Result:
found more than 649 distributions - search limited to the first 2001 files matching your query
( run in 1.493 )
Bio-GMOD
view release on metacpan or search on metacpan
GMOD/Admin/Update.pm view on Meta::CPAN
my ($mount_point, $available_space);
my $counter;
while (<IN>) {
next unless /^\//;
my ($filesystem, $blocks, $used, $available, $use_percent, $mounted_on) = split(/\s+/);
$mount_point = $mounted_on;
$available_space = sprintf("%.2f", $available/1048576);
$counter++;
}
Bio-GeneDesign
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lib/Bio/GeneDesign.pm view on Meta::CPAN
object.
the count function counts the bases in a DNA sequence and returns a hash
reference where each base (including the ambiguous bases) are keys and the
values are the number of times they appear in the sequence. There are also the
special values GCp and ATp for GC and AT percentage.
=cut
sub count
{
lib/Bio/GeneDesign.pm view on Meta::CPAN
=head2 GC_windows
takes a nucleotide sequence, a window size, and minimum and maximum values.
returns lists of real coordinates of subsequences that violate mimimum or
maximum GC percentages.
Values are returned inside an array reference such that the first value is an
array ref of minimum violators (as array refs of left/right coordinates), and
the second value is an array ref of maximum violators.
lib/Bio/GeneDesign.pm view on Meta::CPAN
my ($self, @args) = @_;
my ($rlen, $rgc, $rstop)
= $self->_rearrange([qw(
length
gc_percentage
no_stops)], @args);
$self->throw("no codon table has been defined")
if ($rstop && ! $self->{codontable});
$rgc = $rgc || 50;
$self->throw("gc_percentage must be between 0 and 100")
if ($rgc && ($rgc < 0 || $rgc > 100));
if (! $rlen || $rlen < 1)
{
return q{};
Bio-Graphics
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lib/Bio/Graphics/Glyph/merged_alignment.pm view on Meta::CPAN
=head2 SAMPLE CONFIGURATION
Sample gbrowse configuration stanzas for an alignment feature
using this glyph. The scores are assumed to be expressed
as percent identity (0-100).
# base configuration
[BLASTZ]
feature = blastz_alignment
glyph = merged_alignment
Bio-Grep
view release on metacpan or search on metacpan
lib/Bio/Grep/Backend/Vmatch.pm view on Meta::CPAN
end => $upstream + $fields[$COL_LENGTH],
alignment => Bio::SimpleAlign->new(),
sequence_id => $internal_seq_id,
remark => q{},
evalue => $fields[$COL_EVALUE],
percent_identity => $fields[$COL_IDENTITY],
query => Bio::Seq->new(
-id => $query->id,
-desc => $query->desc . $rct,
-seq => $rcs,
),
Bio-Grid-Run-SGE
view release on metacpan or search on metacpan
bin/distribution view on Meta::CPAN
$barWidth->[$i] = log($count) / $maxLog;
} else {
$barWidth->[$i] = $count / $maxVal;
}
# determine the percent of key frequency
my $percentile = $count / $totalValues * 100;
# graph axis labels, really
$ctText->[$i] = sprintf ("%d", $count);
$pctText->[$i] = $count > 0 ? sprintf ("(%3.02f%%)", $percentile) : '';
$preBarLen = length ($ctText->[$i]) + length ($pctText->[$i]);
# determine the longest key name and longest count/percent text for
# aligning the output
if ($preBarLen > $maxPreBarLen) { $maxPreBarLen = $preBarLen; }
if (length ($sortedKeys[$i]) > $maxKeyLen) { $maxKeyLen = length ($sortedKeys[$i]); }
}
bin/distribution view on Meta::CPAN
}
# the arrays, hashes, variables must be all-correct for this to
# work, TODO: list out which ones they are, convert to functional
# keyText->[] - list of the keys
# pctText->[] - list of the percents
# ctText->[] - list of the counts
# barWidth->[] - list of the widths of the bars
sub outputGraph {
