| line |
true |
false |
branch |
|
393
|
3 |
2 |
if (@_) |
|
394
|
0 |
3 |
if (scalar @_ == 1) { } |
|
401
|
3 |
0 |
if (exists $options{'file'} or $options{'table'}) |
|
405
|
1 |
2 |
if (exists $options{'do_gene'}) |
|
408
|
3 |
0 |
if (exists $options{'do_exon'}) |
|
411
|
1 |
2 |
if (exists $options{'do_cds'}) |
|
414
|
1 |
2 |
if (exists $options{'do_utr'}) |
|
417
|
0 |
3 |
if (exists $options{'do_codon'}) |
|
420
|
0 |
3 |
if (exists $options{'do_name'}) |
|
423
|
0 |
3 |
if (exists $options{'share'}) |
|
426
|
0 |
3 |
if (exists $options{'source'}) |
|
429
|
0 |
3 |
if (exists $options{'refseqsum'}) { } |
|
|
0 |
3 |
elsif (exists $options{'summary'}) { } |
|
435
|
0 |
3 |
if (exists $options{'refseqstat'}) { } |
|
|
0 |
3 |
elsif (exists $options{'status'}) { } |
|
441
|
0 |
3 |
if (exists $options{'kgxref'}) |
|
444
|
0 |
3 |
if (exists $options{'ensembltogenename'}) { } |
|
|
0 |
3 |
elsif (exists $options{'ensname'}) { } |
|
450
|
0 |
3 |
if (exists $options{'ensemblsource'}) { } |
|
|
1 |
2 |
elsif (exists $options{'enssrc'}) { } |
|
456
|
2 |
1 |
if (exists $options{'class'}) |
|
472
|
5 |
118 |
if (@_) |
|
485
|
3 |
92 |
if (@_) |
|
493
|
4 |
89 |
if (@_) |
|
501
|
1 |
54 |
if (@_) |
|
509
|
1 |
52 |
if (@_) |
|
517
|
0 |
54 |
if (@_) |
|
525
|
0 |
231 |
if (@_) |
|
533
|
0 |
394 |
if (@_) |
|
541
|
7 |
227 |
if (@_) |
|
552
|
0 |
7 |
unless ($filename) |
|
558
|
0 |
7 |
unless my $fh = 'Bio::ToolBox::Data::file'->open_to_read_fh($filename) |
|
564
|
7 |
7 |
if $line =~ /^#/ |
|
565
|
0 |
7 |
unless $line =~ /\w+/ |
|
570
|
0 |
0 |
unless ($ncol == 16 or $ncol == 15 or $ncol == 12 or $ncol == 11 or $ncol == 10) |
|
574
|
0 |
7 |
if ($ncol == 10) |
|
584
|
5 |
2 |
if ($filename =~ /ensgene/i and $self->source eq 'UCSC') { } |
|
|
0 |
2 |
elsif ($filename =~ /xenorefgene/i and $self->source eq 'UCSC') { } |
|
|
0 |
2 |
elsif ($filename =~ /refgene/i and $self->source eq 'UCSC') { } |
|
|
0 |
2 |
elsif ($filename =~ /refseq/i and $self->source eq 'UCSC') { } |
|
|
0 |
4 |
elsif ($filename =~ /knowngene/i and $self->source eq 'UCSC') { } |
|
604
|
2 |
5 |
if ($self->fh) |
|
624
|
0 |
5 |
unless ($file) |
|
630
|
2 |
3 |
if ($type =~ /ensembltogene|ensname/i) { } |
|
|
3 |
0 |
elsif ($type =~ /ensemblsource|enssrc/i) { } |
|
|
0 |
0 |
elsif ($type =~ /refseqstat|status/i) { } |
|
|
0 |
0 |
elsif ($type =~ /refseqsum|summary/i) { } |
|
|
0 |
0 |
elsif ($type =~ /kgxref/i) { } |
|
651
|
0 |
5 |
unless ($fh) |
|
658
|
5 |
0 |
if ($type =~ /ensembl/) { } |
|
660
|
2 |
3 |
$type eq 'ensembltogene' ? : |
