| line |
!l |
l&&!r |
l&&r |
condition |
|
466
|
414 |
13474 |
0 |
$self->in_element('hit') || $self->in_element('hsp') and /Score\s*=\s*(\S+)\s*bits\s* # Bit score
(?:\((\d+)\))?, # Raw score
\s+Log\-Length\sScore\s*=\s*(\d+) # Log-Length score
/ox |
|
|
414 |
13474 |
0 |
$self->in_element('hit') || $self->in_element('hsp') and /Score\s*=\s*([^,\s]+), # Raw score
\s*Expect\s*=\s*([^,\s]+), # E-value
\s*P(?:\(\S+\))?\s*=\s*([^,\s]+) # P-value
/ox |
|
|
414 |
13051 |
423 |
$self->in_element('hit') || $self->in_element('hsp') and /Score\s*=\s*(\S+)\s* # Bit score
\(([\d\.]+)\s*bits\), # Raw score
\s*Expect\s*=\s*([^,\s]+), # E-value
\s*(?:Sum)?\s* # SUM
P(?:\(\d+\))?\s*=\s*([^,\s]+) # P-value
(?:\s*,\s+Group\s*\=\s*(\d+))? # HSP Group
/ox |
|
|
414 |
12981 |
70 |
$self->in_element('hit') || $self->in_element('hsp') and /^\sFeatures\s\w+\sthis\spart/mosx |
|
|
414 |
11781 |
1200 |
$self->in_element('hit') || $self->in_element('hsp') and /Score\s*=\s*(\S+)\s*bits\s* # Bit score
(?:\((\d+)\))?, # Missing for BLAT pseudo-BLAST fmt
\s*Expect(?:\((\d+\+?)\))?\s*=\s*([^,\s]+) # E-value
/ox |
|
|
414 |
10158 |
1623 |
$self->in_element('hsp') and m[Identities\s*=\s*(\d+)\s*/\s*(\d+)\s*[\d\%\(\)]+\s*
(?:,\s*Positives\s*=\s*(\d+)/(\d+)\s*[\d\%\(\)]+\s*)? # pos only valid for Protein alignments
(?:\,\s*Gaps\s*=\s*(\d+)/(\d+))? # Gaps
]iox |
|
|
414 |
9786 |
372 |
$self->in_element('hsp') and m[Strand\s*=\s*(Plus|Minus)\s*/\s*(Plus|Minus)]i |
|
|
414 |
9444 |
342 |
$self->in_element('hsp') and /Links\s*=\s*(\S+)/ox |
|
|
414 |
9136 |
308 |
$self->in_element('hsp') and m[Frame\s*=\s*([\+\-][1-3])\s*(/\s*([\+\-][1-3]))?] |
|
|
409 |
9058 |
0 |
$self->in_element('hsp') and /WARNING|NOTE/ |
|
474
|
0 |
85 |
0 |
$reportversion and $reportversion =~ /WashU$/ |
|
597
|
10 |
25 |
13 |
$q =~ /\w$/ && $_ =~ /^\w/ |
|
626
|
67 |
0 |
27 |
defined $version && length $version |
|
748
|
0 |
26 |
923 |
defined($_ = $self->_readline) and not /^\s+$/ |
|
877
|
165 |
359 |
12 |
$restofline =~ /\w$/ && $_ =~ /^\w/ |
|
1184
|
0 |
3 |
1 |
$frame1 and $frame2 |
|
1299
|
2708 |
96 |
15 |
/^\s+[\d+\.]+\s+[\d+\.]+\s+[\d+\.]/ and $last eq '' |
|
1397
|
0 |
26 |
108 |
defined $_ and not /^\s+$/ |
|
1400
|
48 |
36 |
24 |
$firstgapinfo and s/Q=(\d+),R=(\d+)\s+//x |
|
1506
|
0 |
26 |
0 |
defined $_ and not /^\s+/ |
|
1903
|
0 |
9058 |
27150 |
defined $_ and $i < 3 |
|
1905
|
18092 |
9058 |
0 |
$i == 0 and /^\s+$/ |
|
1932
|
0 |
0 |
9034 |
defined $_ and defined $len |
