| line |
true |
false |
branch |
|
241
|
115 |
0 |
if (not defined $self->sequence_factory) |
|
280
|
113 |
76 |
if index($buffer, 'LOCUS ') == 0 |
|
282
|
6 |
113 |
unless defined $buffer |
|
283
|
0 |
113 |
unless $buffer =~ /^LOCUS\s+(\S.*)$/o |
|
295
|
0 |
113 |
if (exists $VALID_ALPHABET{$seqlength}) { } |
|
316
|
113 |
0 |
exists $VALID_ALPHABET{$alphabet} ? : |
|
320
|
10 |
103 |
if ($params{'-alphabet'} eq 'protein') { } |
|
328
|
4 |
109 |
if ($params{'-molecule'} eq 'dna' or $params{'-molecule'} eq 'rna') |
|
332
|
0 |
113 |
unless exists $VALID_MOLTYPE{$params{'-molecule'}} |
|
335
|
8 |
105 |
if ($circ eq 'circular') { } |
|
341
|
34 |
71 |
length $circ == 3 ? : |
|
352
|
107 |
6 |
if ($date =~ s/\s*((\d{1,2})-(\w{3})-(\d{2,4})).*/$1/) |
|
353
|
0 |
107 |
if (length $date < 11) { } |
|
357
|
0 |
0 |
if (length $d == 1) |
|
362
|
0 |
0 |
if (length $y == 2) |
|
363
|
0 |
0 |
if ($y > 60) { } |
|
385
|
2 |
111 |
unless ($builder->want_object) |
|
391
|
106 |
5 |
if ($builder->want_slot('annotation')) |
|
398
|
110 |
629 |
if ($line =~ /^DEFINITION\s+(\S.*\S)/) |
|
401
|
62 |
110 |
if ($line =~ /^\s+(.*)/) |
|
415
|
110 |
629 |
if ($line =~ /^ACCESSION\s+(\S.*\S)/) { } |
|
|
1 |
628 |
elsif ($line =~ /^PID\s+(\S+)/) { } |
|
|
91 |
537 |
elsif ($line =~ /^VERSION\s+(\S.+)$/) { } |
|
|
107 |
430 |
elsif ($line =~ /^KEYWORDS\s+(\S.*)/) { } |
|
|
106 |
324 |
elsif ($line =~ /^SOURCE\s+\S/) { } |
|
|
109 |
215 |
elsif ($line =~ /^REFERENCE\s+\S/) { } |
|
|
2 |
213 |
elsif ($line =~ /^PROJECT\s+(\S.*)/) { } |
|
|
60 |
153 |
elsif ($line =~ /^COMMENT\s+(\S.*)/) { } |
|
|
20 |
133 |
elsif ($line =~ /^DB(?:SOURCE|LINK)\s+(\S.+)/) { } |
|
418
|
3 |
110 |
if ($line =~ /^\s+(.*)/) |
|
436
|
87 |
4 |
if ($acc =~ /^\w+\.(\d+)/) |
|
440
|
89 |
2 |
if ($gi and index($gi, 'GI:') == 0) |
|
450
|
31 |
107 |
if ($line =~ /^\s+(.*)/) |
|
457
|
107 |
0 |
if @kw |
|
465
|
101 |
5 |
if ($builder->want_slot('species')) { } |
|
471
|
5 |
13 |
if substr($buffer, 0, 1) ne ' ' |
|
479
|
100 |
9 |
if ($annotation) { } |
|
487
|
9 |
38 |
if substr($buffer, 0, 1) ne ' ' |
|
495
|
2 |
0 |
if ($annotation) |
|
506
|
58 |
2 |
if ($annotation) { } |
|
509
|
58 |
423 |
if $line =~ /^\S/ |
|
514
|
2 |
56 |
if (my($text, $table) = $comment =~ /([^#]*)(##\S+Data-START##.+?##\S+Data-END##)/is) { } |
|
517
|
1 |
1 |
if $text |
|
537
|
2 |
5 |
if substr($buffer, 0, 1) ne ' ' |
|
545
|
20 |
0 |
if ($annotation) { } |
|
548
|
20 |
65 |
if $line =~ /^\S/ |
|
553
|
5 |
15 |
if ($dbsource =~ s/(UniProt(?:KB)?|swissprot):\s+locus\s+(\S+)\,.+\n//) { } |
|
564
|
5 |
0 |
if ($dbsource =~ s/\s+created:\s+([^\.]+)\.\n//) |
|
585
|
5 |
0 |
if ($dbsource =~ s/\s+xrefs:\s+((?:\S+,\s+)+\S+)\s+xrefs/xrefs/) { } |
|
|
0 |
0 |
