| line |
true |
false |
branch |
|
111
|
0 |
7 |
if ($arg{'-file'} =~ /^>.*/) { } |
|
123
|
0 |
7 |
if ($self->validate) |
|
144
|
1 |
67 |
if ($f) |
|
148
|
2 |
65 |
if $self->fasta_mode |
|
153
|
0 |
68 |
if $gff_string =~ /^\s*$/ |
|
154
|
3 |
65 |
if $gff_string =~ /^\#[^#]/ |
|
158
|
0 |
65 |
unless $gff_string |
|
161
|
2 |
63 |
if ($gff_string =~ /^>/) { } |
|
|
6 |
57 |
elsif ($gff_string =~ /^##/) { } |
|
169
|
2 |
0 |
if ($pos >= 0) { } |
|
227
|
6 |
24 |
if (ref $anno_ID) |
|
230
|
0 |
6 |
if exists $seen_ids{$attr_ID} |
|
239
|
24 |
6 |
if (@parents) { } |
|
242
|
0 |
24 |
unless exists $seen_ids{$parent_id} |
|
262
|
5 |
12 |
unless $self->fasta_mode |
|
265
|
6 |
6 |
unless ($self->seqio) |
|
284
|
0 |
0 |
unless ($feature) |
|
287
|
0 |
0 |
unless $feature->isa('Bio::SeqFeature::Annotated') |
|
289
|
0 |
0 |
if ($self->version == 1) { } |
|
|
0 |
0 |
elsif ($self->version == 2) { } |
|
|
0 |
0 |
elsif ($self->version == 2.5) { } |
|
|
0 |
0 |
elsif ($self->version == 3) { } |
|
324
|
7 |
84 |
if defined $val |
|
326
|
7 |
84 |
if ($val and $val == 1) |
|
346
|
6 |
24 |
if defined $val |
|
362
|
1 |
0 |
if (defined $k and defined $v) { } |
|
|
0 |
0 |
elsif (defined $k) { } |
|
388
|
0 |
0 |
if defined $val |
|
405
|
7 |
73 |
if defined $val |
|
422
|
7 |
0 |
if (defined $val and $valid{$val}) { } |
|
|
0 |
0 |
elsif (defined $val) { } |
|
449
|
1 |
74 |
if ($f) { } |
|
|
2 |
72 |
elsif ($self->{'buffer'}) { } |
|
474
|
6 |
12 |
if ($directive eq 'gff-version') { } |
|
|
1 |
11 |
elsif ($directive eq 'sequence-region') { } |
|
|
1 |
10 |
elsif ($directive eq 'feature-ontology') { } |
|
|
1 |
9 |
elsif ($directive eq 'attribute-ontology') { } |
|
|
1 |
8 |
elsif ($directive eq 'source-ontology') { } |
|
|
5 |
3 |
elsif ($directive eq 'FASTA' or $directive =~ /^>/) { } |
|
|
3 |
0 |
elsif ($directive eq '#') { } |
|
|
0 |
0 |
elsif ($directive eq 'organism') { } |
|
476
|
0 |
6 |
if ($version != 3) |
|
486
|
0 |
1 |
unless $arg[1] and $arg[2] |
|
556
|
57 |
0 |
unless $start eq '.' |
|
557
|
57 |
0 |
unless $end eq '.' |
|
558
|
54 |
0 |
$strand eq '-' ? : |
|
|
3 |
54 |
$strand eq '+' ? : |
|
564
|
0 |
57 |
if ($self->validate) { } |
|
567
|
0 |
0 |
if ($seq =~ /[^a-zA-Z0-9\.\-\:\^\*\$\@\!\+\_\?]/) |
|
571
|
0 |
0 |
if ($seq =~ /\s/) |
|
576
|
0 |
0 |
if ($seq =~ /^>/) |
|
583
|
0 |
0 |
if ($start > $end) |
|
591
|
0 |
0 |
if (defined $region and $start < $region->start or $end > $region->end) |
|
597
|
0 |
0 |
if $strand =~ /^[^\+\-\.\?]$/ |
|
600
|
0 |
0 |
if $phase =~ /^[^\.012]$/ |
|
603
|
0 |
0 |
if ($type =~ /^\D+:\d+$/) { } |
|
611
|
0 |
0 |
unless ($feature_type) |
|
617
|
0 |
57 |
if ($type =~ /^\D+:\d+$/) { } |
