| line |
true |
false |
branch |
|
162
|
31 |
0 |
if (not defined $self->sequence_factory) |
|
190
|
1 |
24 |
unless (defined $line) |
|
194
|
1 |
23 |
if ($line =~ /^\s+$/) |
|
196
|
1 |
0 |
if $line =~ /^\S/ |
|
200
|
0 |
1 |
unless $line |
|
204
|
0 |
24 |
unless $line =~ /^ID\s+\S+/ |
|
209
|
10 |
14 |
if ($line =~ tr/;// == 6) { } |
|
217
|
7 |
3 |
if ($line =~ /^ID (\S+);\s+SV (\d+); (\w+); ([^;]+); (\w{3}); (\w{3}); (\d+) BP./) |
|
220
|
7 |
3 |
if (defined $sv) |
|
225
|
0 |
10 |
if (defined $topology and $topology eq 'circular') |
|
229
|
7 |
3 |
if (defined $mol) |
|
230
|
6 |
1 |
if ($mol =~ /DNA/) { } |
|
|
1 |
0 |
elsif ($mol =~ /RNA/) { } |
|
|
0 |
0 |
elsif ($mol =~ /AA/) { } |
|
241
|
12 |
2 |
if ($line =~ /^ID\s+(\S+)[^;]*;\s+(\S+)[^;]*;\s+(\S+)[^;]*;/) |
|
245
|
12 |
2 |
if ($mol) |
|
246
|
0 |
12 |
if ($mol =~ /circular/) |
|
250
|
12 |
0 |
if (defined $mol) |
|
251
|
10 |
2 |
if ($mol =~ /DNA/) { } |
|
|
2 |
0 |
elsif ($mol =~ /RNA/) { } |
|
|
0 |
0 |
elsif ($mol =~ /AA/) { } |
|
262
|
5 |
19 |
unless (defined $name and length $name) |
|
274
|
24 |
475 |
if (/^(F[HT]|SQ)/) |
|
275
|
2 |
22 |
if $1 eq 'SQ' or $1 eq 'FT' |
|
279
|
22 |
453 |
if (/^DE\s+(\S.*\S)/) |
|
280
|
2 |
20 |
$desc ? : |
|
284
|
24 |
451 |
if (/^AC\s+(.*)?/ or /^PA\s+(.*)?/) |
|
287
|
23 |
1 |
unless defined $params{'-accession_number'} |
|
292
|
6 |
469 |
if (/^SV\s+\S+\.(\d+);?/) |
|
300
|
26 |
449 |
if (/^DT\s+(.+)$/) |
|
304
|
24 |
2 |
if ($version) |
|
305
|
11 |
13 |
if ($version =~ /\(Rel\. (\d+), Created\)/ms) { } |
|
|
11 |
2 |
elsif ($version =~ /\(Rel\. (\d+), Last updated, Version (\d+)\)/ms) { } |
|
329
|
29 |
446 |
if (/^KW (.*)\S*$/) { } |
|
|
21 |
425 |
elsif (/^O[SC]/) { } |
|
|
3 |
422 |
elsif (/^OX/) { } |
|
|
99 |
323 |
elsif (/^R/) { } |
|
|
5 |
318 |
elsif (/^DR/) { } |
|
|
15 |
303 |
elsif (/^CC\s+(.*)/) { } |
|
343
|
3 |
0 |
if (/NCBI_TaxID=(\d+)/) |
|
374
|
242 |
15 |
if (/^CC\s+(.*)/) { } |
|
392
|
22 |
24 |
if /^FT\s{3}\w/ |
|
393
|
2 |
22 |
if /^SQ / |
|
394
|
0 |
22 |
if /^CO / |
|
398
|
22 |
2 |
if (defined $buffer and $buffer =~ /^FT /) |
|
410
|
12 |
6 |
if ($params{'-species'} and $feat->primary_tag eq 'source' and $feat->has_tag('db_xref') and not $params{'-species'}->ncbi_taxid) |
|
414
|
12 |
0 |
if (index($tagval, 'taxon:') == 0) |
|
424
|
22 |
234 |
unless ($buffer =~ /^FT/) |
|
430
|
2 |
19 |
if ($params{'-species'} and defined $ncbi_taxid and not $params{'-species'}->ncbi_taxid) |
|
440
|
4 |
20 |
if ($buffer =~ /^CO/) |
|
445
|
4 |
0 |
unless ($buffer and $buffer =~ /^CO/) |
|
451
|
20 |
4 |
unless ($buffer =~ m[^//]) |
|
452
|
1 |
19 |
unless ($buffer =~ /^SQ/) |
|
454
|
0 |
0 |
if /^SQ/ |
|
459
|
18 |
2906 |
if m[^//] |
|
500
|
0 |
11 |
if ($self->_id_generation_func) { } |
|
508
|
5 |
6 |
if (not defined $name or $name eq 'unknown') |
|
513
|
0 |
11 |
if $name =~ /\s/ |
|
522
|
2 |
9 |