|
665
|
0 |
85 |
if $line =~ /^#/ |
|
667
|
0 |
85 |
if (scalar @line_data != 2) |
|
712
|
0 |
0 |
if $line =~ /^#/ |
|
720
|
0 |
0 |
if (exists $self->{$type}{$id}) |
|
739
|
0 |
0 |
if $self->{'counts'}{$k} > 0 |
|
741
|
0 |
3 |
if (@items) { } |
|
746
|
2 |
1 |
$self->do_gene ? : |
|
754
|
0 |
92 |
unless ($self->fh) |
|
760
|
27 |
87 |
if ($line =~ /^#/ or not $line =~ /\w+/) |
|
766
|
0 |
87 |
unless ($builder) |
|
774
|
70 |
17 |
if ($self->do_gene) { } |
|
792
|
0 |
25 |
unless ($self->{'eof'}) |
|
800
|
0 |
2 |
unless ($self->{'eof'}) |
|
804
|
2 |
0 |
wantarray ? : |
|
811
|
2 |
3 |
if (@_) |
|
812
|
0 |
2 |
unless $self->open_file(shift()) |
|
814
|
0 |
5 |
unless ($self->fh) |
|
818
|
0 |
5 |
if $self->{'eof'} |
|
826
|
85 |
0 |
unless ($gene) |
|
833
|
5 |
80 |
unless (exists $self->{'seq_ids'}{$s}) |
|
836
|
25 |
60 |
if $feature->end > $self->{'seq_ids'}{$s} |
|
843
|
0 |
0 |
unless $Bio::ToolBox::parser::ucsc::a->[0] cmp $Bio::ToolBox::parser::ucsc::b->[0] |
|
856
|
0 |
87 |
if (scalar @_ == 0) { } |
|
|
87 |
0 |
elsif (scalar @_ == 1) { } |
|
872
|
0 |
87 |
unless ($name) |
|
878
|
2 |
85 |
if (exists $self->{'gene2seqf'}{lc $name}) |
|
886
|
0 |
2 |
if ($id) |
|
888
|
0 |
0 |
if ($g->primary_id eq $id) |
|
894
|
0 |
0 |
if ($chrom and $start and $end) |
|
896
|
0 |
0 |
if ($g->strand == $strand and not $g->start > $end || $g->end < $start) |
|
910
|
2 |
0 |
if (scalar @$genes == 1) { } |
|
|
0 |
0 |
elsif (scalar @$genes > 1) { } |
|
927
|
2 |
0 |
wantarray ? : |
|
932
|
0 |
0 |
unless $string |
|
934
|
0 |
0 |
unless $builder |
|
935
|
0 |
0 |
if ($self->do_gene) { } |
|
946
|
0 |
0 |
wantarray ? : |
|
969
|
3 |
170 |
if ($ucsc->{'sfclass'} ne $SFCLASS) |
|
971
|
0 |
3 |
unless eval "require $SFCLASS" |
|
981
|
87 |
86 |
if (scalar @linedata == 16) { } |
|
|
0 |
86 |
elsif (scalar @linedata == 15) { } |
|
|
0 |
86 |
elsif (scalar @linedata == 12) { } |
|
|
0 |
86 |
elsif (scalar @linedata == 11) { } |
|
|
86 |
0 |
elsif (scalar @linedata == 10) { } |
|
1020
|
0 |
87 |
if ($linedata[1] =~ /^N[MR]_\d+/) |
|
1062
|
0 |
0 |
if ($linedata[0] =~ /^N[MR]_\d+/) |
|
1138
|
0 |
0 |
if ($linedata[1] =~ /^N[MR]_\d+/) |
|
1173
|
0 |
86 |
if ($linedata[0] =~ /^N[MR]_\d+/) |
|
1185
|
0 |
173 |
unless $self{'strand'} =~ /^[\+\-]$/ |
|
1186
|
0 |
173 |
unless $self{'txStart'} =~ /^\d+$/ |
|
1187
|
0 |
173 |
unless $self{'txEnd'} =~ /^\d+$/ |
|
1188
|
0 |
173 |
unless $self{'cdsStart'} =~ /^\d+$/ |
|
1189
|
0 |
173 |
unless $self{'cdsEnd'} =~ /^\d+$/ |
|
1190
|
0 |
173 |