# print a header with alignment from key names
print STDERR "min";
bin/distribution view on Meta::CPAN
print " num ^\\d+\$ - tokens/lines must be entirely numeric\n";
print " --numonly[=N] input is numerics, simply graph values without labels\n";
print " abs input is absolute values (default)\n";
print " mon input monotonically-increasing, graph differences (of 2nd and later values)\n";
print " --palette=P comma-separated list of ANSI colour values for portions of the output\n";
print " in this order: regular, key, count, percent, graph. implies --color.\n";
print " --rcfile=F use this rcfile instead of \$HOME/.distributionrc - must be first argument!\n";
print " --size=S size of histogram, can abbreviate to single character, overridden by --width/--height\n";
print " small 40x10\n";
print " medium 80x20\n";
print " large 120x30\n";
Bio-Homology-InterologWalk
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lib/Bio/Homology/InterologWalk.pm view on Meta::CPAN
#lastly I store those new ids never seen in the starting dataset
$new_id_set{$idOUT} = 1 unless(exists($start_data_set{$idOUT}));
}
my $number_of_old_IDs = keys %old_id_present;
my $percentage = ($number_of_old_IDs / $number_of_elements_start_ds) * 100;
print("Number of IDs from the original dataset that appear in the network: $number_of_old_IDs\n");
print("Percentage of IDs from the original dataset that appear in the final dataset: $percentage\n");
my $number_of_new_IDs = keys %new_id_set;
my $number_of_network_nodes = keys %all_seen;
$percentage= ($number_of_new_IDs / $number_of_network_nodes) * 100;
if($onetoone_only){
print("Number of total UNIQUE IDs in interaction dataset (considering ONE-TO-ONE ortologies only): $number_of_network_nodes\n");
}else{
print("Number of total UNIQUE IDs in interaction dataset: $number_of_network_nodes\n");
}
print("Number of NEW ids (e.g. not seen in starting data set): $number_of_new_IDs\n");
print("Percentage of new ids over the total: $percentage\n");
#I save all the new ids in a flat file. This might be useful to do some analysis of their functional annotation
foreach my $id (sort keys %new_id_set){
#print ("$id\t$new_id_set{$id}\n");
lib/Bio/Homology/InterologWalk.pm view on Meta::CPAN
$DF_oname = $homology_member->display_label;
#OPI
my $pairwise_alignment_from_multiple = $homology->get_SimpleAlign;
$DF_opi = $pairwise_alignment_from_multiple->overall_percentage_identity;
#$opi = sprintf("%.3f", $overall_pid); #rounded
$DF_orthologue_id = '-' if(!$DF_orthologue_id);
$DF_oname = '-' if(!$DF_oname);
$DF_odesc = '-' if(!$DF_odesc);
lib/Bio/Homology/InterologWalk.pm view on Meta::CPAN
We can divide the metadata features in two broad classes:
- features related to the interaction. These include: Interaction Type, Interaction
Detection Method, Interaction coming from a SPOKE-expanded complex, interaction recon-
firmed through multiple taxa, interaction reconfirmed through multiple detection methods
- features related to the two orthology mappings. These include: orthology type
(one-to-one, one-to-many, many-to-one, many-to-many), OPI (percentage identity of the
conserved columns - see Bio::SimpleAlign), node to node distance, distance from the
first shared ancestor, (under development) dN/dS ratio
The IPX computation will also involve a normalisation stage. The subroutine requires
five arguments (meanscore_x) representing mean values to be used for normalisation.
