| line |
true |
false |
branch |
|
113
|
4 |
1 |
if $gene |
|
114
|
4 |
1 |
if $numbering |
|
141
|
5 |
20 |
if (defined $value) |
|
142
|
0 |
5 |
if (not $value->isa('Bio::LiveSeq::Gene')) { } |
|
150
|
25 |
0 |
if (exists $self->{'gene'}) { } |
|
176
|
6 |
23 |
if (defined $value) |
|
177
|
6 |
0 |
if ($value =~ /(coding)( )?(\d+)?/ or $value eq 'entry' or $value eq 'gene') { } |
|
183
|
28 |
1 |
if (exists $self->{'numbering'}) { } |
|
205
|
0 |
5 |
if ($value->isa('Bio::Liveseq::Mutation')) |
|
210
|
0 |
5 |
unless ($value->pos) |
|
214
|
0 |
0 |
unless ($value->seq or $value->len) |
|
258
|
5 |
250 |
if (defined $value) |
|
259
|
0 |
5 |
if (not $value->isa('Bio::LiveSeq::Mutation')) { } |
|
267
|
255 |
0 |
if (exists $self->{'mutation'}) { } |
|
292
|
5 |
60 |
if (defined $value) |
|
293
|
0 |
5 |
if (not $value->isa('Bio::LiveSeq::DNA') || $value->isa('Bio::LiveSeq::Transcript')) { } |
|
301
|
65 |
0 |
if (exists $self->{'DNA'}) { } |
|
328
|
5 |
111 |
if (defined $value) |
|
329
|
0 |
5 |
if (not $value->isa('Bio::LiveSeq::Transcript')) { } |
|
337
|
116 |
0 |
if (exists $self->{'RNA'}) { } |
|
365
|
5 |
17 |
if (defined $value) |
|
366
|
0 |
5 |
if (not $value->isa('Bio::Variation::DNAMutation')) { } |
|
374
|
22 |
0 |
if (exists $self->{'dnamut'}) { } |
|
402
|
5 |
15 |
if (defined $value) |
|
403
|
0 |
5 |
if (not $value->isa('Bio::Variation::RNAChange')) { } |
|
411
|
20 |
0 |
if (exists $self->{'rnachange'}) { } |
|
439
|
5 |
10 |
if (defined $value) |
|
440
|
0 |
5 |
if (not $value->isa('Bio::Variation::AAChange')) { } |
|
448
|
15 |
0 |
if (exists $self->{'aachange'}) { } |
|
476
|
5 |
10 |
if (defined $value) |
|
479
|
15 |
0 |
if (exists $self->{'exons'}) { } |
|
518
|
0 |
0 |
unless $aln->isa('Bio::SimpleAlign') |
|
520
|
0 |
0 |
if $aln->no_sequences != 2 |
|
526
|
0 |
0 |
unless ($aln->get_seq_by_pos(1)->id eq 'QUERY') |
|
527
|
0 |
0 |
if $aln->get_seq_by_pos(2)->id ne 'QUERY' |
|
593
|
0 |
0 |
unless $refseq->isa('Bio::PrimarySeqI') |
|
595
|
0 |
0 |
unless $queryseq->isa('Bio::PrimarySeqI') |
|
597
|
0 |
0 |
unless $pos =~ /^\+?\d+$/ |
|
599
|
0 |
0 |
unless $len =~ /^\+?\d+$/ |
|
606
|
0 |
0 |
if ($len == 1 and $refstring =~ /[^\.\-\*\?]/ and $varstring =~ /[^\.\-\*\?]/) { } |
|
|
0 |
0 |
elsif ($refstring =~ /^[^\.\-\*\?]+$/ and not $varstring =~ /^[^\.\-\*\?]+$/) { } |
|
|
0 |
0 |
elsif (not $refstring =~ /^[^\.\-\*\?]+$/ and $varstring =~ /^[^\.\-\*\?]+$/) { } |
|
685
|
0 |
5 |
unless ($self->gene) |
|
696
|
0 |
5 |
if $self->gene->get_DNA->alphabet eq 'rna' and $self->numbering eq 'gene' |