unless $self{'exonCount'} =~ /^\d+$/ |
|
1191
|
0 |
173 |
unless $self{'exonStarts'} =~ /^[\d,]+$/ |
|
1192
|
0 |
173 |
unless $self{'exonEnds'} =~ /^[\d,]+$/ |
|
1193
|
0 |
173 |
if (@errors) |
|
1199
|
155 |
18 |
$self{'strand'} eq '+' ? : |
|
1206
|
63 |
110 |
if ($self{'cdsStart'} - 1 == $self{'cdsEnd'}) { } |
|
1211
|
21 |
42 |
if ($type) { } |
|
|
0 |
42 |
elsif ($self{'name2'} =~ /^mir/i) { } |
|
|
0 |
42 |
elsif ($self{'name2'} =~ /^snr/i) { } |
|
|
0 |
42 |
elsif ($self{'name2'} =~ /^sno/i) { } |
|
1237
|
32 |
78 |
defined $type ? : |
|
1300
|
0 |
243 |
exists $self->{'refseq'} ? : |
|
1305
|
243 |
0 |
exists $self->{'note'} ? : |
|
1310
|
173 |
0 |
exists $self->{'status'} ? : |
|
1315
|
173 |
0 |
exists $self->{'completeness'} ? : |
|
1332
|
48 |
22 |
if ($gene) { } |
|
1334
|
0 |
48 |
if ($self->txStart < $gene->start) |
|
1338
|
4 |
44 |
if ($self->txEnd > $gene->end) |
|
1359
|
0 |
22 |
if (exists $$id2count{lc $id}) { } |
|
1374
|
12 |
10 |
if ($self->name2 ne $self->gene_name) |
|
1402
|
0 |
173 |
if (exists $$id2count{lc $id}) { } |
|
1416
|
173 |
0 |
if (exists $$ensembldata{$self->name}) { } |
|
1418
|
26 |
147 |
if ($t and $t =~ /protein.coding/i) { } |
|
|
15 |
132 |
elsif ($t and $t =~ /rna|transcript/i) { } |
|
|
12 |
120 |
elsif ($t) { } |
|
1452
|
36 |
137 |
if ($self->gene_name ne $self->name2) |
|
1460
|
0 |
173 |
if (defined $self->completeness) |
|
1463
|
0 |
173 |
if (defined $self->status) |
|
1466
|
53 |
120 |
if ($biotype) |
|
1471
|
122 |
51 |
if ($ucsc->do_exon) |
|
1476
|
110 |
63 |
if ($self->cdsStart - 1 != $self->cdsEnd) |
|
1478
|
10 |
100 |
if ($ucsc->do_utr) |
|
1482
|
0 |
110 |
if ($ucsc->do_codon) |
|
1486
|
10 |
100 |
if ($ucsc->do_cds) |
|
1502
|
0 |
243 |
if (defined $self->note) |
|
1507
|
0 |
243 |
if (defined $self->refseq) |
|
1512
|
0 |
243 |
if (exists $self->{'spid'} and defined $self->{'spid'}) |
|
1517
|
0 |
243 |
if (exists $self->{'spdid'} and defined $self->{'spdid'}) |
|
1522
|
0 |
243 |
if (exists $self->{'protacc'} and defined $self->{'protacc'}) |
|
1533
|
0 |
0 |
if ($_ eq $value) |
|
1540
|
0 |
0 |
if $check |
|
1552
|
277 |
318 |
if ($ucsc->share and $gene) |
|
1555
|
156 |
121 |
if ($exon) |
|
1566
|
427 |
12 |
if ($transcript->strand == 1) { } |
|
1587
|
0 |
439 |
if ($ucsc->do_name) |
|
1608
|
76 |
0 |
if ($transcript->strand == 1) { } |
|
1626
|
0 |
76 |
if ($self->exonStarts->[$i] < $self->cdsStart and $self->exonEnds->[$i] > $self->cdsEnd) { } |
|
|
3 |
73 |
elsif ($self->exonStarts->[$i] < $self->cdsStart and $self->exonEnds->[$i] < $self->cdsStart) { } |