if ($seq->can('division') and defined $seq->division and $self->_is_valid_division($seq->division)) { } |
|
531
|
0 |
11 |
if ($seq->can('molecule') and defined $seq->molecule and $self->_is_valid_molecule_type($seq->molecule)) { } |
|
|
6 |
7 |
elsif ($seq->can('primary_seq') and defined $seq->primary_seq->alphabet) { } |
|
540
|
6 |
0 |
if ($alphabet eq 'dna') { } |
|
|
0 |
0 |
elsif ($alphabet eq 'rna') { } |
|
|
0 |
0 |
elsif ($alphabet eq 'protein') { } |
|
551
|
0 |
11 |
if ($seq->is_circular) |
|
641
|
0 |
13 |
unless defined $seq |
|
642
|
4 |
9 |
unless (ref $seq and $seq->isa('Bio::SeqI')) |
|
643
|
0 |
4 |
if $self->verbose >= 0 |
|
645
|
2 |
2 |
unless (ref $seq and $seq->isa('Bio::PrimarySeqI')) |
|
658
|
0 |
11 |
if (my $func = $self->_ac_generation_func) { } |
|
|
4 |
7 |
elsif ($seq->isa('Bio::Seq::RichSeqI') and defined $seq->accession_number) { } |
|
|
7 |
0 |
elsif ($seq->can('accession_number')) { } |
|
668
|
11 |
0 |
if (defined $acc) |
|
669
|
0 |
11 |
unless $self->_print("AC $acc;\n", "XX\n") |
|
676
|
4 |
7 |
if ($seq->can('get_dates')) |
|
684
|
0 |
0 |
unless ($cr and $ur and $ur) |
|
689
|
0 |
0 |
if (not $date_flag) { } |
|
690
|
0 |
0 |
if $ct == 1 |
|
693
|
0 |
0 |
if $ct == 2 |
|
703
|
0 |
4 |
if ($switch == 1) |
|
704
|
0 |
0 |
unless $self->_print("XX\n") |
|
709
|
0 |
11 |
unless $self->_write_line_EMBL_regex('DE ', 'DE ', $seq->desc, '\\s+|$', 80) |
|
710
|
0 |
11 |
unless $self->_print("XX\n") |
|
715
|
0 |
11 |
if (my $func = $self->_kw_generation_func) { } |
|
|
4 |
7 |
elsif ($seq->can('keywords')) { } |
|
720
|
4 |
7 |
if (defined $kw) |
|
721
|
0 |
4 |
unless $self->_write_line_EMBL_regex('KW ', 'KW ', $kw, '\\s+|$', 80) |
|
722
|
0 |
4 |
unless $self->_print("XX\n") |
|
728
|
6 |
5 |
if ($seq->can('species') and my $spec = $seq->species) |
|
735
|
0 |
6 |
if ($spec->common_name) |
|
738
|
0 |
6 |
unless $self->_print("OS $OS\n") |
|
740
|
0 |
6 |
unless $self->_write_line_EMBL_regex('OC ', 'OC ', $OC, '; |$', 80) |
|
741
|
0 |
6 |
if ($spec->organelle) |
|
742
|
0 |
0 |
unless $self->_write_line_EMBL_regex('OG ', 'OG ', $spec->organelle, '; |$', 80) |
|
745
|
2 |
4 |
if ($ncbi_taxid) |
|
746
|
0 |
2 |
unless $self->_print("OX NCBI_TaxID=$ncbi_taxid\n") |
|
748
|
0 |
6 |
unless $self->_print("XX\n") |
|
752
|
9 |
2 |
if ($seq->can('annotation') and defined $seq->annotation) |
|
754
|
0 |
6 |
unless $self->_print("RN [$t]\n") |
|
758
|
0 |
6 |
if ($ref->comment) |
|
759
|
0 |
0 |
unless $self->_write_line_EMBL_regex('RC ', 'RC ', $ref->comment, '\\s+|$', 80) |
|
763
|
6 |
0 |
if ($start and $end) { } |
|
|
0 |
0 |
elsif ($start or $end) { } |
|
764
|
0 |
6 |
unless $self->_print("RP $start-$end\n") |
|
770
|
0 |
6 |
if (my $med = $ref->medline) |
|
771
|
0 |
0 |
unless $self->_print("RX MEDLINE; $med.\n") |
|
773
|
0 |
6 |
if (my $pm = $ref->pubmed) |
|
774
|
0 |
0 |
unless $self->_print("RX PUBMED; $pm.\n") |
