| line |
true |
false |
branch |
|
1114
|
1 |
44 |
if ($args{'stream'}) |
|
1124
|
7 |
37 |
if ($args{'file'} and $args{'parse'}) { } |
|
|
5 |
32 |
elsif ($args{'file'}) { } |
|
|
0 |
32 |
elsif (exists $args{'db'} and $args{'features'}) { } |
|
1127
|
5 |
2 |
unless ($self->parse_table(\%args)) |
|
1129
|
0 |
5 |
unless $l |
|
1130
|
5 |
0 |
if ($self->database =~ /^Parsed:(.+)$/ and $self->feature_type eq 'named') |
|
1142
|
0 |
5 |
unless ($self->load_file($args{'file'}, $args{'noheader'})) |
|
1152
|
0 |
0 |
if ($args{'features'} eq 'genome') { } |
|
1158
|
0 |
0 |
unless ($result) |
|
1168
|
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'}) { } |
|
1172
|
0 |
1 |
if exists $args{'feature'} |
|
1180
|
0 |
0 |
unless ($self->extension =~ /g[tf]f/) |
|
1182
|
0 |
0 |
$args{'gff'} == 3 ? : |
|
|
0 |
0 |
$args{'gff'} == 2.5 ? : |
|
1187
|
0 |
0 |
unless ($args{'bed'} =~ /^\d{1,2}$/ and $args{'bed'} >= 3) |
|
1192
|
0 |
0 |
unless ($self->extension =~ /bed|peak/) |
|
1199
|
0 |
0 |
unless ($u) |
|
1203
|
0 |
0 |
unless ($self->extension =~ /ucsc|ref+lat|genepred/) |
|
1217
|
0 |
1 |
unless my $Dupe = $self->new('columns', $columns) |
|
1241
|
12 |
6 |
if (ref $args) { } |
|
1246
|
0 |
12 |
exists $args->{'simplify'} && defined $args->{'simplify'} ? : |
|
1256
|
0 |
18 |
unless ($file) |
|
1262
|
5 |
13 |
unless my $flavor = $self->taste_file($file) |
|
1265
|
0 |
13 |
if ($@) |
|
1271
|
0 |
13 |
unless my $parser = $class->new |
|
1272
|
0 |
13 |
unless $parser->open_file($file) |
|
1276
|
6 |
7 |
unless ($feature) |
|
1277
|
2 |
4 |
if ($typelist =~ /gene/i) { } |
|
|
3 |
1 |
elsif ($typelist eq 'region') { } |
|
1290
|
2 |
11 |
if ($subfeature) |
|
1291
|
1 |
1 |
if $subfeature =~ /exon/i |
|
1292
|
1 |
1 |
if $subfeature =~ /cds/i |
|
1293
|
0 |
2 |
if $subfeature =~ /utr|untranslated/i |
|
1294
|
0 |
2 |
if $subfeature =~ /codon/i |
|
1296
|
4 |
9 |
if ($feature =~ /gene$/i) { } |
|
1303
|
0 |
1 |
if (lc $feature eq 'mrna' and not $parser->typelist =~ /mrna/i and not $self->last_row) |
|
1312
|
0 |
13 |
unless $parser->parse_file |
|
1315
|
5 |
8 |
if ($self->last_row > 0) { } |
|
1324
|
65 |
0 |
if ($f) |
|
1329
|
0 |
5 |
unless ($count == $self->last_row) |
|
1345
|
2 |
6 |
if ($args) |
|
1351
|
0 |
120 |
if ($chr_exclude) |
|
1352
|
0 |
0 |
if $f->seq_id =~ /$chr_exclude/i |
|
1355
|
113 |
7 |
if ($f->type =~ /$feature/i or $mrna_check and is_coding($f)) |
|
1360
|
0 |
8 |
unless ($self->last_row) |
|
1366
|
0 |
8 |
if $chr_exclude |
|
1385
|
0 |
2 |
unless defined $column |
|
1386
|
0 |
2 |
unless exists $self->{$column}{'name'} |
