| line |
true |
false |
branch |
|
319
|
8 |
3 |
if (@_) |
|
320
|
0 |
8 |
if (scalar @_ == 1) { } |
|
321
|
0 |
0 |
unless $self->open_file($_[0]) |
|
325
|
4 |
4 |
if (exists $options{'simplify'}) |
|
328
|
4 |
4 |
if (exists $options{'do_gene'}) |
|
331
|
2 |
6 |
if (exists $options{'do_exon'}) |
|
334
|
4 |
4 |
if (exists $options{'do_cds'}) |
|
337
|
0 |
8 |
if (exists $options{'do_utr'}) |
|
340
|
0 |
8 |
if (exists $options{'do_codon'}) |
|
343
|
0 |
8 |
if (exists $options{'version'}) |
|
346
|
8 |
0 |
if (exists $options{'file'} or $options{'table'}) |
|
348
|
0 |
8 |
unless $self->open_file($options{'file'}) |
|
351
|
8 |
0 |
if (exists $options{'class'}) |
|
353
|
8 |
0 |
if (eval "require $class; 1") { } |
|
369
|
7 |
586 |
if (@_) |
|
377
|
6 |
182 |
if (@_) |
|
385
|
5 |
267 |
if (@_) |
|
393
|
0 |
0 |
if (@_) |
|
401
|
0 |
34 |
if (@_) |
|
419
|
7 |
78 |
if (defined $_[0]) |
|
427
|
11 |
13 |
if (@_) |
|
429
|
7 |
4 |
if ($v eq '3') { } |
|
|
4 |
0 |
elsif ($v eq '2.5' or $v eq '2.2') { } |
|
|
0 |
0 |
elsif ($v eq '2' or $v eq '1') { } |
|
452
|
0 |
11 |
unless ($filename) |
|
459
|
0 |
11 |
unless ($typelist =~ /\w+/) |
|
466
|
0 |
11 |
unless my $fh = "Bio::ToolBox::Data::file"->open_to_read_fh($filename) |
|
471
|
11 |
0 |
if ($first =~ /^##gff.version\s+([\d\.]+)\s*$/i) { } |
|
481
|
0 |
0 |
if ($filename =~ /\.gtf.*$/i) { } |
|
|
0 |
0 |
elsif ($filename =~ /\.gff3.*$/i) { } |
|
506
|
0 |
587 |
unless ($self->fh) |
|
509
|
0 |
587 |
if $self->{'eof'} |
|
512
|
11 |
576 |
unless (defined $self->{'convertor_sub'}) |
|
523
|
25 |
745 |
if ($firstchar eq '#') { } |
|
|
0 |
745 |
elsif ($firstchar eq '>') { } |
|
524
|
0 |
25 |
if ($line =~ /^###$/) { } |
|
|
0 |
25 |
elsif ($line =~ /^##sequence.region/i) { } |
|
533
|
0 |
0 |
if (defined $seq_id and $start =~ /^\d+$/ and $stop =~ /^\d+$/) { } |
|
559
|
0 |
745 |
unless scalar @fields == 9 |
|
563
|
265 |
480 |
if ($type eq 'cds') { } |
|
|
178 |
302 |
elsif ($type eq 'exon') { } |
|
|
0 |
302 |
elsif ($type =~ /utr|untranslated/) { } |
|
|
32 |
270 |
elsif ($type =~ /codon/) { } |
|
|
165 |
105 |
elsif ($type =~ /gene$/) { } |
|
|
36 |
69 |
elsif ($type =~ /transcript|rna/) { } |
|
|
7 |
62 |
elsif ($type =~ /chromosome|contig|scaffold/) { } |
|
564
|
199 |
66 |
if ($self->do_cds) { } |
|
571
|
178 |
0 |
if ($self->do_exon) { } |
|
578
|
0 |
0 |
if ($self->do_utr) { } |
|
585
|
0 |
32 |
if ($self->do_codon) { } |
|
592
|
165 |
0 |
if ($self->do_gene) { } |
|
610
|
2 |
60 |
unless $self->simplify |
|
622
|
0 |
70 |
unless ($self->fh) |
|
625
|
0 |
70 |
unless ($self->{'eof'}) |
|
626
|
0 |
0 |
unless $self->parse_file |
|
633
|
0 |
4 |
unless ($self->{'eof'}) |
|
637
|
4 |
0 |
wantarray ? : |
|
645
|
0 |
7 |
unless ($self->fh) |
|
648
|
0 |
7 |
if $self->{'eof'} |
|
657
|
2 |
0 |
$self->version =~ /2\../ ? : |
|
|
5 |
2 |
$self->version eq '3' ? : |
|
671
|
404 |
172 |
if ($id) |
|
673
|
0 |
404 |
if (exists $self->{'loaded'}{$id}) { } |
|
677
|
0 |
0 |
if ($feature->primary_tag =~ /gene|rna|transcript/) |
|
682
|
0 |
0 |
if (ref $self->{'loaded'}{$id} eq 'ARRAY') { } |
|
700
|
411 |
165 |
if ($feature->has_tag('Parent')) { } |
|
704
|
411 |
0 |
if (exists $self->{'loaded'}{$parent_id}) { } |
|
713
|
312 |
99 |
if ($self->{'gtf'}) |
|
714
|
0 |
312 |
if ($feature->start < $parent->start) |
|
717
|
1 |
311 |
if ($feature->end > $parent->end) |
|
721
|
278 |
34 |
if ($parent->has_tag("Parent")) |
|
726
|
0 |
278 |
if ($feature->start < $grandparent->start) |
|
729
|
0 |
278 |
if ($feature->end > $grandparent->end) |
|
750
|
0 |
7 |
if (scalar @{$self->{'orphans'};}) |
|
753
|
0 |
0 |
if (scalar @{$self->{'orphans'};}) |
|
760
|
0 |
7 |
if (keys %{$$self{"duplicate_ids"};}) |
|
781
|
12 |
0 |
if ($fields->[8] =~ /gene_name "([^"]+)";?/) { } |
|
789
|
2 |
10 |
unless ($self->simplify) |
|
790
|
0 |
2 |
if ($fields->[8] =~ /gene_biotype "([^"]+)";?/) { } |
|
|
0 |
2 |
elsif ($fields->[8] =~ /gene_type "([^"]+)";?/) { } |
|
796
|
0 |
2 |
if ($fields->[8] =~ /gene_source "([^"]+)";?/) |
|
816
|
0 |
0 |
if ($fields->[8] =~ /transcript_name "([^"]+)";?/) { } |
|
824
|
0 |
0 |
unless ($self->simplify) |
|
825
|
0 |
0 |
if ($fields->[8] =~ /transcript_biotype "([^"]+)";?/) { } |
|
|
0 |
0 |
elsif ($fields->[8] =~ /transcript_type "([^"]+)";?/) { } |
|
831
|
0 |
0 |
if ($fields->[8] =~ /transcript_source "([^"]+)";?/) |
|
843
|
5 |
32 |
unless (exists $self->{'gene2seqf'}) |
|
844
|
0 |
5 |
unless $self->{'eof'} |
|
848
|
0 |
107 |
if (exists $self->{'gene2seqf'}{$name}) { } |
|
859
|
0 |
37 |
if (scalar @_ == 0) { } |
|
|
4 |
33 |
elsif (scalar @_ == 1) { } |
|
875
|
0 |
37 |
unless ($name) |
|
881
|
37 |
0 |
if (exists $self->{'gene2seqf'}{lc $name}) |
|
889
|
33 |
4 |
if ($id) |
|
891
|
33 |
0 |
if ($g->primary_id eq $id) |
|
897
|
0 |
0 |
if ($chrom and $start and $end) |
|
899
|
0 |
0 |
if ($g->strand == $strand and not $g->start > $end || $g->end < $start) |
|
913
|
4 |
0 |
if (scalar @$genes == 1) { } |
|
|
0 |
0 |
elsif (scalar @$genes > 1) { } |
|
933
|
0 |
0 |
unless ($string) |
|
940
|
0 |
0 |
unless (defined $self->{'convertor_sub'}) |
|
951
|
7 |
4 |
if ($self->{'gff3'}) { } |
|
|
4 |
0 |
elsif ($self->{'gtf'}) { } |
|
955
|
2 |
2 |
if ($self->simplify) { } |
|
962
|
0 |
4 |
unless ($self->typelist =~ /transcript|rna/i) |
|
964
|
0 |
0 |
unless ($self->do_exon or $self->do_cds) |
|
968
|
4 |
0 |