The actual means are computed in get_mean_scores(), which is pre-requisite to
lib/Bio/Homology/InterologWalk.pm view on Meta::CPAN
-meanscore_me_dm : mean 'multiple detection methods' score for normalisation
-meanscore_me_taxa : mean 'multiple taxa' score for normalisation
Throws : -
Comment : -
See Also : L<http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/SimpleAlign.pm#overall_percentage_identity>, L</get_mean_scores>, C<doScores.pl> for sample usage
=cut
sub compute_prioritisation_index{
Bio-KBase
view release on metacpan or search on metacpan
lib/Bio/KBase/CDMI/CDMI_APIImpl.pm view on Meta::CPAN
in which hundreds of corresponding genes are detected, but they all come from
very closely related genomes.
The significance of the score relates to the number of genomes in the database.
We recommend that you take the time to look at a set of scored pairs and determine
approximately what percentage appear to be actually related for a few cutoff values.
=back
=cut
Bio-Kmer
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lib/Bio/Kmer.pm view on Meta::CPAN
software like jellyfish.
gt 1 If the count of kmers is fewer
than this, ignore the kmer. This
might help speed analysis if you
do not care about low-count kmers.
sample 1 Retain only a percentage of kmers.
1 is 100%; 0 is 0%
Only works with the perl kmer counter.
verbose 0 Print more messages.
Examples:
Bio-MAGE
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MAGE/Measurement/ConcentrationUnit.pm view on Meta::CPAN
use constant UNITNAMECV_PM => 'pM';
use constant UNITNAMECV_MG_PER_ML => 'mg_per_mL';
use constant UNITNAMECV_OTHER => 'other';
use constant UNITNAMECV_UM => 'uM';
use constant UNITNAMECV_M => 'M';
use constant UNITNAMECV_MASS_PER_VOLUME_PERCENT => 'mass_per_volume_percent';
use constant UNITNAMECV_GRAM_PERCENT => 'gram_percent';
use constant UNITNAMECV_MASS_PER_MASS_PERCENT => 'mass_per_mass_percent';
use constant UNITNAMECV_NM => 'nM';
=head1 NAME
Bio::MAGE::Measurement::ConcentrationUnit - Class for the MAGE-OM API
MAGE/Measurement/ConcentrationUnit.pm view on Meta::CPAN
=item $val = $concentrationunit->setUnitNameCV($val)
The restricted setter method for the C<unitNameCV> attribute.
C<unitNameCV> is an B<enumerated> attribute - it can only be set to C<undef> or one of the following values: M mM uM nM pM fM mg_per_mL mL_per_L g_per_L gram_percent mass_per_volume_percent mass_per_mass_percent other
Input parameters: the value to which the C<unitNameCV> attribute will be set
Return value: the current value of the C<unitNameCV> attribute
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$val> is not one of the accepted enumeration values: M mM uM nM pM fM mg_per_mL mL_per_L g_per_L gram_percent mass_per_volume_percent mass_per_mass_percent other
=cut
sub setUnitNameCV {
MAGE/Measurement/ConcentrationUnit.pm view on Meta::CPAN
croak(__PACKAGE__ . "::setUnitNameCV: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setUnitNameCV: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setUnitNameCV: expected one of enum values : M mM uM nM pM fM mg_per_mL mL_per_L g_per_L gram_percent mass_per_volume_percent mass_per_mass_percent other, got $val")
unless (not defined $val) or (grep {$val eq $_} qw(M mM uM nM pM fM mg_per_mL mL_per_L g_per_L gram_percent mass_per_volume_percent mass_per_mass_percent other));
return $self->{__UNITNAMECV} = $val;
}
MAGE/Measurement/ConcentrationUnit.pm view on Meta::CPAN
The restricted getter method for the C<unitNameCV> attribute.
Input parameters: none
Return value: the current value of the C<unitNameCV> attribute : an instance of type C<M mM uM nM pM fM mg_per_mL mL_per_L g_per_L gram_percent mass_per_volume_percent mass_per_mass_percent other>.