|
1388
|
0 |
2 |
wantarray ? : |
|
1393
|
0 |
28 |
unless $name |
|
1398
|
2 |
26 |
if ($name_ref eq 'ARRAY') { } |
|
|
0 |
26 |
elsif ($name_ref eq 'Bio::DB::GFF::Typename') { } |
|
|
26 |
0 |
elsif ($name_ref eq '') { } |
|
1399
|
2 |
0 |
if ($self->last_row > 1) { } |
|
1401
|
2 |
0 |
if ($self->last_row == scalar @$name - 1) { } |
|
1452
|
0 |
28 |
if exists $self->{'column_indices'} |
|
1453
|
0 |
28 |
if ($self->gff or $self->bed or $self->ucsc or $self->vcf) |
|
1463
|
0 |
1 |
unless defined $index |
|
1477
|
191 |
40 |
if ($_[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/) { } |
|
1489
|
0 |
231 |
if (scalar @row_data > $self->{'number_columns'}) |
|
1504
|
0 |
5 |
unless defined $self->{'data_table'}[$row_number] |
|
1509
|
4 |
1 |
if (exists $self->{'SeqFeatureObjects'} and defined $self->{'SeqFeatureObjects'}[$row_number]) |
|
1525
|
0 |
1 |
if (exists $self->{'SeqFeatureObjects'}) |
|
1535
|
237 |
0 |
wantarray ? : |
|
1540
|
0 |
508 |
unless defined $row and defined $column |
|
1541
|
0 |
508 |
if (defined $value) |
|
1555
|
0 |
6 |
unless (ref $code eq 'CODE') |
|
1570
|
0 |
178 |
unless (defined $row_i and ref $seqfeature) |
|
1573
|
0 |
178 |
unless $row_i <= $self->last_row |
|
1581
|
0 |
0 |
unless $row_i <= $self->last_row |
|
1582
|
0 |
0 |
unless $self->{'SeqFeatureObjects'} |
|
1588
|
0 |
0 |
unless ($self->feature_type eq 'named') |
|
1596
|
0 |
0 |
if ($@) |
|
1603
|
0 |
0 |
if (exists $self->{'SeqFeatureObjects'}) { } |
|
1606
|
0 |
0 |
unless my $feature = $self->{'SeqFeatureObjects'}[$i] |
|
1607
|
0 |
0 |
unless my $collSeqFeat = collapse_transcripts($feature) |
|
1614
|
0 |
0 |
unless my $db = $self->open_meta_database(1) |
|
1620
|
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) |
|
1626
|
0 |
0 |
unless my $collSeqFeat = collapse_transcripts($feature) |
|
1637
|
0 |
0 |
unless (exists $self->{'SeqFeatureObjects'}) |
|
1645
|
0 |
0 |
if ($@) |
|
1653
|
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') { } |
|
1676
|
0 |
0 |
if (exists $self->{'SeqFeatureObjects'}) { } |
|
1679
|
0 |
0 |
unless my $feature = $self->{'SeqFeatureObjects'}[$i] |
|
1687
|
0 |
0 |
unless my $db = $self->open_meta_database(1) |
|
1693
|
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) |
|
1720
|
0 |
1 |
unless exists $self->{$index}{'name'} |
|
1721
|
0 |
1 |
unless ($direction =~ /^[id]/i) |
|
1733
|
1 |
0 |
if (defined $v and not $v =~ m[^(?:\.|n/?a|nan|\-?inf)$]i) |
|
1742
|
1 |
0 |
if ($example =~ /[a-z]/i) { } |
|
|
0 |
0 |
elsif ($example =~ /^\-?\d+\.?\d*$/) { } |
|
1766
|
0 |
1 |
