| line |
true |
false |
branch |
|
149
|
0 |
0 |
if ($method and not $method =~ /fgenesh/i) |
|
200
|
1 |
4 |
unless $self->_predictions_parsed |
|
205
|
4 |
1 |
if ($gene) |
|
212
|
4 |
0 |
unless ($seqobj) |
|
215
|
0 |
4 |
if ($id =~ /mrna/ or $id =~ /cds/) { } |
|
221
|
4 |
0 |
if ($seqobj) |
|
230
|
0 |
4 |
if (not $id =~ /_predicted_(\w+)_$prednr/) { } |
|
234
|
4 |
0 |
if ($1 eq 'protein') { } |
|
|
0 |
0 |
elsif ($1 eq 'mrna' or $1 eq 'cds') { } |
|
242
|
0 |
0 |
if ($id =~ /_cds_/) |
|
276
|
27 |
14 |
if (/^\s*(\d+)\s+([+\-])/) |
|
281
|
6 |
21 |
$2 eq '+' ? : |
|
283
|
4 |
23 |
unless (defined $gene) |
|
300
|
19 |
8 |
if ($is_exon) { } |
|
333
|
19 |
8 |
if ($is_exon) { } |
|
|
4 |
4 |
elsif ($flds[3] eq 'PolA') { } |
|
|
4 |
0 |
elsif ($flds[3] eq 'TSS') { } |
|
338
|
4 |
15 |
if ($predobj->strand == 1) { } |
|
342
|
3 |
1 |
if $cod_offset < 1 |
|
352
|
15 |
0 |
if $cod_offset >= 0 |
|
379
|
4 |
10 |
if (/^\s*$/ and defined $gene) |
|
387
|
0 |
10 |
if (/^(FGENESH)\s+([\d\.]+)/) |
|
390
|
0 |
0 |
if (/\s(\S+)\sgenomic DNA/) |
|
396
|
1 |
9 |
if (/^\s*Seq name:\s+(\S+)/) |
|
401
|
1 |
8 |
if (/^Predicted protein/) |
|
424
|
1 |
4 |
unless exists $self->{'_preds'} and @{$self->{'_preds'};} |
|
441
|
0 |
4 |
unless (exists $self->{'_preds'}) |
|
460
|
1 |
5 |
if $val |
|
461
|
0 |
6 |
unless (exists $self->{'_preds_parsed'}) |
|
480
|
0 |
0 |
if $val |
|
481
|
0 |
0 |
unless (exists $self->{'_has_cds'}) |
|
506
|
0 |
4 |
unless $entry |
|
507
|
1 |
3 |
if $entry =~ /^Predicted protein/ |
|
511
|
4 |
0 |
if ($entry =~ /^>FGENESH:/) |
|
512
|
4 |
0 |
if ($entry =~ /^>FGENESH:\s+(\d+)/) { } |
|
|
0 |
0 |
elsif ($entry =~ /^>FGENESH:\[mRNA\]\s*(\d+)/) { } |
|
|
0 |
0 |
elsif ($entry =~ /^>FGENESH:\[exon\]\s+Gene:\s*(\d+)/) { } |
|
528
|
0 |
19 |
if ($entry =~ /^>FGENESH:\[exon\]/ and $id =~ /^_predicted_cds_/) { } |
|
536
|
1 |
18 |
unless $entry = $self->_readline |
|
537
|
3 |
15 |
if ($entry =~ /^>/ and not $entry =~ /^>FGENESH:\[exon\]/ && $id =~ /^_predicted_cds_/) |