elsif ($dbsource =~ s/\s+xrefs:\s+(.+)\s+xrefs/xrefs/i) { } |
|
592
|
49 |
0 |
if ($dbsrc =~ /(\S+)\.(\d+)/ or $dbsrc =~ /(\S+)/) |
|
596
|
11 |
38 |
unless defined $version |
|
597
|
20 |
23 |
$i++ % 2 ? : |
|
|
6 |
43 |
$id =~ /^\d\S{3}/ ? : |
|
618
|
0 |
0 |
if ($id =~ /gi:\s+(\d+)/) { } |
|
|
0 |
0 |
elsif ($id =~ /pdb\s+accession\s+(\S+)/) { } |
|
620
|
0 |
0 |
$i++ % 2 ? : |
|
643
|
5 |
0 |
if ($dbsource =~ s/xrefs\s+
\(non\-sequence\s+databases\):\s+
((?:\S+,\s+)+\S+)//x) |
|
656
|
16 |
70 |
unless (exists $DBSOURCE{$db}) |
|
672
|
4 |
11 |
if ($dbsource =~ /^(\S*?):?\s*accession\s+(\S+)\.(\d+)/) { } |
|
|
1 |
10 |
elsif ($dbsource =~ /^(\S*?):?\s*accession\s+(\S+)/) { } |
|
|
10 |
0 |
elsif ($dbsource =~ /(\S+)([\.:])\s*(\S+)/) { } |
|
700
|
9 |
1 |
if ($2 eq ':') { } |
|
736
|
0 |
0 |
if substr($buffer, 0, 1) ne ' ' |
|
743
|
111 |
116 |
if ($line =~ /^(FEATURES|ORIGIN)/) |
|
746
|
111 |
116 |
if $line =~ /^(FEATURES|ORIGIN)/ |
|
751
|
0 |
111 |
unless defined $buffer |
|
759
|
106 |
5 |
if $annotation |
|
763
|
0 |
111 |
unless ($builder->want_object) |
|
769
|
104 |
1 |
if ($builder->want_slot('features') and defined $buffer and $buffer =~ /^FEATURES/o) |
|
787
|
104 |
8280 |
if $buffer =~ /^BASE|ORIGIN|CONTIG|WGS/o |
|
807
|
0 |
8280 |
unless (defined $ftunit) |
|
813
|
0 |
0 |
unless ($buffer =~ /^\s{5,5}\S+/o or $buffer =~ /^\S+/o) |
|
827
|
95 |
6 |
if ($species and $feat->primary_tag eq 'source' and $feat->has_tag('db_xref') and !$species->ncbi_taxid || $species->ncbi_taxid && $species->ncbi_taxid =~ /^list/) |
|
835
|
95 |
1 |
if (index($tagval, 'taxon:') == 0) |
|
848
|
111 |
0 |
if (defined $buffer) |
|
850
|
7 |
104 |
if ($buffer =~ /^CONTIG\s+(.*)/o) { } |
|
|
1 |
103 |
elsif ($buffer =~ /^WGS|WGS_SCAFLD\s+/o) { } |
|
|
53 |
50 |
elsif (not $buffer =~ m[^ORIGIN|//]o) { } |
|
853
|
7 |
22 |
if $buffer =~ m[^ORIGIN|//]o |
|
857
|
7 |
0 |
if ($ctg) |
|
880
|
52 |
96 |
if $buffer =~ m[^(ORIGIN|//)] |
|
884
|
0 |
111 |
unless ($builder->want_object) |
|
888
|
101 |
10 |
if ($builder->want_slot('seq')) { } |
|
|
10 |
0 |
elsif (defined $buffer and substr($buffer, 0, 2) ne '//') { } |
|
891
|
93 |
8 |
if (defined $buffer and $buffer =~ s/^ORIGIN\s+//) |
|
892
|
1 |
92 |
if ($annotation and length $buffer > 0) |
|
903
|
92 |
32643 |
if $buffer =~ m[^//] |
|
915
|
10 |
162 |
if substr($buffer, 0, 2) eq '//' |
|
923
|
0 |
111 |
unless $seq |
|
944
|
0 |
25 |
unless defined $seq |
|
946
|
0 |
25 |
unless (ref $seq and $seq->isa('Bio::SeqI')) |
|
955
|
2 |
23 |
unless ($seq->can('division') and defined($div = $seq->division)) |
|
960
|
2 |
23 |
unless ($seq->can('molecule') and defined($mol = $seq->molecule)) |
|
966
|
2 |
23 |
$seq->is_circular ? : |
|
971
|
0 |
25 |
if ($self->_id_generation_func) { } |
|
976
|
23 |
2 |