|
|
9 |
64 |
elsif ($self->exonStarts->[$i] < $self->cdsStart and $self->exonEnds->[$i] >= $self->cdsStart) { } |
|
|
50 |
14 |
elsif ($self->exonStarts->[$i] >= $self->cdsStart and $self->exonEnds->[$i] <= $self->cdsEnd) { } |
|
|
7 |
7 |
elsif ($self->exonStarts->[$i] <= $self->cdsEnd and $self->exonEnds->[$i] > $self->cdsEnd) { } |
|
|
7 |
0 |
elsif ($self->exonStarts->[$i] > $self->cdsEnd and $self->exonEnds->[$i] > $self->cdsEnd) { } |
|
1638
|
0 |
0 |
$transcript->strand == 1 ? : |
|
1643
|
0 |
0 |
$transcript->strand == 1 ? : |
|
1655
|
3 |
0 |
$transcript->strand == 1 ? : |
|
1668
|
9 |
0 |
$transcript->strand == 1 ? : |
|
1691
|
7 |
0 |
$transcript->strand == 1 ? : |
|
1704
|
7 |
0 |
$transcript->strand == 1 ? : |
|
1722
|
26 |
0 |
if ($ucsc->share and $gene) |
|
1727
|
19 |
7 |
unless ($utr) |
|
1738
|
0 |
19 |
if $ucsc->do_name |
|
1746
|
0 |
26 |
if ($start2) |
|
1750
|
0 |
0 |
if ($ucsc->share) |
|
1755
|
0 |
0 |
unless ($utr2) |
|
1766
|
0 |
0 |
if $ucsc->do_name |
|
1796
|
76 |
0 |
if ($transcript->strand == 1) { } |
|
1814
|
0 |
76 |
if ($self->exonStarts->[$j] < $self->cdsStart and $self->exonEnds->[$j] > $self->cdsEnd) { } |
|
|
3 |
73 |
elsif ($self->exonStarts->[$j] < $self->cdsStart and $self->exonEnds->[$j] < $self->cdsStart) { } |
|
|
9 |
64 |
elsif ($self->exonStarts->[$j] < $self->cdsStart and $self->exonEnds->[$j] >= $self->cdsStart) { } |
|
|
50 |
14 |
elsif ($self->exonStarts->[$j] >= $self->cdsStart and $self->exonEnds->[$j] <= $self->cdsEnd) { } |
|
|
7 |
7 |
elsif ($self->exonStarts->[$j] <= $self->cdsEnd and $self->exonEnds->[$j] > $self->cdsEnd) { } |
|
|
7 |
0 |
elsif ($self->exonStarts->[$j] > $self->cdsEnd and $self->exonEnds->[$j] > $self->cdsEnd) { } |
|
1912
|
46 |
20 |
if $phase > 2 |
|
1927
|
0 |
0 |
if ($transcript->strand == 1) { } |
|
1931
|
0 |
0 |
if ($ucsc->share and $gene) |
|
1939
|
0 |
0 |
unless ($start_codon) |
|
1950
|
0 |
0 |
if $ucsc->do_name |
|
1955
|
0 |
0 |
unless ($stop_codon) |
|
1966
|
0 |
0 |
if $ucsc->do_name |
|
1975
|
0 |
0 |
if ($ucsc->share and $gene) |
|
1983
|
0 |
0 |
unless ($stop_codon) |
|
1994
|
0 |
0 |
if $ucsc->do_name |
|
1999
|
0 |
0 |
unless ($start_codon) |
|
2011
|
0 |
0 |
if $ucsc->do_name |
|
2025
|
48 |
22 |
if (exists $self->ucsc->{'gene2seqf'}{lc $self->gene_name}) |
|
2037
|
48 |
0 |
if ($g->strand == $self->strand and not $g->start > $self->txEnd || $g->end < $self->txStart) |
|
2061
|
163 |
5189 |
if ($subfeature->primary_tag eq $type and $subfeature->start == $start and $subfeature->end == $stop) |