| line |
true |
false |
branch |
|
169
|
0 |
0 |
if (defined $format and $format eq 'Glimmer' || $format eq 'GlimmerM' || $format eq 'GlimmerHMM') |
|
177
|
2 |
3 |
if (defined $detail) |
|
183
|
1 |
4 |
if defined $seqname |
|
186
|
1 |
4 |
if defined $seqlength |
|
205
|
0 |
0 |
if ($method and not $method =~ /glimmer/i) |
|
259
|
5 |
109 |
unless $self->_predictions_parsed |
|
291
|
3 |
2 |
unless ($format) |
|
295
|
1 |
232 |
if ($line =~ /^Glimmer\S*\s+\(Version\s*\S+\)/) { } |
|
|
1 |
231 |
elsif ($line =~ /^Glimmer\S*$/) { } |
|
|
1 |
230 |
elsif ($line =~ /^Putative Genes:$/) { } |
|
|
0 |
230 |
elsif ($line =~ /^>(\S+)/) { } |
|
321
|
5 |
0 |
exists $method{$format} ? : |
|
345
|
1 |
309 |
if (/^(Glimmer\S*)\s+\(Version\s*(\S+)\)/) { } |
|
|
1 |
308 |
elsif (/^(GlimmerHMM\S*)$/) { } |
|
|
2 |
306 |
elsif (/^Sequence name:\s+(.+)$/) { } |
|
|
2 |
304 |
elsif (/^Sequence length:\s+(\S+)/) { } |
|
|
66 |
238 |
elsif (/^(Predicted genes)|(Gene)|\s+\#/ or /^\s+$/) { } |
|
|
238 |
0 |
elsif (/^\s+(\d+)\s+ # gene num
(\d+)\s+ # exon num
([\+\-])\s+ # strand
(\S+)\s+ # exon type
(\d+)\s+(\d+) # exon start, end
\s+(\d+) # exon length
/ox) { } |
|
370
|
54 |
184 |
if (not $lastgenenum or $lastgenenum != $genenum) |
|
371
|
52 |
2 |
if $gene |
|
380
|
39 |
199 |
$strand eq '-' ? : |
|
393
|
2 |
0 |
if $gene |
|
431
|
1 |
2 |
if (defined $seqlength) |
|
438
|
2 |
1 |
if (defined $detail_file) |
|
444
|
2 |
220 |
if ($_ =~ /^>(\S+)/) |
|
449
|
2 |
218 |
if (defined $seqname and $_ =~ /^Sequence length = (\d+)$/) |
|
462
|
1 |
58 |
if ($_ =~ /^Putative Genes:$/) { } |
|
|
2 |
56 |
elsif ($_ =~ /^>(\S+)/) { } |
|
|
56 |
0 |
elsif (/^\s+(\d+)\s+ # gene num
(\d+)\s+(\d+)\s+ # start, end
\[([\+\-])(\d{1})\s+ # strand, frame
/ox or /^[^\d]+(\d+)\s+ # orf (numeric portion)
(\d+)\s+(\d+)\s+ # start, end
([\+\-])(\d{1})\s+ # strand, frame
([\d\.]+) # score
/ox) { } |
|
492
|
43 |
13 |
if ($strand eq '+') { } |
|
493
|
2 |
41 |
if ($start > $end) |
|
498
|
0 |
13 |
if ($start < $end) |
|
503
|
2 |
54 |
if ($circular_prediction) |
|
504
|
0 |
2 |
unless (defined $seqlength) |
|
514
|
25 |
31 |
if ($source eq 'Glimmer_2.X') |
|
515
|
19 |
6 |
if ($strand eq '+') { } |
|
530
|
1 |
111 |
if ($coord < 1) { } |
|
|
1 |
110 |
elsif (defined $seqlength and $coord > $seqlength) { } |
|
541
|
2 |
54 |
if ($circular_prediction) { } |
|
542
|
2 |
0 |
if ($strand eq '+') { } |
|
551
|
13 |
0 |
if ($strand eq '-' and not $fst and not $fend and $start > $end) |
|
563
|
13 |
43 |
$strand eq '-' ? : |
|
596
|
4 |
110 |
unless exists $self->{'_preds'} and @{$self->{'_preds'};} |
|
613
|
0 |
110 |
unless (exists $self->{'_preds'}) |
|
632
|
5 |
114 |
if $val |
|
633
|
0 |
119 |
unless (exists $self->{'_preds_parsed'}) |
|
652
|
1 |
3 |
if $val |
|
653
|
2 |
2 |
unless (exists $self->{'_seqname'}) |
|
672
|
1 |
3 |
if $val |
|
689
|
2 |
5 |
if $val |
|
707
|
2 |
3 |
if $val |