|
2188
|
38749 |
4162 |
96 |
defined $type and $type eq 'result' |
|
2226
|
15374 |
18530 |
32019 |
$self->in_element('hsp') and $data->{'Name'} =~ /^Hsp\_(qseq|hseq|midline)$/ |
|
2232
|
68 |
2 |
65853 |
defined $data->{'Data'} and not $data->{'Data'} =~ /^\s+$/ |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
466
|
85 |
0 |
15240 |
/^((?:\S+?)?BLAST[NPX]?)\s+(.+)$/i or /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i |
|
|
922 |
12552 |
414 |
$self->in_element('hit') || $self->in_element('hsp') |
|
|
922 |
12552 |
414 |
$self->in_element('hit') || $self->in_element('hsp') |
|
|
922 |
12552 |
414 |
$self->in_element('hit') || $self->in_element('hsp') |
|
|
829 |
12222 |
414 |
$self->in_element('hit') || $self->in_element('hsp') |
|
|
825 |
12156 |
414 |
$self->in_element('hit') || $self->in_element('hsp') |
|
|
26 |
42 |
9482 |
/^Parameters:/ or /^\s+Database:\s+?/ |
|
|
68 |
0 |
9482 |
/^Parameters:/ or /^\s+Database:\s+?/ or /^\s+Subset/ |
|
|
42 |
15 |
9467 |
/^Parameters:/ or /^\s+Database:\s+?/ or /^\s+Subset/ or /^\s*Lambda/ |
|
|
15 |
0 |
9467 |
/^Parameters:/ or /^\s+Database:\s+?/ or /^\s+Subset/ or /^\s*Lambda/ or /^\s*Histogram/ |
|
|
15 |
0 |
9467 |
/^Parameters:/ or /^\s+Database:\s+?/ or /^\s+Subset/ or /^\s*Lambda/ or /^\s*Histogram/ or $self->in_element('hsp') and /WARNING|NOTE/ |
|
517
|
69 |
3 |
147 |
$_ =~ /^$/ or $_ =~ /^RID:/ |
|
|
3 |
1 |
146 |
$_ =~ /^$/ or $_ =~ /^RID:/ or $_ =~ /^Database:/ |
|
|
1 |
0 |
146 |
$_ =~ /^$/ or $_ =~ /^RID:/ or $_ =~ /^Database:/ or $_ =~ /^Query=/ |
|
590
|
84 |
10 |
48 |
/\((\-?[\d,]+)\s+letters.*\)/ or /^Length=(\-?[\d,]+)/ |
|
1224
|
95 |
0 |
26 |
$reporttype eq 'TBLASTN' or $reporttype eq 'PSITBLASTN' |
|
|
26 |
0 |
0 |
$reporttype eq 'BLASTX' or $reporttype eq 'RPS-BLAST(BLASTP)' |
|
1299
|
5 |
0 |
2799 |
/^((?:\S+)?BLAST[NPX]?)\s+(.+)$/i or /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i |
|
1323
|
52 |
73 |
2670 |
/Number of Sequences:\s+([\d\,]+)/i or /of sequences in database:\s+(\-?[\d,]+)/i |
|
1896
|
9049 |
9 |
0 |
$self->{'_reporttype'} ||= $Bio::SearchIO::blast::DEFAULTREPORTTYPE |
|
1905
|
0 |
0 |
27150 |
$i == 0 and /^\s+$/ or /^\s*(?:Lambda|Minus|Plus|Score)/i |
|
2113
|
83 |
3 |
0 |
$self->{'_reporttype'} ||= $Bio::SearchIO::blast::DEFAULTREPORTTYPE |
|
2254
|
2214 |
0 |
0 |
defined $name || defined $self->{'_elements'} |
|
|
0 |
2 |
2212 |
not defined $name || defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |