| line |
true |
false |
branch |
|
77
|
0 |
0 |
if (defined $getswissprotinfo) { } |
|
78
|
0 |
0 |
if ($getswissprotinfo ne 0 and $getswissprotinfo ne 1) |
|
86
|
0 |
0 |
unless ($hashref) |
|
89
|
0 |
0 |
if ($test_transl) |
|
151
|
0 |
6 |
unless ($gene_name or $cds_position) |
|
155
|
0 |
6 |
if ($gene_name and $cds_position) { } |
|
|
6 |
0 |
elsif ($gene_name) { } |
|
164
|
0 |
6 |
if (defined $getswissprotinfo) { } |
|
165
|
0 |
0 |
if ($getswissprotinfo ne 0 and $getswissprotinfo ne 1) |
|
173
|
0 |
6 |
if (defined $flanking) { } |
|
174
|
0 |
0 |
unless ($flanking >= 0) |
|
182
|
0 |
6 |
unless ($hashref) |
|
184
|
0 |
6 |
unless ($gene) |
|
204
|
0 |
0 |
unless ($obj_transl eq $hash_transl) |
|
234
|
0 |
0 |
if ($getswissprotinfo) |
|
244
|
0 |
0 |
if ($swisshashes[$j]) |
|
271
|
0 |
6 |
if (index($input, 'cds-position:') == 0) { } |
|
273
|
0 |
0 |
if ($cds_position >= 1 and $cds_position <= scalar @cds) |
|
280
|
0 |
6 |
unless ($genefeatureshash and scalar @{$genefeatureshash->{'genefeatures'};}) |
|
293
|
6 |
0 |
if ($min - $flanking < 1) { } |
|
298
|
6 |
0 |
if ($max + $flanking > $seqlength) { } |
|
317
|
0 |
6 |
unless (@transcripts) |
|
331
|
0 |
6 |
if ($ttables[$j]) |
|
336
|
0 |
6 |
if ($swisshashes[$j]) |
|
355
|
1 |
5 |
if (@exons) |
|
360
|
9 |
0 |
if ($object != -1) { } |
|
361
|
9 |
0 |
if defined $exondescs[$exoncount] |
|
372
|
1 |
5 |
if (@introns) |
|
377
|
8 |
0 |
if ($object != -1) { } |
|
388
|
5 |
1 |
if (@prim_transcripts) |
|
392
|
7 |
0 |
if ($object != -1) |
|
398
|
0 |
6 |
if (@repeat_regions) |
|
403
|
0 |
0 |
if ($object != -1) { } |
|
415
|
0 |
6 |
if (@repeat_units) |
|
420
|
0 |
0 |
if ($object != -1) { } |
|
447
|
0 |
110 |
unless defined $element |
|
448
|
0 |
110 |
if ($element < $min) |
|
451
|
6 |
104 |
if ($element > $max) |
|
479
|
6 |
0 |
if ($transcriptobj != -1) |
|
509
|
0 |
0 |
unless ($entry) |
|
526
|
0 |
0 |
if ($entry->{'Features'}) |
|
551
|
0 |
0 |
unless ($entry) |
|
580
|
0 |
0 |
if ($featurename eq 'CDS') { } |
|
618
|
0 |
0 |
unless ($entry) |
|
625
|
0 |
0 |
if ($genename) |
|
626
|
0 |
0 |
if (index($genenames, $genename) == -1) |
|
648
|
0 |
0 |
if ($entry->{'Features'}) |
|
654
|
0 |
0 |
if ($feature->{'name'} eq 'INIT_MET' and $feature->{'location'} eq '0 0') { } |
|
669
|
0 |
0 |
if (index($liveseq_aa, '-') != -1 or index($swiss_aa, '-') != -1) |
|
682
|
0 |
0 |
if ($aarangeobj != -1) |
|
730
|
6 |
0 |
if (scalar @cds == 1) |
|
736
|
0 |
6 |
if ($cds_position) |
|
741
|
0 |
0 |
unless ($skipgenematch) |
|
748
|
0 |
0 |
if ($skipgenematch or $cds_position and $self->_checkfeatureproximity($entryfeature->{'range'}, $cds_begin, $cds_end, $proximity) or not $cds_position and $entryfeature->{'qualifiers'}{'gene'} eq "$gene_name") |
|
754
|
6 |
24 |
if ($name eq 'CDS') { } |
|
758
|
6 |
0 |
if ($getswissprotinfo) |
|
777
|
0 |
24 |
if ($entryfeature->{'locationtype'} and $entryfeature->{'locationtype'} eq 'joined') |
|
781
|
9 |
15 |
if ($name eq 'exon') |
|
783
|
3 |
6 |
if ($entryfeature->{'qualifiers'}{'note'}) |
|
784
|
0 |
3 |
if ($desc) { } |
|
793
|
8 |
16 |
if ($name eq 'intron') |
|
795
|
0 |
8 |
if ($desc) { } |
|
803
|
7 |
17 |
if ($name eq 'prim_transcript' or $name eq 'mRNA') |
|
804
|
0 |
24 |
if ($name eq 'repeat_unit') |
|
808
|
0 |
24 |
if ($name eq 'repeat_region') |
|
815
|
0 |
6 |
unless ($gene_name) |
|
846
|
0 |
0 |
if (ref $range[0] eq 'ARRAY') { } |
|
851
|
0 |
0 |
if ($cds_begin > $cds_end) |
|
854
|
0 |
0 |
if ($strand == -1) |
|
857
|
0 |
0 |
if ($cds_begin - $end > $proximity) |
|
861
|
0 |
0 |
if ($begin - $cds_end > $proximity) |
|
877
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
882
|
0 |
0 |
unless open my $TMPFASTAFILE1, '>', $fastafile1 |
|
883
|
0 |
0 |
unless open my $TMPFASTAFILE2, '>', $fastafile2 |
|
923
|
0 |
0 |
if (@alt_codons) { } |
|
946
|
0 |
0 |
if ($dice < $relativeusage + $partial) { } |
|
953
|
0 |
0 |
unless ($chosen_codon) |
|
975
|
0 |
0 |
unless ($gene) |