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
Bio-MAGETAB
view release on metacpan or search on metacpan
lib/Bio/MAGETAB/Util/DBLoader.pm view on Meta::CPAN
}
}
# Warn the user about a known Tangram bug.
if ( $value && $value =~ /\%/ ) {
warn("Warning: ID fields containing the percent character (%) may"
." lead to problems with object retrieval. See the documentation for "
.__PACKAGE__." for a discussion of this bug.\n");
}
{
Bio-MLST-Check
view release on metacpan or search on metacpan
lib/Bio/MLST/Blast/BlastN.pm view on Meta::CPAN
my ($start, $end) = ($row[8], $row[9]);
($start, $end, my $reverse) = $start <= $end ? ($start, $end, 0) : ($end, $start, 1);
return {
'allele_name' => $row[0],
'source_name' => $row[1],
'percentage_identity' => $row[2],
'sample_alignment_length' => $row[3],
'matches' => $row[12],
'source_start' => $start,
'source_end' => $end,
'reverse' => $reverse,
lib/Bio/MLST/Blast/BlastN.pm view on Meta::CPAN
sub _filter_best_hits
{
my($self, $hits, $tollerance) = @_;
$tollerance = defined($tollerance) ? $tollerance : 2.0;
my @percentages = map { $_->{'percentage_identity'} } @$hits;
my $top_percentage = max @percentages;
my @top_hits = grep { $_->{'percentage_identity'} >= $top_percentage - $tollerance } @$hits;
return \@top_hits;
}
sub _group_overlapping_hits
{
lib/Bio/MLST/Blast/BlastN.pm view on Meta::CPAN
sub _best_hit_in_group
{
###
# The best hit has the greatest number of matching bases. If two hits have
# the same number of matching bases, the one with the greater
# percentage identity is selected.
###
my($self, $hits) = @_;
my @lengths = map { $_->{'matches'} } @$hits;
my $max_length = max @lengths;
my @longest_hits = grep { $_->{'matches'} == $max_length } @$hits;
my $best_hit = reduce { $a->{'percentage_identity'} > $b->{'percentage_identity'} ? $a : $b } @longest_hits;
return $best_hit;
}
sub _blastn_cmd
{
lib/Bio/MLST/Blast/BlastN.pm view on Meta::CPAN
$bins = $self->_merge_similar_bins($bins);
my $groups = $self->_bins_to_groups($bins);
# Find the best match
my @best_in_groups = map { $self->_best_hit_in_group($_) } @$groups;
$top_hit = reduce { $a->{'percentage_identity'} > $b->{'percentage_identity'} ? $a : $b } @best_in_groups;
if (defined $top_hit)
{
$top_hit->{'percentage_identity'} = int($top_hit->{'percentage_identity'});
delete $top_hit->{'sample_alignment_length'};
delete $top_hit->{'matches'};
}
else {
$top_hit = {};
lib/Bio/MLST/Blast/BlastN.pm view on Meta::CPAN
Returns a hash containing details about the top blast result.
The attributes returned in the hash are:
allele_name
percentage_identity
source_name
source_start
source_end
reverse
contamination
Bio-MUST-Apps-FortyTwo
view release on metacpan or search on metacpan
bin/compress-db.pl view on Meta::CPAN
=for Euclid: n.type: n > 15
n.default: 40
=item --cap3-p=<n>
Overlap percent identity cutoff for CAP3 (should be > 65) [default: 90].
=for Euclid: n.type: n > 65
n.default: 90
=item --verbosity=<level>
Bio-MUST-Apps-Physeter
view release on metacpan or search on metacpan
bin/physeter.pl view on Meta::CPAN
next HIT;
}
# skip weak hits (classical mode)
next HIT if $hit->hsp_length < $ARGV_tax_min_len;
next HIT if $hit->percent_identity < $ARGV_tax_min_ident;
next HIT if $hit->bit_score < $ARGV_tax_min_score;
# fetch hit taxonomy and org
# optimized code (requires taxon_id|accession seq_ids)
my $taxon_id = ( split m{\|}xms, $hit->hit_id )[0];
bin/physeter.pl view on Meta::CPAN
Enable greedy behavior when interpreting the ambiguous taxa provided in the
required argument C<--taxon-list> [default: no].
