| line |
true |
false |
branch |
|
201
|
16 |
0 |
unless $noparse |
|
204
|
0 |
16 |
unless ($self->gff_version($gff_version)) |
|
235
|
0 |
46 |
if /^\s+$/ |
|
236
|
42 |
4 |
if ($line =~ /^\#\#sequence-region\s+(\S+)\s+(\S+)\s+(\S+)\s*/) { } |
|
|
0 |
4 |
elsif ($line =~ /^(\#\#feature-ontology)/) { } |
|
|
0 |
4 |
elsif ($line =~ /^(\#\#attribute-ontology)/) { } |
|
|
0 |
4 |
elsif ($line =~ /^(\#\#source-ontology)/) { } |
|
|
0 |
4 |
elsif ($line =~ /^(\#\#\#)/) { } |
|
|
0 |
4 |
elsif ($line =~ /^(\#\#FASTA)/) { } |
|
260
|
0 |
0 |
unless ($line =~ /^\>(\S+)/) |
|
265
|
0 |
46 |
if ($line =~ /^\>(.*)/) |
|
268
|
0 |
0 |
if ($seq) |
|
274
|
4 |
42 |
unless ($handled) |
|
279
|
3 |
43 |
unless $line =~ /^\#/ |
|
292
|
0 |
0 |
if ($line =~ /^\>(.*)/) { } |
|
297
|
0 |
0 |
if ($seqid =~ /(\S+)\s+(.*)/) |
|
302
|
0 |
0 |
if ($line =~ /^\#/) |
|
305
|
0 |
0 |
if ($line =~ /^\>/) |
|
312
|
0 |
0 |
if $self->ignore_sequence |
|
319
|
0 |
0 |
if ($self->features_attached_to_seqs) |
|
349
|
1 |
0 |
if defined $self->{'segments'} |
|
375
|
0 |
3 |
if ($gff_string =~ /^\#\#\#/) |
|
378
|
0 |
3 |
if $gff_string =~ /^\#/ or $gff_string =~ /^\s*$/ or $gff_string =~ m[^//] |
|
384
|
0 |
0 |
if ($seq) |
|
387
|
0 |
0 |
unless $gff_string |
|
392
|
1 |
3 |
unless $gff_string |
|
397
|
0 |
3 |
if ($self->features_attached_to_seqs) |
|
407
|
0 |
0 |
if @_ |
|
409
|
0 |
0 |
unless $self->{'__feature_idx_by_seq_id'} |
|
434
|
1 |
2 |
if ($self->gff_version == 1) { } |
|
|
1 |
1 |
elsif ($self->gff_version == 3) { } |
|
462
|
0 |
1 |
unless (defined $frame) |
|
465
|
1 |
0 |
unless $frame =~ /^\d+$/ |
|
472
|
0 |
1 |
if ($score eq '.') { } |
|
477
|
1 |
0 |
if ($strand eq '-') |
|
478
|
0 |
1 |
if ($strand eq '+') |
|
479
|
0 |
1 |
if ($strand eq '.') |
|
481
|
0 |
0 |
if ($g =~ /(\S+)=(\S+)/) { } |
|
523
|
0 |
1 |
unless (defined $frame) |
|
532
|
0 |
1 |
if ($score eq '.') { } |
|
537
|
1 |
0 |
if ($strand eq '-') |
|
538
|
0 |
1 |
if ($strand eq '+') |
|
539
|
0 |
1 |
if ($strand eq '.') |
|
558
|
1 |
1 |
$flag == 0 ? : |
|
|
2 |
59 |
if ($a eq '"') { } |
|
|
1 |
58 |
elsif ($a eq ';' and $flag) { } |
|
|
0 |
116 |
elsif ($a eq '#' and not $flag) { } |
|
577
|
3 |
0 |
if (defined $values) |
|
594
|
2 |
0 |
if (length $othervalue > 0) |
|
616
|
0 |
1 |
unless (defined $frame) |
|
625
|
1 |
0 |
if ($score eq '.') { } |
|
630
|
0 |
1 |
if ($strand eq '-') |
|
631
|
1 |
0 |
if ($strand eq '+') |
|
632
|
0 |
1 |
if ($strand eq '.') |
|
664
|
0 |
3 |
unless @features |
|
665
|
1 |
2 |
if ($self->{'_first'} and $self->gff_version == 3) |
|
693
|
1 |
10 |
if ($self->gff_version == 1) { } |
|
|
8 |
2 |
elsif ($self->gff_version == 3) { } |
|
|
0 |
2 |
elsif ($self->gff_version == 2.5) { } |
|
720
|
1 |
0 |
if ($feat->can('score')) |
|
723
|
0 |
1 |
unless defined $score |
|
725
|
1 |
0 |
if ($feat->can('frame')) |
|
728
|
1 |
0 |
unless defined $frame |
|
731
|
0 |
1 |
if (not $strand) { } |
|
|
0 |
1 |
elsif ($strand == 1) { } |
|
|
1 |
0 |
elsif ($feat->strand == -1) { } |
|
739
|
1 |
0 |
if ($feat->can('seqname')) { } |
|
757
|
1 |
3 |
if exists $SKIPPED_TAGS{$tag} |
|
759
|
3 |
0 |
if $value |
|
781
|
0 |
2 |
if ($origfeat->isa('Bio::SeqFeature::FeaturePair')) { } |
|
788
|
2 |
0 |
if ($feat->can('score')) |
|
791
|
1 |
1 |
unless defined $score |
|
793
|
2 |
0 |
if ($feat->can('frame')) |
|
796
|
2 |
0 |
unless defined $frame |
|
799
|
0 |
2 |
if (not $strand) { } |
|
|
1 |
1 |
elsif ($strand == 1) { } |
|
|
1 |
0 |
elsif ($feat->strand == -1) { } |
|
807
|
2 |
0 |
if ($feat->can('seqname')) |
|
834
|
1 |
6 |
if exists $SKIPPED_TAGS{$tag} |
|
837
|
6 |
0 |
defined $value && length $value ? : |
|
854
|
0 |
2 |
if (not $feat->has_tag('Target') || $feat->has_tag('Group') and $origfeat->isa('Bio::SeqFeature::FeaturePair')) |
|
857
|
0 |
0 |
$origfeat->feature1->strand < 0 ? : |
|
|
0 |
0 |
$str2 ? : |
|
883
|
0 |
0 |
if ($origfeat->isa('Bio::SeqFeature::FeaturePair')) { } |
|
890
|
0 |
0 |
if ($feat->can('score')) |
|
893
|
0 |
0 |
unless defined $score |
|
895
|
0 |
0 |
if ($feat->can('frame')) |
|
898
|
0 |
0 |
unless defined $frame |
|
901
|
0 |
0 |
if (not $strand) { } |
|
|
0 |
0 |
elsif ($strand == 1) { } |
|
|
0 |
0 |
elsif ($feat->strand == -1) { } |
|
909
|
0 |
0 |
if ($feat->can('seqname')) { } |
|
927
|
0 |
0 |
if (@all_tags) |
|
931
|
0 |
0 |
if exists $SKIPPED_TAGS{$tag} |
|
932
|
0 |
0 |
defined $value && length $value ? : |
|
946
|
0 |
0 |
if ($tag eq 'Group' or $tag eq 'Target') { } |
|
955
|
0 |
0 |
if (not $feat->has_tag('Target') || $feat->has_tag('Group') and $origfeat->isa('Bio::SeqFeature::FeaturePair')) |
|
958
|
0 |
0 |
$origfeat->feature1->strand < 0 ? : |
|
|
0 |
0 |
$str2 ? : |
|
984
|
0 |
8 |
if ($origfeat->isa('Bio::SeqFeature::FeaturePair')) { } |
|
994
|
8 |
0 |
if ($feat->can('score')) |
|
997
|
1 |
7 |
unless defined $score |
|
999
|
8 |
0 |
if ($feat->can('frame')) |
|
1002
|
1 |
7 |
unless defined $frame |
|
1006
|
0 |
8 |
if (not $strand) { } |
|
|
8 |
0 |
elsif ($strand == 1) { } |
|
|
0 |
0 |
elsif ($feat->strand == -1) { } |
|
1014
|
8 |
0 |
if ($feat->can('seqname')) { } |
|
1027
|
19 |
5 |
if $feat->has_tag($t) |
|
1031
|
7 |
29 |
if exists $SKIPPED_TAGS{$tag} |
|
1033
|
7 |
22 |
if ($tag eq 'Target' and not $origfeat->isa('Bio::SeqFeature::FeaturePair')) |
|
1035
|
0 |
7 |
if (scalar @values > 1) |
|
1038
|
0 |
0 |
unless defined $e and defined $b and $target_id |
|
1039
|
0 |
0 |
if defined $strand and $strand < 0 |
|
1041
|
0 |
0 |
if ($strand) { } |
|
1053
|
27 |
2 |
if (defined $value and length $value) { } |
|
1055
|
0 |
27 |
if (ref $value eq 'Bio::Annotation::Comment') |
|
1059
|
8 |
19 |
if ($value =~ /[^a-zA-Z0-9\,\;\=\.:\%\^\*\$\@\!\+\_\?\-]/) |
|
1075
|
3 |
26 |
unless $tag =~ /^(ID|Name|Alias|Parent|Gap|Target|Derives_from|Note|Dbxref|Ontology_term)$/ |
|
1081
|
0 |
7 |
if ($feat->has_tag('Target') and not $feat->has_tag('Group') and $origfeat->isa('Bio::SeqFeature::FeaturePair')) |
|
1088
|
0 |
0 |
$origfeat->feature1->strand < 0 ? : |
|
1099
|
0 |
8 |
if ($feat->can('name') and defined $feat->name) |
|
1105
|
0 |
8 |
if ($feat->location->isa('Bio::Location::SplitLocationI')) { } |
|
1150
|
16 |
31 |
if (defined $value and grep {$value == $_;} 1, 2, 2.5, 3) |
|
1174
|
0 |
0 |
unless my $self = $class->new(@_) |
|
1211
|
0 |
0 |
if @_ |
|
1213
|
0 |
0 |
unless $self->{'_seq_by_id_h'} |
|
1259
|
0 |
3 |
if @_ |
|
1282
|
0 |
0 |
if @_ |
|
1299
|
0 |
0 |
unless wantarray |