|
779
|
0 |
6 |
unless $self->_write_line_EMBL_regex('RA ', 'RA ', $authors . ';', '\\s+|$', 80) |
|
788
|
0 |
6 |
unless $self->_write_line_EMBL_regex('RT ', 'RT ', $ref_title, '\\s+|$', 80) |
|
789
|
0 |
6 |
unless $self->_write_line_EMBL_regex('RL ', 'RL ', $ref->location, '\\s+|$', 80) |
|
790
|
0 |
6 |
unless $self->_print("XX\n") |
|
795
|
2 |
7 |
if (my(@db_xref) = $seq->annotation->get_Annotations('dblink')) |
|
801
|
0 |
43 |
$opt ? : |
|
802
|
0 |
43 |
unless $self->_write_line_EMBL_regex('DR ', 'DR ', $line, '\\s+|$', 80) |
|
804
|
0 |
2 |
unless $self->_print("XX\n") |
|
809
|
0 |
4 |
unless $self->_write_line_EMBL_regex('CC ', 'CC ', $comment->text, '\\s+|$', 80) |
|
810
|
0 |
4 |
unless $self->_print("XX\n") |
|
817
|
0 |
11 |
unless $self->_print("FH Key Location/Qualifiers\n") |
|
818
|
0 |
11 |
unless $self->_print("FH\n") |
|
820
|
9 |
2 |
$seq->can('top_SeqFeatures') ? : |
|
821
|
6 |
5 |
if ($feats[0]) |
|
822
|
0 |
6 |
if (defined $self->_post_sort) { } |
|
836
|
0 |
0 |
unless $self->_print_EMBL_FTHelper($fth) |
|
845
|
0 |
38 |
if ($fth->key eq 'CONTIG') |
|
848
|
0 |
38 |
unless $self->_print_EMBL_FTHelper($fth) |
|
854
|
0 |
11 |
if ($self->_show_dna == 0) |
|
855
|
0 |
0 |
unless $self->_print("//\n") |
|
858
|
0 |
11 |
unless $self->_print("XX\n") |
|
863
|
9 |
2 |
if ($seq->can('annotation') and defined $seq->annotation) |
|
865
|
0 |
0 |
if ($ctg->value) |
|
866
|
0 |
0 |
unless $self->_write_line_EMBL_regex('CO ', 'CO ', $ctg->value, '[,]|$', 80) |
|
872
|
8 |
3 |
if (length $str) |
|
883
|
0 |
8 |
if ($olen < 0) |
|
887
|
0 |
8 |
unless $self->_print("SQ Sequence $len BP; $alen A; $clen C; $glen G; $tlen T; $olen other;\n") |
|
903
|
0 |
162 |
unless $self->_print(sprintf(" $blocks%9d\n", $i + $nuc)) |
|
907
|
8 |
0 |
if (my $last = substr($str, $i)) |
|
912
|
0 |
8 |
unless $self->_print(sprintf(" $blocks%9d\n", $length)) |
|
917
|
0 |
11 |
unless $self->_print("//\n") |
|
919
|
11 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
938
|
0 |
38 |
unless (ref $fth and $fth->isa('Bio::SeqIO::FTHelper')) |
|
946
|
0 |
38 |
if ($fth->key eq 'CONTIG') |
|
947
|
0 |
0 |
unless $self->_print("XX\n") |
|
948
|
0 |
0 |
unless $self->_write_line_EMBL_regex('CO ', 'CO ', $fth->loc, '\\,|$', 80) |
|
953
|
0 |
38 |
unless $self->_write_line_EMBL_regex(sprintf('FT %-15s ', $fth->key), 'FT ', $fth->loc, '\\,|$', 80) |
|
957
|
0 |
108 |
unless (defined $fth->field->{$tag}) |
|
962
|
0 |
139 |
if ($value eq '_no_value') { } |
|
|
139 |
0 |
elsif (not $Bio::SeqIO::embl::FTQUAL_NO_QUOTE{$tag} or length "/$tag=$value" >= 60) { } |
|
963
|
0 |
0 |
unless $self->_write_line_EMBL_regex('FT ', 'FT ', "/$tag", '.|$', 80) |
|
972
|
80 |
59 |
$value =~ /\s+/ ? : |
|
973
|
0 |
139 |
unless $self->_write_line_EMBL_regex('FT ', 'FT ', qq[/$tag="$value"], $pat, 80) |
|
977
|
0 |
0 |
unless $self->_write_line_EMBL_regex('FT ', 'FT ', "/$tag=$value", '.|$', 80) |