if ($sortmethod eq 'numeric') { } |
|
|
1 |
0 |
elsif ($sortmethod eq 'ascii') { } |
|
1786
|
0 |
0 |
if ($direction =~ /^i/i) { } |
|
1815
|
0 |
78 |
if (exists $datahash{$value}) { } |
|
1835
|
0 |
1 |
if ($direction eq 'i' or $direction eq 'I') { } |
|
|
1 |
0 |
elsif ($direction eq 'd' or $direction eq 'D') { } |
|
1866
|
0 |
1 |
unless ($self->feature_type eq 'coordinate') |
|
1888
|
0 |
78 |
if ($self->value($row, $chromo_i) =~ /^(?:chr)?(\d+)$/) { } |
|
1944
|
0 |
1 |
unless ($part and $total_parts) |
|
1950
|
0 |
1 |
if (exists $self->{'SeqFeatureObjects'}) |
|
1958
|
0 |
1 |
if ($part == 1) { } |
|
|
1 |
0 |
elsif ($part == $total_parts) { } |
|
1964
|
0 |
0 |
if (exists $self->{'SeqFeatureObjects'}) |
|
1978
|
0 |
1 |
if (exists $self->{'SeqFeatureObjects'}) |
|
2002
|
0 |
0 |
if (exists $self->{'SeqFeatureObjects'}) |
|
2019
|
0 |
1 |
if (exists $self->{'db_connection'}) |
|
2032
|
0 |
1 |
unless @files |
|
2037
|
0 |
1 |
if ($@) |
|
2045
|
0 |
1 |
unless ($Stream) |
|
2081
|
0 |
2 |
if ($Stream->number_columns != $self->number_columns) |
|
2111
|
0 |
0 |
if ($args{'dataset'} and ref $args{'dataset'} eq 'ARRAY') { } |
|
|
0 |
0 |
elsif ($args{'dataset'} and ref $args{'dataset'} eq 'SCALAR') { } |
|
2118
|
0 |
0 |
if ($args{'startcolumn'} and ref $args{'startcolumn'} eq 'ARRAY') { } |
|
|
0 |
0 |
elsif ($args{'startcolumn'} and ref $args{'startcolumn'} eq 'SCALAR') { } |
|
2126
|
0 |
0 |
if ($args{'endcolumn'} and ref $args{'endcolumn'} eq 'ARRAY') { } |
|
|
0 |
0 |
elsif ($args{'endcolumn'} and ref $args{'endcolumn'} eq 'SCALAR') { } |
|
2135
|
0 |
0 |
unless ($self->verify) |
|
2139
|
0 |
0 |
unless (defined $outfile) |
|
2140
|
0 |
0 |
if ($self->basename) { } |
|
2161
|
0 |
0 |
unless (exists $skip{lc $self->{$i}{'name'}}) |
|
2163
|
0 |
0 |
if (defined $d) { } |
|
2176
|
0 |
0 |
unless (@datasets) |
|
2177
|
0 |
0 |
if (scalar keys %possibles > 1) |
|
2186
|
0 |
0 |
if (scalar @startcolumns != scalar @datasets) |
|
2195
|
0 |
0 |
if (scalar @endcolumns != scalar @datasets) |
|
2239
|
0 |
0 |
if (substr($self->name($column), -1) eq '%') |
|
2243
|
0 |
0 |
if ($do_percentile and substr($self->name($column), -2) eq 'bp') |
|
2252
|
0 |
0 |
$v eq '.' ? : |
|
2257
|
0 |
0 |
if ($log) |
|
2263
|
0 |
0 |
if ($log) |
|
2268
|
0 |
0 |
if ($d == 0) { } |
|
2275
|
0 |
0 |
if ($summed_data->value($row, 1) != $midpoint) |
|
2317
|
6 |
148 |
if $self->{'index'} > $self->{'data'}{'last_row'} |
|
2324
|
0 |
148 |
if (exists $self->{'data'}{'SeqFeatureObjects'} and defined $self->{'data'}{'SeqFeatureObjects'}[$i]) |
|
2335
|
0 |
0 |
if @_ |