|
698
|
1 |
4 |
if ($self->numbering =~ /(coding)( )?(\d+)?/) { } |
|
701
|
1 |
0 |
if $3 |
|
702
|
0 |
1 |
if ($transnumber and $transnumber >= 0 and $transnumber <= $#transcripts) { } |
|
705
|
0 |
1 |
if $transnumber |
|
719
|
1 |
4 |
if ($refseq->isa('Bio::LiveSeq::Transcript')) { } |
|
747
|
0 |
5 |
unless $self->_mutationpos2label($refseq, $seqDiff) |
|
759
|
0 |
5 |
unless $mutation->label > 0 |
|
766
|
1 |
4 |
if ($self->numbering =~ /coding/) { } |
|
776
|
0 |
5 |
if ($mutation->len == 0) { } |
|
|
5 |
0 |
elsif ($mutation->len == 1) { } |
|
790
|
5 |
0 |
if ($self->_rnaAffected) { } |
|
|
0 |
0 |
elsif ($seqDiff->offset != 0 and $dnamut->region ne 'intron') { } |
|
814
|
1 |
4 |
if ($refseq->isa('Bio::LiveSeq::Transcript')) { } |
|
855
|
4 |
1 |
if ($self->numbering eq 'entry') |
|
858
|
0 |
4 |
if $tmp < 1 |
|
863
|
5 |
0 |
if $label > 0 |
|
896
|
0 |
5 |
if $dnamut_start <= 0 |
|
898
|
5 |
0 |
$self->mutation->len == 0 || $self->mutation->len == 1 ? : |
|
908
|
5 |
0 |
if $self->mutation->seq |
|
918
|
5 |
0 |
if $allele_ori |
|
920
|
0 |
5 |
$self->mutation->len == 0 ? : |
|
927
|
4 |
1 |
if ($seqDiff->numbering eq 'entry' or $seqDiff->numbering eq 'gene') { } |
|
938
|
5 |
0 |
if ($uplabel > 0) { } |
|
969
|
0 |
5 |
if ($self->mutation->prelabel > $DNAend or $self->mutation->postlabel > $DNAend) { } |
|
974
|
0 |
0 |
if ($self->mutation->postlabel == $RNAstart or follows($self->mutation->postlabel, $RNAstart)) { } |
|
|
0 |
0 |
elsif ($RNAend == $self->mutation->prelabel or follows($RNAend, $self->mutation->prelabel)) { } |
|
|
0 |
0 |
elsif (scalar @exons == 1) { } |
|
990
|
0 |
0 |
if (follows($self->mutation->prelabel, $before) or $after == $self->mutation->prelabel or follows($after, $self->mutation->prelabel) or follows($after, $self->mutation->postlabel)) |
|
1004
|
0 |
5 |
if ($strand == 1 and $self->mutation->postlabel <= $RNAstart or $strand != 1 and $self->mutation->postlabel >= $RNAstart) { } |
|
|
0 |
5 |
elsif ($strand == 1 and $self->mutation->prelabel >= $RNAend or $strand != 1 and $self->mutation->prelabel <= $RNAend) { } |
|
|
1 |
4 |
elsif (scalar @exons == 1) { } |
|
1014
|
0 |
0 |
if ($strand == 1) { } |
|
1028
|
0 |
4 |
if ($strand == 1 and $self->mutation->prelabel < $before or $strand == -1 and $self->mutation->prelabel > $before) { } |
|
1039
|
0 |
0 |
if ($afterdist < $beforedist) { } |
|
1053
|
0 |
14 |
if ($strand == 1 and $self->mutation->prelabel >= $before and $self->mutation->postlabel <= $after or $strand == -1 and $self->mutation->prelabel <= $before and $self->mutation->postlabel >= $after) { } |