|
1002
|
0 |
4 |
unless ($$buffer =~ /^CO/) |
|
1007
|
3 |
353 |
unless /^C/ |
|
1008
|
353 |
0 |
if (/^CO\s+(.*)/) |
|
1036
|
0 |
99 |
unless ($$buffer =~ /^RN/) |
|
1049
|
99 |
628 |
unless /^R/ |
|
1050
|
40 |
588 |
if (/^RP (\d+)-(\d+)/) |
|
1051
|
55 |
573 |
if (/^RX MEDLINE;\s+(\d+)/) |
|
1052
|
10 |
618 |
if (/^RX PUBMED;\s+(\d+)/) |
|
1053
|
193 |
435 |
if (/^RA (.*)/) |
|
1056
|
164 |
271 |
if (/^RT (.*)/) |
|
1059
|
156 |
115 |
if (/^RL (.*)/) |
|
1062
|
3 |
112 |
if (/^RC (.*)/) |
|
1105
|
21 |
71 |
if (/^OS\s+(.+)/) { } |
|
|
50 |
21 |
elsif (s/^OC\s+(.+)$//) { } |
|
|
0 |
21 |
elsif (/^OG\s+(.*)/) { } |
|
1106
|
0 |
21 |
$sci_name ? : |
|
1122
|
0 |
21 |
unless $sci_name |
|
1132
|
21 |
0 |
if $class[-2] |
|
1133
|
21 |
0 |
if ($sci_name =~ /^($possible_genus)/) { } |
|
1141
|
21 |
0 |
if ($genus) |
|
1142
|
0 |
21 |
if $genus =~ /^(Unknown|None)$/i |
|
1147
|
0 |
21 |
if ($species =~ /subsp\.|var\./) |
|
1155
|
21 |
0 |
unless ($class[-1] eq 'Viruses') |
|
1157
|
11 |
10 |
if $common |
|
1161
|
21 |
0 |
unless ($class[-1] eq $sci_name) |
|
1169
|
0 |
21 |
unless $sci_name |
|
1184
|
21 |
0 |
unless ($class[-1] eq 'Viruses') |
|
1185
|
21 |
0 |
if $genus |
|
1186
|
11 |
10 |
if $species |
|
1187
|
0 |
21 |
if $sub_species |
|
1188
|
11 |
10 |
if $common |
|
1190
|
0 |
21 |
if $org |
|
1211
|
25 |
5 |
if (/^DR ([^\s;]+);\s*([^\s;]+);?\s*([^\s;]+)?\.$/) { } |
|
1245
|
1 |
3 |
if (/^OX (\S+)=(\d+);$/) { } |
|
1274
|
0 |
0 |
if (defined $value) |
|
1301
|
256 |
0 |
if ($$buffer =~ /^FT\s{3}(\S+)\s+(\S+)/) { } |
|
|
0 |
0 |
elsif ($$buffer =~ /^CO\s+(\S+)/) { } |
|
1306
|
2016 |
22 |
if (/^FT(\s+)(.+?)\s*$/) { } |
|
1309
|
1782 |
234 |
if (length $1 > 4) { } |
|
1311
|
1523 |
259 |
if (@qual) { } |
|
|
254 |
5 |
elsif (substr($2, 0, 1) eq '/') { } |
|
1336
|
0 |
0 |
if (/^CO\s+(\S+)\s*$/) { } |
|
1365
|
0 |
1091 |
unless (($qualifier, $value) = $data =~ m[^/([^=]+)(?:=\s*(.*))?]) |
|
1366
|
0 |
0 |
if (defined $last_unquoted_qualifier) { } |
|
1371
|
0 |
0 |
if $qualifier ne 'translation' |
|
1383
|
0 |
1091 |
unless defined $qualifier |
|
1386
|
1091 |
0 |
if (defined $value) { } |
|
1388
|
971 |
120 |
if (substr($value, 0, 1) eq '"') { } |
|
1395
|
0 |
686 |
unless (defined $next) |
|
1405
|
569 |
117 |
if ($qualifier eq 'translation') { } |
|
1445
|
0 |
0 |
unless $length |
|
1452
|
0 |
0 |
unless $self->_print("$pre1$sub\n") |
|
1456
|
0 |
0 |
unless $self->_print("$pre2$sub\n") |
|
1483
|
0 |
263 |
unless $length |
|
1490
|
401 |
0 |
if ($line =~ /^(.{1,$subl})($pat)(.*)/) |
|
1492
|
8 |
393 |
if $pre1 eq 'RA ' |
|
1499
|
0 |
401 |
if $l eq '' |
|
1511
|
256 |
7 |
if $s |
|
1513
|
0 |
145 |
unless $self->_print("$pre2$s\n") |
|
1532
|
0 |
6 |
if (@_) |
|
1553
|
31 |
11 |
if (@_) |
|
1574
|
0 |
11 |
if (@_) |
|
1595
|
0 |
11 |
if (@_) |
|
1616
|
0 |
0 |
if (@_) |
|
1637
|
0 |
11 |
if (@_) |