| line |
true |
false |
branch |
|
145
|
0 |
19 |
if defined $opts{'prefix'} and $opts{'prefix'} =~ /^$/ |
|
163
|
0 |
19 |
$filename eq 'STDIN' ? : |
|
256
|
0 |
0 |
if $i == $j |
|
268
|
0 |
0 |
if (&_internal_stop_or_x($pep)) |
|
278
|
0 |
0 |
if scalar @$cd_set > 1 |
|
296
|
0 |
0 |
if ($num) |
|
313
|
0 |
0 |
if ($num) |
|
333
|
0 |
0 |
if $type eq "dna" and $mon =~ /[atcg]/i or $type eq "protein" and $mon =~ /[ACDEFGHIKLMNPQRSTVWY]/i or $type eq "protein" and $mon =~ /\*\s*$/ |
|
335
|
0 |
0 |
if ($seen_gaps{$mon}) { } |
|
349
|
0 |
0 |
if ($optStr =~ /^id:(\S+);(\S+)$/) { } |
|
363
|
0 |
0 |
if ($names{$id}) { } |
|
379
|
0 |
0 |
unless ($pep_string =~ /\*[A-Z]/) |
|
388
|
0 |
0 |
unless ($opts{'no-revcom'}) |
|
390
|
0 |
0 |
unless ($pep_rev =~ /\*[A-Z]/) |
|
413
|
0 |
0 |
if $opts{'no-revcom'} and $fm < 0 |
|
414
|
0 |
0 |
$fm > 0 ? : |
|
425
|
0 |
0 |
$longest->{'frame'} > 0 ? : |
|
444
|
0 |
0 |
if ($pep_string =~ /\*[A-Z]/) { } |
|
449
|
0 |
0 |
if $pep_string =~ /X/ |
|
455
|
0 |
0 |
unless $aas[$i] eq "*" or $i == $#aas |
|
456
|
0 |
0 |
if ($i - $start + 2 > $ref->{'aa_length'}) |
|
462
|
0 |
0 |
$end > $three_prime ? : |
|
552
|
0 |
0 |
if (&_internal_stop_or_x($seq->translate->seq)) |
|
584
|
0 |
0 |
if @cd_obj <= 1 |
|
590
|
0 |
0 |
unless $sum > 0 |
|
596
|
0 |
0 |
unless $_->{'rel_freq'} > 0 |
|
604
|
0 |
0 |
unless $match =~ /length|id|file/ |
|
611
|
0 |
0 |
if ($match eq "id") |
|
615
|
0 |
0 |
if ($match eq "length") |
|
619
|
0 |
0 |
if ($match =~ /file:(\S+)/) |
|
626
|
0 |
0 |
unless /(\S+)/ |
|
631
|
0 |
0 |
unless $order{$_->{'id'}} |
|
650
|
0 |
0 |
if ($line =~ /^>(\S+)\s+(\d+)/) { } |
|
704
|
0 |
4 |
unless $match =~ /^([^:]+):(\S+)$/ |
|
710
|
0 |
4 |
unless defined $filter_dispatch{$callsub} |
|
712
|
4 |
0 |
if ($tag eq 'order') { } |
|
|
0 |
0 |
elsif ($tag eq 'id') { } |
|
|
0 |
0 |
elsif ($tag eq 'file') { } |
|
716
|
0 |
7 |
if $_ > $ct |
|
721
|
0 |
0 |
if $id_list{$_} == 1 |
|
729
|
0 |
0 |
if $list{$_} == 1 |
|
816
|
0 |
7 |
if $end eq "-" |
|
817
|
0 |
7 |
if $end > $seq->length |
|
836
|
0 |
7 |
if (@nonStandardAA) |
|
840
|
7 |
0 |
if (@internalStops) |
|
844
|
7 |
0 |
@internalStops ? : |
|
862
|
7 |
0 |
if ($frame == 1) { } |
|
|
0 |
0 |
elsif ($frame == 3) { } |
|
|
0 |
0 |
elsif ($frame == 6) { } |
|
863
|
7 |
0 |
if (&_internal_stop_or_x($seq->translate->seq)) { } |
|
884
|
0 |
0 |
if ($dir eq 'F') { } |
|
971
|
0 |
1 |
defined $opts{'prefix'} ? : |
|
973
|
0 |
1 |
if $char_len < 1 |
|
980
|
0 |
7 |
if length $serial > $char_len |
|
991
|
0 |
1 |
if $length_warn |
|
1029
|
0 |
0 |
if ($string =~ /^[atcg]{3}$/i) { } |
|
|
0 |
0 |
elsif (&_in_list($string, [keys %aas])) { } |
|
1061
|
0 |
1 |
unless $in_format eq "genbank" |
|
1064
|
28 |
38 |
if ($feat->primary_tag eq "CDS") |
|
1066
|
0 |
28 |
if $location->isa("Bio::Location::Split") |
|
1071
|
28 |
153 |
if $tag eq "locus_tag" |
|
1072
|
2 |
179 |
if $tag eq "gene" |
|
1073
|
28 |
153 |
if $tag eq "product" |
|
1078
|
14 |
14 |
if ($feat->strand > 0) { } |
|
1099
|
0 |
0 |
if $mono[$i] ne "-" |
|
1100
|
0 |
0 |
if not $see_aa and $mono[$i] eq "-" |
|
1165
|
14 |
192 |
if ($myCodonTable->is_ter_codon($codon)) |
|
1180
|
0 |
0 |
if $_ eq $scalar |
|
1191
|
1 |
4 |
if ($val =~ /^(\d+)-(\d+)$/) { } |
|
1193
|
0 |
1 |
unless $last > $first |
|
1204
|
0 |
1 |
if $filename eq "-" |
|
1207
|
0 |
1 |
unless open my $sedout, ">", $sedfile |
|
1231
|
0 |
0 |
if ($id_list->{$seq_id}) |
|
1233
|
0 |
0 |
if $id_list->{$seq_id} > 2 |
|
1240
|
0 |
0 |
if ($id_list->{$seq_id}) { } |
|
1254
|
6 |
15 |
if $order_list->{$ct} |
|
1259
|
1 |
6 |
if ($order_list->{$ct}) { } |
|
1272
|
0 |
0 |
if ($id_list->{$seq_id}) |
|
1274
|
0 |
0 |
if $id_list->{$seq_id} > 2 |
|
1282
|
0 |
0 |
if ($id_list->{$seq_id}) { } |
|
1297
|
0 |
0 |
if $seq_id =~ /$regex/ |
|
1303
|
0 |
0 |
if ($seq_id =~ /$regex/) { } |
|
1319
|
0 |
0 |
if $percent_ambig > $cutoff |
|
1326
|
0 |
0 |
if ($ct >= $cutoff) { } |
|
1337
|
0 |
0 |
if $currseq->length <= $value |
|
1343
|
0 |
0 |
if ($currseq->length <= $value) { } |