| line |
!l |
l&&!r |
l&&r |
condition |
|
1136
|
33 |
5 |
7 |
$args{'file'} and $args{'parse'} |
|
|
32 |
1 |
0 |
exists $args{'db'} and $args{'features'} |
|
1142
|
0 |
0 |
5 |
$self->database =~ /^Parsed:(.+)$/ and $self->feature_type eq "named" |
|
1173
|
0 |
0 |
0 |
$exclusion_Data and $exclusion_Data->feature_type eq "coordinate" |
|
1200
|
31 |
0 |
0 |
exists $args{'gff'} and $args{'gff'} |
|
|
31 |
0 |
0 |
exists $args{'bed'} and $args{'bed'} |
|
|
31 |
0 |
0 |
exists $args{'ucsc'} and $args{'ucsc'} |
|
1219
|
0 |
0 |
0 |
$args{'bed'} =~ /^\d{1,2}$/ and $args{'bed'} >= 3 |
|
1278
|
12 |
0 |
0 |
exists $args->{'simplify'} && defined $args->{'simplify'} |
|
1336
|
12 |
1 |
0 |
lc $feature eq "mrna" and not $parser->typelist =~ /mrna/i |
|
|
13 |
0 |
0 |
lc $feature eq "mrna" and not $parser->typelist =~ /mrna/i and not $self->last_row |
|
1388
|
7 |
0 |
0 |
$mrna_check and is_coding($f) |
|
1510
|
0 |
40 |
313 |
$_[0] and ref $_[0] eq "ARRAY" |
|
|
0 |
0 |
40 |
$_[0] and ref $_[0] eq "Bio::ToolBox::Data::Feature" |
|
|
0 |
0 |
0 |
$_[0] and $_[0] =~ /\t/ |
|
1542
|
4 |
0 |
5 |
exists $self->{'SeqFeatureObjects'} and defined $self->{'SeqFeatureObjects'}[$row_number] |
|
1573
|
0 |
0 |
272 |
defined $row and defined $column |
|
1603
|
0 |
0 |
178 |
defined $row_i and ref $seqfeature |
|
1766
|
0 |
0 |
1 |
defined $v and not $v =~ m[^(?:\.|n/?a|nan|\-?inf)$]i |
|
1951
|
0 |
0 |
1 |
$part and $total_parts |
|
2118
|
0 |
0 |
0 |
$args{'dataset'} and ref $args{'dataset'} eq "ARRAY" |
|
|
0 |
0 |
0 |
$args{'dataset'} and ref $args{'dataset'} eq "SCALAR" |
|
2125
|
0 |
0 |
0 |
$args{'startcolumn'} and ref $args{'startcolumn'} eq "ARRAY" |
|
|
0 |
0 |
0 |
$args{'startcolumn'} and ref $args{'startcolumn'} eq "SCALAR" |
|
2133
|
0 |
0 |
0 |
$args{'endcolumn'} and ref $args{'endcolumn'} eq "ARRAY" |
|
|
0 |
0 |
0 |
$args{'endcolumn'} and ref $args{'endcolumn'} eq "SCALAR" |
|
2250
|
0 |
0 |
0 |
$do_percentile and substr($self->name($column), -2) eq "bp" |
|
2331
|
88 |
60 |
0 |
exists $self->{'data'}{'SeqFeatureObjects'} and defined $self->{'data'}{'SeqFeatureObjects'}[$i] |
| line |
l |
!l |
condition |
|
1119
|
3 |
43 |
$args{'feature'} || 'gene' |
|
1120
|
0 |
45 |
$args{'Stream'} || 0 |
|
1121
|
1 |
33 |
$args{'in'} || undef |
|
1122
|
7 |
39 |
$args{'parse'} ||= 0 |
|
1123
|
0 |
46 |
$args{'noheader'} ||= 0 |
|
1138
|
2 |
5 |
$args{'subfeature'} ||= "" |
|
1167
|
0 |
1 |
$args{'exclude'} || undef |
|
1199
|
0 |
31 |
$args{'datasets'} || undef |
|
1274
|
12 |
0 |
$args->{'file'} || '' |
|
1275
|
7 |
5 |
$args->{'feature'} || '' |
|
1276
|
2 |
10 |
$args->{'subfeature'} || '' |
|
1379
|
0 |
2 |
$args->{'chrskip'} || undef |
|
1607
|
165 |
13 |
$self->{'SeqFeatureObjects'} ||= [] |
|
1653
|
0 |
0 |
$self->value($i, $name_i) || undef |
|
|
0 |
0 |
$self->value($i, $type_i) || undef |
|
|
0 |
0 |
$self->value($i, $id_i) || undef |
|
1669
|
0 |
0 |
shift() || 'exon' |
|
1726
|
0 |
0 |
$self->value($i, $name_i) || undef |
|
|
0 |
0 |
$self->value($i, $type_i) || undef |
|
|
0 |
0 |
$self->value($i, $id_i) || undef |
|
1750
|
1 |
0 |
shift() || 'i' |
|
1911
|
77 |
1 |
$chrom2row{$c} ||= [] |
|
2116
|
0 |
0 |
$args{'filename'} || undef |
|
2169
|
0 |
0 |
$self->metadata($i, 'dataset') || undef |
|
2172
|
0 |
0 |
$possibles{$d} ||= [] |
|
2263
|
0 |
0 |
$self->metadata($column, 'log2') || 0 |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
1119
|
0 |
46 |
0 |
$args{'features'} ||= $args{'feature'} || 'gene' |
|
1120
|
1 |
0 |
45 |
$args{'stream'} ||= $args{'Stream'} || 0 |
|
1121
|
12 |
1 |
33 |
$args{'file'} ||= $args{'in'} || undef |
|
1167
|
0 |
0 |
1 |
$args{'blacklist'} ||= $args{'exclude'} || undef |
|
1199
|
1 |
0 |
31 |
$args{'columns'} ||= $args{'datasets'} || undef |
|
1388
|
113 |
0 |
7 |
$f->type =~ /$feature/i or $mrna_check and is_coding($f) |
|
1486
|
0 |
0 |
31 |
$self->gff or $self->bed |
|
|
0 |
0 |
31 |
$self->gff or $self->bed or $self->ucsc |
|
|
0 |
0 |
31 |
$self->gff or $self->bed or $self->ucsc or $self->vcf |
|
1714
|
0 |
0 |
0 |
$length || $feature->length |
|
1733
|
0 |
0 |
0 |
$length || $feature->length |
|
1868
|
0 |
0 |
1 |
$direction eq "i" or $direction eq "I" |
|
|
1 |
0 |
0 |
$direction eq "d" or $direction eq "D" |
|
1905
|
1 |
0 |
0 |
$self->stop_column || $start_i |
|
2132
|
0 |
0 |
0 |
$args{'endcolumn'} ||= $args{'stopcolumn'} |