if ($seq->can('get_dates')) |
|
980
|
0 |
25 |
if $seq->display_id =~ /\s/ |
|
983
|
1 |
24 |
lc $alpha eq 'protein' ? : |
|
995
|
0 |
25 |
if ($self->_ac_generation_func) { } |
|
1002
|
23 |
2 |
if ($seq->isa('Bio::Seq::RichSeqI')) |
|
1010
|
0 |
25 |
if ($seq->isa('Bio::Seq::RichSeqI') and $seq->pid) |
|
1015
|
0 |
25 |
if (defined $self->_sv_generation_func) { } |
|
|
18 |
9 |
elsif ($seq->isa('Bio::Seq::RichSeqI') and defined $seq->seq_version) { } |
|
1017
|
0 |
0 |
if ($temp_line) |
|
1023
|
18 |
0 |
defined $id && $id =~ /^\d+$/ ? : |
|
1037
|
1 |
1 |
$db eq 'Project' ? : |
|
1038
|
1 |
1 |
$db eq 'Project' ? : |
|
|
0 |
2 |
$db eq 'GenBank' ? : |
|
1045
|
0 |
25 |
if (defined $self->_kw_generation_func) { } |
|
|
23 |
2 |
elsif ($seq->can('keywords')) { } |
|
1051
|
23 |
0 |
unless $kw =~ /\.$/ |
|
1062
|
22 |
3 |
if (my $spec = $seq->species) |
|
1063
|
22 |
0 |
$spec->can('organelle') ? : |
|
1067
|
22 |
0 |
if ($spec->isa('Bio::Species')) { } |
|
1082
|
22 |
0 |
$spec->name('abbreviated') ? : |
|
1084
|
4 |
18 |
$on ? : |
|
1085
|
6 |
16 |
$cn ? : |
|
1097
|
47 |
0 |
if ($ref->start) { } |
|
|
0 |
0 |
elsif ($ref->gb_reference) { } |
|
1098
|
3 |
44 |
$seq->alphabet eq 'protein' ? : |
|
1109
|
9 |
38 |
if $ref->consortium |
|
1115
|
5 |
42 |
if ($ref->medline) |
|
1122
|
13 |
34 |
if ($ref->pubmed) |
|
1127
|
0 |
47 |
if ($ref->comment) |
|
1143
|
0 |
25 |
if (defined $self->_post_sort) { } |
|
1164
|
0 |
430 |
unless ($fth->isa('Bio::SeqIO::FTHelper')) |
|
1173
|
0 |
25 |
if ($seq->annotation->get_Annotations('wgs')) |
|
1183
|
1 |
24 |
if ($seq->annotation->get_Annotations('contig')) |
|
1187
|
1 |
0 |
if (not $ct) { } |
|
1197
|
1 |
24 |
if ($seq->length == 0) |
|
1201
|
1 |
24 |
if ($self->_show_dna == 0) |
|
1211
|
0 |
24 |
$o ? : |
|
1233
|
19 |
5 |
if (my $last = substr($str, $i)) |
|
1246
|
24 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
1265
|
0 |
430 |
unless (ref $fth and $fth->isa('Bio::SeqIO::FTHelper')) |
|
1271
|
0 |
430 |
length $fth->key >= 15 ? : |
|
1278
|
0 |
997 |
if ($tag eq 'db_xref' and grep /HASH/, @{$fth->field->{$tag};}) { } |
|
1291
|
0 |
1085 |
if ($value eq '_no_value') { } |
|
|
976 |
109 |
elsif (not $FTQUAL_NO_QUOTE{$tag} or length "/$tag=$value" >= $FTQUAL_LINE_LENGTH) { } |
|
1303
|
330 |
646 |
$value =~ /\s/ ? : |
|
1334
|
0 |
100 |
unless ($$buffer =~ /^REFERENCE/) |
|
1344
|
402 |
977 |
if ($line =~ /^\s{2}AUTHORS\s+(.*)/o) |
|
1347
|
638 |
402 |
if ($line =~ /^\s{9,}(.*)/o) |
|
1356
|
35 |
1344 |
if ($line =~ /^\s{2}CONSRTM\s+(.*)/o) |
|
1359
|
1 |
35 |
if ($line =~ /^\s{9,}(.*)/o) |
|
1368
|
408 |
971 |
if ($line =~ /^\s{2}TITLE\s+(.*)/o) |
|
1371
|
285 |
408 |
if ($line =~ /^\s{9,}(.*)/o) |
|
1380
|
416 |
963 |
if ($line =~ /^\s{2}JOURNAL\s+(.*)/o) |