=item --tax-min-ident=<n>
Minimum identity percentage to consider a hit when computing a LCA [default:
n.default].
=for Euclid: n.type: +number
n.default: 0
Bio-MUST-Core
view release on metacpan or search on metacpan
bin/classify-ali.pl view on Meta::CPAN
Other conditions are available: 'min_org_count' and 'max_org_count' deal with
organisms instead of sequences, whereas 'min_copy_mean' and 'max_copy_mean'
allow bounding the mean number of gene copies per organism. Moreover, there
exist 'perc' variants ('min_seq_perc', 'max_seq_perc', 'min_org_perc',
'max_org_perc') that count in percents (either of total sequences or total
organisms). All default to no bound.
An example YAML file follows:
categories:
Bio-MUST-Drivers
view release on metacpan or search on metacpan
bin/annotate-ali.pl view on Meta::CPAN
use Bio::MUST::Drivers;
# TODO: add support for prebuilt reference database (e.g. nr)
# convert fractional identity threshold to percentage (see Euclid)
$ARGV_identity *= 100.0 if 0 < $ARGV_identity && $ARGV_identity <= 1;
### Building database: $ARGV_ref_file
my $blastdb = Bio::MUST::Drivers::Blast::Database::Temporary->new(
seqs => $ARGV_ref_file
bin/annotate-ali.pl view on Meta::CPAN
my $curr_id = q{};
HIT:
while ( my $hit = $parser->next_hit ) {
my ($qid, $hid, $identity)
= map { $hit->$_ } qw(query_id hit_id percent_identity);
next HIT if $identity < $ARGV_identity; # skip weak-identity hits
unless ($ARGV_hit_list) { # optionally
next HIT if $qid eq $curr_id; # skip non-first hits
bin/annotate-ali.pl view on Meta::CPAN
=item --identity [=] <number>
Identity threshold for annotating a sequence [default: 0]. When specified as a
fraction between 0 and 1 (included), it is first multiplied by 100 to be
interpreted in percentage.
=for Euclid: number.type: number
number.default: 0
=item --max-hits [=] <number>
bin/annotate-ali.pl view on Meta::CPAN
=item --fields [=] <str>...
List of whitespace-separated BLAST fields to be displayed in final report
[default: no].
Valid fields are: percent_identity, hsp_length, mismatches, gaps, query_from,
query_to, hit_from, hit_to, evalue, bit_score, query_start, query_end,
hit_start, hit_end.
=for Euclid: str.type: string, str eq "percent_identity" || str eq "hsp_length" || str eq "mismatches" || str eq "gaps" || str eq "query_from" || str eq "query_to" || str eq "hit_from" || str eq "hit_to" || str eq "evalue" || str eq "bit_score" || st...
str.default: []
=item --out[-suffix] [=] <suffix>
Suffix to append to infile basenames for deriving outfile names [default:
Bio-MUST-Tools-Mcl
view release on metacpan or search on metacpan
bin/tag-loc-ids.pl view on Meta::CPAN
HIT:
# loop through first hits for each query
while (my $hit = $report->next_query) {
# consider only hits over percent_id threshold
next HIT if $hit->percent_identity < $ARGV_percent_id;
# strict check of length unless percent_id filter only
unless ($ARGV_pid_only) {
next HIT
unless ( $hit->query_end - $hit->query_start )
== ( $hit->hit_end - $hit->hit_start )
;
bin/tag-loc-ids.pl view on Meta::CPAN
infile (e.g., IDM files) and outfile names [default: none].
=for Euclid: str.type: string
repeatable
=item --percent-id=<n>
Min percentage identity to consider a hit.
