0 87 $line =~ /^#/ or not $line =~ /\w+/
896 0 0 0 $g->start > $end || $g->end < $start
1083 0 0 0 $ucsc->{'kgxref'}{$linedata[0]}[0] || $linedata[0]
1096 0 0 0 $ucsc->{'kgxref'}{$linedata[0]}[3] || $ucsc->{'kgxref'}{$linedata[0]}[0] || $ucsc->{'kgxref'}{$linedata[0]}[4] || $linedata[0]
2037 0 0 48 $g->start > $self->txEnd || $g->end < $self->txStart