|
1386
|
149 |
416 |
if ($line =~ /^\s{9,}(.*)/o) |
|
1396
|
59 |
904 |
if ($line =~ /^\s{2}REMARK\s+(.*)/o) |
|
1399
|
24 |
59 |
if ($line =~ /^\s{9,}(.*)/o) |
|
1409
|
130 |
774 |
if ($line =~ /^\s{2}MEDLINE\s+(.*)/) |
|
1412
|
0 |
130 |
if ($line =~ /^\s{9,}(.*)/) |
|
1422
|
237 |
537 |
if ($line =~ /^\s{3}PUBMED\s+(.*)/) |
|
1425
|
0 |
237 |
if ($line =~ /^\s{9,}(.*)/) |
|
1435
|
417 |
120 |
if ($line =~ /^REFERENCE/o) |
|
1437
|
317 |
100 |
if defined $ref |
|
1451
|
286 |
131 |
if ($line =~ /^REFERENCE\s+\d+\s+\([a-z]+ (\d+) to (\d+)\)/) { } |
|
|
14 |
117 |
elsif ($line =~ /^REFERENCE\s+\d+\s+\((.*)\)/) { } |
|
1460
|
100 |
437 |
if $line =~ /^(FEATURES)|(COMMENT)/o |
|
1466
|
100 |
0 |
if defined $ref |
|
1494
|
402 |
15 |
if $au |
|
1495
|
408 |
9 |
if $title |
|
1557
|
303 |
214 |
if ($line =~ /^(?:\s{0,2})(\w+)\s+(.+)?$/ox) { } |
|
1559
|
101 |
202 |
if $tag and not exists $source{$tag} |
|
1562
|
0 |
214 |
unless $tag |
|
1565
|
101 |
7 |
if $tag ne 'CLASSIFICATION' and $tag eq 'ORGANISM' and $line =~ /(?
|
|
1571
|
113 |
303 |
exists $ann->{$tag} ? : |
|
1579
|
0 |
101 |
unless $sci_name |
|
1584
|
101 |
0 |
if ($sl =~ /^(mitochondrion|chloroplast|plastid)?
\s*(.*?)
\s*(?: \( (.*?) \) )?\.?
$
/msx) { } |
|
1606
|
101 |
0 |
$class[-2] ? : |
|
1608
|
88 |
13 |
if ($sci_name =~ /^($possible_genus)/) { } |
|
1620
|
5 |
96 |
if ($species and $species =~ /(.+)\s+((?:subsp\.|var\.).+)/) |
|
1629
|
0 |
101 |
unless defined $species || defined $genus and $unkn == 0 |
|
1637
|
101 |
0 |
if @class > 0 |
|
1638
|
32 |
69 |
if $common |
|
1639
|
101 |
0 |
if $abbr_name |
|
1640
|
9 |
92 |
if $organelle |
|
1664
|
8280 |
0 |
if ($$buffer =~ /^\s{5}(\S+)\s+(.+?)\s*$/o) { } |
|
1669
|
88489 |
103 |
if ($line =~ /^(\s+)(.+?)\s*$/o) { } |
|
1672
|
80312 |
8177 |
if (length $1 > 6) { } |
|
1675
|
68121 |
12191 |
if (@qual or index($2, '/') == 0) { } |
|
1719
|
0 |
55807 |
unless my($qualifier, $value) = $data =~ m[^/([^=]+)(?:=\s*(.+))?] |
|
1722
|
0 |
55807 |
unless defined $qualifier |
|
1724
|
54903 |
904 |
if (defined $value) { } |
|
1726
|
52083 |
2820 |
if (substr($value, 0, 1) eq '"') { } |
|
|
27 |
2793 |
elsif ($value =~ /^\(/) { } |
|
1730
|
0 |
12312 |
if ($i >= $#qual) |
|
1746
|
9870 |
2442 |
unless ($qualifier =~ /^translation$/i) |
|
1763
|
0 |
2 |
if ($i >= $#qual) |
|
1802
|
0 |
0 |
unless $length |
|
1840
|
0 |
1765 |
unless $length |
|
1848
|
2129 |
0 |
if ($line =~ /^(.{0,$subl})($pat)(.*)/) |
|
1854
|
0 |
2129 |
if $l eq '' |
|
1866
|
1760 |
5 |
if $s |
|
1884
|
0 |
25 |
if (defined $value) |
|
1902
|
116 |
25 |
if (defined $value) |
|
1920
|
0 |
25 |
if (defined $value) |
|
1938
|
0 |
25 |
if (defined $value) |
|
1956
|
0 |
25 |
if (defined $value) |
|
1974
|
0 |
25 |
if (defined $value) |