|
|
4 |
10 |
elsif ($strand == 1 and $exons[$i]->start < $self->mutation->prelabel and $exons[$i]->end > $self->mutation->prelabel or $strand == 1 and $exons[$i]->start < $self->mutation->postlabel and $exons[$i]->end > $self->mutation->postlabel or $strand == -1 and $exons[$i]->start > $self->mutation->prelabel and $exons[$i]->end < $self->mutation->prelabel or $strand == -1 and $exons[$i]->start > $self->mutation->postlabel and $exons[$i]->end < $self->mutation->postlabel) { } |
|
1065
|
0 |
0 |
if ($afterdist < $beforedist) { } |
|
1098
|
2 |
2 |
if ($afterdist < $beforedist) { } |
|
1151
|
0 |
5 |
$self->mutation->len == 0 ? : |
|
1160
|
1 |
4 |
if ($seqDiff->numbering eq 'coding') { } |
|
1184
|
5 |
0 |
if ($self->RNA->valid($uplabel)) { } |
|
1187
|
0 |
0 |
if $self->RNA->valid($RNAprelabel) |
|
1200
|
0 |
5 |
if ($self->mutation->len == 0) { } |
|
1207
|
0 |
5 |
if ($dnstreamseq eq '-1') { } |
|
1234
|
5 |
0 |
if $dnamut->allele_ori->seq |
|
1240
|
5 |
0 |
if $self->mutation->seq |
|
1245
|
0 |
5 |
if $rnachange->length == 0 |
|
1252
|
5 |
0 |
if $aa_allele_ori |
|
1284
|
0 |
0 |
$self->mutation->len == 0 ? : |
|
1294
|
0 |
0 |
if $dnamut->allele_ori->seq |
|
1297
|
0 |
0 |
if $dnamut->allele_mut->seq |
|
1305
|
0 |
0 |
if ($seqDiff->numbering eq 'coding') { } |
|
1312
|
0 |
0 |
if ($rnachange->end < 0) { } |
|
1319
|
0 |
0 |
if $dist < 1 |
|
1327
|
0 |
0 |
if $dist > 0 |
|
1341
|
5 |
0 |
if ($self->rnachange and $self->rnachange->region eq 'coding') { } |
|
1355
|
5 |
0 |
if substr $mut_translation, $aa_start - 1 |
|
1365
|
5 |
0 |
if ($rlenori == 1 and $rlenmut == 1 and $aachange->allele_ori->seq ne '*') { } |
|
|
0 |
0 |
elsif ($rlenori == $rlenmut and $aachange->allele_ori->seq ne '*') { } |
|
|
0 |
0 |
elsif (int($rlenori - $rlenmut) % 3 == 0) { } |
|
1367
|
5 |
0 |
if ($aachange->allele_mut->seq) |
|
1382
|
0 |
0 |
if ($aachange->RNAChange->allele_mut->seq and $aachange->RNAChange->allele_ori->seq) { } |
|
|
0 |
0 |
elsif ($aachange->RNAChange->codon_pos == 1) { } |
|
1387
|
0 |
0 |
unless $rna_len % 3 == 0 |
|
1392
|
0 |
0 |
if ($aachange->RNAChange->allele_mut->seq eq '') { } |
|
|
0 |
0 |
elsif ($aachange->RNAChange->allele_ori->seq eq '') { } |
|
1407
|
0 |
0 |
if (not $aachange->RNAChange->allele_mut->seq) { } |
|
|
0 |
0 |
elsif (not $aachange->RNAChange->allele_ori->seq) { } |
|
1429
|
0 |
5 |
if (scalar @beforeexons ne scalar @afterexons) { } |
|
1436
|
0 |
25 |
if ($beforeexons[$i] ne $afterexons[$i]) |