| line |
true |
false |
branch |
|
1114
|
25 |
21 |
if (ref $class) |
|
1126
|
1 |
45 |
if ($args{'stream'}) |
|
1136
|
7 |
38 |
if ($args{'file'} and $args{'parse'}) { } |
|
|
5 |
33 |
elsif ($args{'file'}) { } |
|
|
1 |
32 |
elsif (exists $args{'db'} and $args{'features'}) { } |
|
1139
|
5 |
2 |
unless ($self->parse_table(\%args)) |
|
1141
|
0 |
5 |
unless $l |
|
1142
|
5 |
0 |
if ($self->database =~ /^Parsed:(.+)$/ and $self->feature_type eq "named") |
|
1154
|
0 |
5 |
unless ($self->load_file($args{'file'}, $args{'noheader'})) |
|
1164
|
1 |
0 |
if ($args{'features'} eq 'genome') { } |
|
1168
|
0 |
1 |
if (defined $args{'blacklist'}) |
|
1173
|
0 |
0 |
if ($exclusion_Data and $exclusion_Data->feature_type eq 'coordinate') { } |
|
1190
|
0 |
1 |
unless ($result) |
|
1200
|
1 |
31 |
if (defined $args{'columns'}) { } |
|
|
0 |
31 |
elsif (exists $args{'gff'} and $args{'gff'}) { } |
|
|
0 |
31 |
elsif (exists $args{'bed'} and $args{'bed'}) { } |
|
|
0 |
31 |
elsif (exists $args{'ucsc'} and $args{'ucsc'}) { } |
|
1204
|
0 |
1 |
if exists $args{'feature'} |
|
1212
|
0 |
0 |
unless ($self->extension =~ /g[tf]f/) |
|
1214
|
0 |
0 |
$args{'gff'} == 3 ? : |
|
|
0 |
0 |
$args{'gff'} == 2.5 ? : |
|
1219
|
0 |
0 |
unless ($args{'bed'} =~ /^\d{1,2}$/ and $args{'bed'} >= 3) |
|
1224
|
0 |
0 |
unless ($self->extension =~ /bed|peak/) |
|
1231
|
0 |
0 |
unless ($u) |
|
1235
|
0 |
0 |
unless ($self->extension =~ /ucsc|ref+lat|genepred/) |
|
1249
|
0 |
1 |
unless my $Dupe = $self->new("columns", $columns) |
|
1273
|
12 |
6 |
if (ref $args) { } |
|
1278
|
0 |
12 |
exists $args->{'simplify'} && defined $args->{'simplify'} ? : |
|
1288
|
0 |
18 |
unless ($file) |
|
1294
|
5 |
13 |
unless my($flavor, $format) = $self->taste_file($file) |
|
1297
|
0 |
13 |
if ($@) |
|
1304
|
0 |
13 |
unless my $parser = $class->new |
|
1305
|
0 |
13 |
unless $parser->open_file($file) |
|
1309
|
6 |
7 |
unless ($feature) |
|
1310
|
2 |
4 |
if ($typelist =~ /gene/i) { } |
|
|
3 |
1 |
elsif ($typelist eq 'region') { } |
|
1323
|
2 |
11 |
if ($subfeature) |
|
1324
|
1 |
1 |
if $subfeature =~ /exon/i |
|
1325
|
1 |
1 |
if $subfeature =~ /cds/i |
|
1326
|
0 |
2 |
if $subfeature =~ /utr|untranslated/i |
|
1327
|
0 |
2 |
if $subfeature =~ /codon/i |
|
1329
|
4 |
9 |
if ($feature =~ /gene$/i) { } |
|
1336
|
0 |
1 |
if (lc $feature eq "mrna" and not $parser->typelist =~ /mrna/i and not $self->last_row) |
|
1345
|
0 |
13 |
unless $parser->parse_file |
|
1348
|
5 |
8 |
if ($self->last_row > 0) { } |
|
1357
|
65 |
0 |
if ($f) |
|
1362
|
0 |
5 |
unless ($count == $self->last_row) |
|
1378
|
2 |
6 |
if ($args) |
|
1384
|
0 |
120 |
if ($chr_exclude) |
|
1385
|
0 |
0 |
if $f->seq_id =~ /$chr_exclude/i |
|
1388
|
113 |
7 |
if ($f->type =~ /$feature/i or $mrna_check and is_coding($f)) |
|
1393
|
0 |
8 |
unless ($self->last_row) |
|
1399
|
0 |
8 |
if $chr_exclude |
|
1418
|
0 |
2 |
unless defined $column |
|
1419
|
0 |
2 |
unless exists $self->{$column}{'name'} |
|
1421
|
0 |
2 |
wantarray ? : |
|
1426
|
0 |
31 |
unless $name |
|
1431
|
2 |
29 |
if ($name_ref eq 'ARRAY') { } |
|
|
0 |
29 |
elsif ($name_ref eq 'Bio::DB::GFF::Typename') { } |
|
|
29 |
0 |
elsif ($name_ref eq '') { } |
|
1432
|
2 |
0 |
if ($self->last_row > 1) { } |
|
1434
|
2 |
0 |
if ($self->last_row == scalar @$name - 1) { } |
|
1485
|
0 |
31 |
if exists $self->{'column_indices'} |
|
1486
|
0 |
31 |
if ($self->gff or $self->bed or $self->ucsc or $self->vcf) |
|
1496
|
0 |
1 |
unless defined $index |
|
1510
|
313 |
40 |
if ($_[0] and ref $_[0] eq 'ARRAY') { } |
|
|
40 |
0 |
elsif ($_[0] and ref $_[0] eq 'Bio::ToolBox::Data::Feature') { } |
|
|
0 |
0 |
elsif ($_[0] and $_[0] =~ /\t/) { } |
|
1522
|
0 |
353 |
if (scalar @row_data > $self->{'number_columns'}) |
|
1537
|
0 |
9 |
unless defined $self->{'data_table'}[$row_number] |
|
1542
|
5 |
4 |
if (exists $self->{'SeqFeatureObjects'} and defined $self->{'SeqFeatureObjects'}[$row_number]) |
|
1558
|
0 |
1 |
if (exists $self->{'SeqFeatureObjects'}) |
|
1568
|
237 |
0 |
wantarray ? : |
|
1573
|
0 |
272 |
unless defined $row and defined $column |
|
1574
|
0 |
272 |
if (defined $value) |
|
1588
|
0 |
6 |
unless (ref $code eq "CODE") |
|
1603
|
0 |
178 |
unless (defined $row_i and ref $seqfeature) |
|
1606
|
0 |
178 |
unless $row_i <= $self->last_row |
|
1614
|
0 |
0 |
unless $row_i <= $self->last_row |
|
1615
|
0 |
0 |
unless $self->{'SeqFeatureObjects'} |
|
1621
|
0 |
0 |
unless ($self->feature_type eq "named") |
|
1629
|
0 |
0 |
if ($@) |
|
1636
|
0 |
0 |
if (exists $self->{'SeqFeatureObjects'}) { } |
|
1639
|
0 |
0 |
unless my $feature = $self->{'SeqFeatureObjects'}[$i] |
|
1640
|
0 |
0 |
unless my $collSeqFeat = collapse_transcripts($feature) |
|
1647
|
0 |
0 |
unless my $db = $self->open_meta_database(1) |
|
1653
|
0 |
0 |
unless my $feature = get_db_feature("db", $db, "name", $self->value($i, $name_i) || undef, "type", $self->value($i, $type_i) || undef, "id", $self->value($i, $id_i) || undef) |
|
1659
|
0 |
0 |
unless my $collSeqFeat = collapse_transcripts($feature) |
|
1670
|
0 |
0 |
unless (exists $self->{'SeqFeatureObjects'}) |
|
1678
|
0 |
0 |
if ($@) |
|
1686
|
0 |
0 |
if ($subfeature eq 'exon') { } |
|
|
0 |
0 |
elsif ($subfeature eq 'cds') { } |
|
|
0 |
0 |
elsif ($subfeature eq '5p_utr') { } |
|
|
0 |
0 |
elsif ($subfeature eq '3p_utr') { } |
|
1709
|
0 |
0 |
if (exists $self->{'SeqFeatureObjects'}) { } |
|
1712
|
0 |
0 |
unless my $feature = $self->{'SeqFeatureObjects'}[$i] |
|
1720
|
0 |
0 |
unless my $db = $self->open_meta_database(1) |
|
1726
|
0 |
0 |
unless my $feature = get_db_feature("db", $db, "name", $self->value($i, $name_i) || undef, "type", $self->value($i, $type_i) || undef, "id", $self->value($i, $id_i) || undef) |
|
1753
|
0 |
1 |
unless exists $self->{$index}{'name'} |
|
1754
|
0 |
1 |
unless ($direction =~ /^[id]/i) |
|
1766
|
1 |
0 |
if (defined $v and not $v =~ m[^(?:\.|n/?a|nan|\-?inf)$]i) |
|
1775
|
1 |
0 |
if ($example =~ /[a-z]/i) { } |
|
|
0 |
0 |
elsif ($example =~ /^\-?\d+\.?\d*$/) { } |
|
1799
|
0 |
1 |
if ($sortmethod eq 'numeric') { } |
|
|
1 |
0 |
elsif ($sortmethod eq 'ascii') { } |
|
1819
|
0 |
0 |
if ($direction =~ /^i/i) { } |
|
1848
|
0 |
78 |
if (exists $datahash{$value}) { } |
|
1868
|
0 |
1 |
if ($direction eq 'i' or $direction eq 'I') { } |
|
|
1 |
0 |
elsif ($direction eq 'd' or $direction eq 'D') { } |
|
1899
|
0 |
1 |
unless ($self->feature_type eq "coordinate") |
|
1925
|
0 |
1 |
if ($self->gff) { } |
|
1931
|
0 |
0 |
unless $Bio::ToolBox::Data::a->[0] <=> $Bio::ToolBox::Data::b->[0] |
|
1940
|
0 |
209 |
unless $Bio::ToolBox::Data::a->[0] <=> $Bio::ToolBox::Data::b->[0] |
|
1951
|
0 |
1 |
unless ($part and $total_parts) |
|
1957
|
0 |
1 |
if (exists $self->{'SeqFeatureObjects'}) |
|
1965
|
0 |
1 |
if ($part == 1) { } |
|
|
1 |
0 |
elsif ($part == $total_parts) { } |
|
1971
|
0 |
0 |
if (exists $self->{'SeqFeatureObjects'}) |
|
1985
|
0 |
1 |
if (exists $self->{'SeqFeatureObjects'}) |
|
2009
|
0 |
0 |
if (exists $self->{'SeqFeatureObjects'}) |
|
2026
|
0 |
1 |
if (exists $self->{'db_connection'}) |
|
2039
|
0 |
1 |
unless @files |
|
2044
|
0 |
1 |
if ($@) |
|
2052
|
0 |
1 |
unless ($Stream) |
|
2088
|
0 |
2 |
if ($Stream->number_columns != $self->number_columns) |
|
2118
|
0 |
0 |
if ($args{'dataset'} and ref $args{'dataset'} eq 'ARRAY') { } |
|
|
0 |
0 |
elsif ($args{'dataset'} and ref $args{'dataset'} eq 'SCALAR') { } |
|
2125
|
0 |
0 |
if ($args{'startcolumn'} and ref $args{'startcolumn'} eq 'ARRAY') { } |
|
|
0 |
0 |
elsif ($args{'startcolumn'} and ref $args{'startcolumn'} eq 'SCALAR') { } |
|
2133
|
0 |
0 |
if ($args{'endcolumn'} and ref $args{'endcolumn'} eq 'ARRAY') { } |
|
|
0 |
0 |
elsif ($args{'endcolumn'} and ref $args{'endcolumn'} eq 'SCALAR') { } |
|
2142
|
0 |
0 |
unless ($self->verify) |
|
2146
|
0 |
0 |
unless (defined $outfile) |
|
2147
|
0 |
0 |
if ($self->basename) { } |
|
2168
|
0 |
0 |
unless (exists $skip{lc $self->{$i}{'name'}}) |
|
2170
|
0 |
0 |
if (defined $d) { } |
|
2183
|
0 |
0 |
unless (@datasets) |
|
2184
|
0 |
0 |
if (scalar keys %possibles > 1) |
|
2193
|
0 |
0 |
if (scalar @startcolumns != scalar @datasets) |
|
2202
|
0 |
0 |
if (scalar @endcolumns != scalar @datasets) |
|
2246
|
0 |
0 |
if (substr($self->name($column), -1) eq "%") |
|
2250
|
0 |
0 |
if ($do_percentile and substr($self->name($column), -2) eq "bp") |
|
2259
|
0 |
0 |
$v eq '.' ? : |
|
2264
|
0 |
0 |
if ($log) |
|
2270
|
0 |
0 |
if ($log) |
|
2275
|
0 |
0 |
if ($d == 0) { } |
|
2282
|
0 |
0 |
if ($summed_data->value($row, 1) != $midpoint) |
|
2324
|
6 |
148 |
if $self->{'index'} > $self->{'data'}{'last_row'} |
|
2331
|
0 |
148 |
if (exists $self->{'data'}{'SeqFeatureObjects'} and defined $self->{'data'}{'SeqFeatureObjects'}[$i]) |
|
2342
|
0 |
0 |
if @_ |