|
630
|
57 |
0 |
unless ($attribute_string eq '.') |
|
642
|
3 |
90 |
if ($attr{$key}) { } |
|
653
|
8 |
49 |
if ($attr{'Dbxref'} or $attr{'dbxref'}) |
|
658
|
0 |
71 |
unless ($db and $accession) |
|
670
|
3 |
54 |
if ($attr{'Ontology_term'}) |
|
674
|
0 |
9 |
if ($self->validate) { } |
|
688
|
3 |
54 |
if ($attr{'Gap'}) |
|
697
|
3 |
54 |
if ($attr{'Target'}) |
|
707
|
0 |
3 |
unless $target_string =~ / / |
|
710
|
0 |
3 |
if (not $tend or $extra) |
|
720
|
0 |
3 |
if ($strand and $strand eq '+') { } |
|
|
0 |
3 |
elsif ($strand and $strand eq '-') { } |
|
728
|
0 |
3 |
if $strand |
|
735
|
11 |
46 |
if ($attr{'ID'}) |
|
736
|
0 |
11 |
if (scalar @{$attr{'ID'};} > 1) |
|
741
|
0 |
11 |
if ($self->{'allIDs'}{do {
$attr{'ID'}
}->[0]} and $self->validate) |
|
753
|
0 |
57 |
if ($attr{'Name'}) |
|
754
|
0 |
0 |
if (scalar @{$attr{'Name'};} > 1) |
|
764
|
62 |
280 |
if ($attr{$other_canonical}) |
|
775
|
8 |
0 |
if $non_reserved_tag eq 'dbxref' |
|
785
|
0 |
57 |
if (@illegal_tags > 0) |
|
815
|
0 |
0 |
if ($tag eq 'comment') { } |
|
835
|
0 |
0 |
if @_ |
|
836
|
0 |
0 |
if defined $organism |
|
874
|
0 |
0 |
unless (defined $group) |
|
881
|
0 |
0 |
ref $feature->seq_id ? : |
|
884
|
0 |
0 |
if $type eq 'exon' |
|
887
|
0 |
0 |
$feature->strand == -1 ? : |
|
|
0 |
0 |
$feature->strand == 1 ? : |
|
888
|
0 |
0 |
ref $feature->score ? : |
|
|
0 |
0 |
defined $feature->score ? : |
|
889
|
0 |
0 |
ref $feature->frame ? : |
|
|
0 |
0 |
ref $feature->phase ? : |
|
|
0 |
0 |
defined $feature->frame ? : |
|
892
|
0 |
0 |
if ($type eq 'EXON' or $type eq 'CDS' or $type eq 'start_codon' or $type eq 'stop_codon') |
|
893
|
0 |
0 |
$gene_id ? : |
|
|
0 |
0 |
$transcript_id ? : |
|
894
|
0 |
0 |
$frame eq '.' ? : |
|
913
|
0 |
0 |
ref $feature->seq_id ? : |
|
915
|
0 |
0 |
if ($feature->source) { } |
|
922
|
0 |
0 |
if ($feature->type) { } |
|
926
|
0 |
0 |
$feature->strand == -1 ? : |
|
|
0 |
0 |
$feature->strand == 1 ? : |
|
927
|
0 |
0 |
ref $feature->score ? : |
|
|
0 |
0 |
defined $feature->score ? : |
|
928
|
0 |
0 |
ref $feature->phase ? : |
|
|
0 |
0 |
defined $feature->phase ? : |
|
931
|
0 |
0 |
if (my(@v) = $feature->get_Annotations('Name')) |
|
935
|
0 |
0 |
if (my(@v) = $feature->get_Annotations('ID')) |
|
938
|
0 |
0 |
if scalar @v > 1 |
|
940
|
0 |
0 |
if (my(@v) = $feature->get_Annotations('Parent')) |
|
944
|
0 |
0 |
if (my(@v) = $feature->get_Annotations('dblink')) |
|
948
|
0 |
0 |
if (my(@v) = $feature->get_Annotations('ontology_term')) |
|
952
|
0 |
0 |
if (my(@v) = $feature->get_Annotations('comment')) |
|
956
|
0 |
0 |
if (my(@v) = $feature->get_Annotations('Target')) |
|
959
|
0 |
0 |
defined $_->strand ? : |