if ($self->do_gene and not $self->typelist =~ /gene/i) |
|
990
|
266 |
1116 |
if ($tag eq 'Name') { } |
|
|
167 |
949 |
elsif ($tag eq 'ID') { } |
|
|
99 |
850 |
elsif ($tag eq 'Parent') { } |
|
|
0 |
850 |
elsif (lc $tag eq 'exon_id') { } |
|
|
2 |
848 |
elsif (not $self->{'simplify'}) { } |
|
998
|
99 |
0 |
unless (not $self->do_gene and $feature->primary_tag =~ /rna|transcript/i) |
|
1027
|
312 |
0 |
if ($group =~ /gene_id "([^"]+)";?/i) |
|
1030
|
312 |
0 |
if ($group =~ /transcript_id "([^"]+)";?/i) |
|
1033
|
0 |
312 |
unless ($gene_id or $transcript_id) |
|
1039
|
278 |
34 |
if ($fields->[2] =~ /cds|exon|utr|codon|untranslated/i) { } |
|
|
34 |
0 |
elsif ($fields->[2] =~ /rna|transcript/i) { } |
|
|
0 |
0 |
elsif ($fields->[2] eq 'gene') { } |
|
1043
|
0 |
278 |
if ($fields->[2] eq "exon" and $group =~ /exon_id "([^"]+)";?/i) |
|
1048
|
0 |
278 |
if ($self->do_gene and not exists $self->{'loaded'}{$gene_id}) |
|
1055
|
0 |
278 |
unless (exists $self->{'loaded'}{$transcript_id}) |
|
1058
|
0 |
0 |
if ($self->do_gene) { } |
|
1075
|
34 |
0 |
if ($group =~ /transcript_name "([^"]+)";?/i) |
|
1080
|
34 |
0 |
if ($self->do_gene) |
|
1082
|
10 |
24 |
unless (exists $self->{'loaded'}{$gene_id}) |
|
1095
|
0 |
0 |
if ($group =~ /gene_name "([^"]+)";?/i) |
|
1121
|
0 |
2 |
if ($fields->[2] =~ /cds|exon|utr|codon|untranslated/i) { } |
|
|
2 |
0 |
elsif ($fields->[2] =~ /transcript|rna/i) { } |
|
|
0 |
0 |
elsif ($fields->[2] eq 'gene') { } |
|
1125
|
0 |
0 |
if ($fields->[2] eq "exon" and exists $attributes{'exon_id'}) |
|
1130
|
0 |
0 |
if ($self->do_gene) |
|
1132
|
0 |
0 |
if ($gene_id and not exists $self->{'loaded'}{$gene_id}) |
|
1141
|
0 |
0 |
if ($transcript_id and not exists $self->{'loaded'}{$transcript_id}) |
|
1144
|
0 |
0 |
if ($self->do_gene) { } |
|
1161
|
2 |
0 |
if (exists $attributes{'transcript_name'}) |
|
1167
|
2 |
0 |
if ($self->do_gene) |
|
1169
|
2 |
0 |
if ($gene_id and not exists $self->{'loaded'}{$gene_id}) |
|
1184
|
0 |
0 |
if (exists $attributes{'gene_name'}) |
|
1209
|
0 |
0 |
unless $tag and $value |
|
1230
|
0 |
580 |
if ($fields->[5] ne ".") |
|
1233
|
199 |
381 |
if ($fields->[7] ne ".") |
|
1262
|
0 |
0 |
unless scalar @{$self->{'orphans'};} |
|
1272
|
0 |
0 |
if (exists $self->{'loaded'}{$parent}) |
|
1280
|
0 |
0 |
if $success |
|
1296
|
0 |
0 |
wantarray ? : |
|
1306
|
0 |
0 |
wantarray ? : |
|
1312
|
0 |
0 |
unless (scalar keys %{$$self{"seq_ids"};}) |
|
1316
|
0 |
0 |
wantarray ? : |
|
1322
|
0 |
0 |
unless (scalar keys %{$$self{"seq_ids"};}) |
|
1330
|
0 |
0 |
unless $self->{'eof'} |
|
1333
|
0 |
0 |
unless (exists $self->{'seq_ids'}{$s}) |
|
1336
|
0 |
0 |
if $_->end > $self->{'seq_ids'}{$s} |