=for Euclid: n.type: n
n.default: 99
=item --fasta[-suffix]=<suffix>
Bio-NEXUS
view release on metacpan or search on metacpan
README_admin view on Meta::CPAN
2. Once you are sure that the package works, change the master version number
in lib/Bio/NEXUS.pm (grep on VERSION). This will change the dist name when
the package is built (but the cvs version has to be changed separately-- see #4).
The initial version was based on the percent completion of NEXUS commands,
starting with 0.66 on 8/22/06. Subsequently we just incremented the minor number
by 1 each time. If you don't change this, you won't get a new version number to
upload to CPAN.
3. Check everything into CVS so that you can tag the current versions. If you
Bio-Phylo
view release on metacpan or search on metacpan
lib/Bio/Phylo/Matrices/MatrixRole.pm view on Meta::CPAN
sub no_sequences {
my $self = shift;
return scalar @{ $self->get_entities };
}
sub percentage_identity { $logger->warn }
# from simplealign
sub average_percentage_identity{
my ($self,@args) = @_;
my @alphabet = ('A','B','C','D','E','F','G','H','I','J','K','L','M',
'N','O','P','Q','R','S','T','U','V','W','X','Y','Z');
lib/Bio/Phylo/Matrices/MatrixRole.pm view on Meta::CPAN
}
return $divisor > 0 ? ($total / $divisor )*100.0 : 0;
}
# from simplealign
sub overall_percentage_identity{
my ($self, $length_measure) = @_;
my @alphabet = ('A','B','C','D','E','F','G','H','I','J','K','L','M',
'N','O','P','Q','R','S','T','U','V','W','X','Y','Z');
Bio-Pipeline-Comparison
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lib/Bio/Pipeline/Comparison/Report/ParseVCFCompare.pm view on Meta::CPAN
{
my ($self,$filename) = @_;
my $number_of_variants = 0;
for my $row_results (@{$self->_raw_venn_diagram_results})
{
my $number_of_files_with_overlap = @{$row_results->{files_to_percentage}};
if($number_of_files_with_overlap > 0)
{
for(my $i = 0; $i < $number_of_files_with_overlap; $i++ )
{
if(defined($row_results->{files_to_percentage}->[$1]->{file_name})
&& $row_results->{files_to_percentage}->[$1]->{file_name} eq $filename)
{
$number_of_variants +=$row_results->{number_of_sites};
last;
}
}
lib/Bio/Pipeline/Comparison/Report/ParseVCFCompare.pm view on Meta::CPAN
sub _number_of_uniques_for_filename
{
my ($self, $filename) = @_;
for my $row_results (@{$self->_raw_venn_diagram_results})
{
if(@{$row_results->{files_to_percentage}} == 1
&& defined($row_results->{files_to_percentage}->[0]->{file_name})
&& $row_results->{files_to_percentage}->[0]->{file_name} eq $filename)
{
return $row_results->{number_of_sites};
}
}
return 0;
lib/Bio/Pipeline/Comparison/Report/ParseVCFCompare.pm view on Meta::CPAN
my $line = $_;
if( $line =~ m/$vd_regex/)
{
my %vd_results;
$vd_results{number_of_sites} = $1;
$vd_results{files_to_percentage} = [ {file_name => $2, percentage => $3} ];
if(defined($4) && defined($5) && defined($6))
{
push(@{$vd_results{files_to_percentage}}, {file_name => $5, percentage => $6} );
}
push(@vd_rows,\%vd_results);
}
}
return \@vd_rows;
Bio-Polloc
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lib/Bio/Polloc/GroupCriteria.pm view on Meta::CPAN
Minimum score for either algorithms B<blast> and B<hmmer>. 20 by default.
=item -consensusperc I<float>
Minimum percentage a residue must appear in order to include it in the
consensus used as query. 60 by default. Only if -algorithm blast.
=item -e I<float>
If C<-algorithm> B<blast>, maximum e-value. 0.1 by default.
Bio-Prospect
view release on metacpan or search on metacpan
exercising rights under, and complying with all of the terms of, this
License. For legal entities, "You" includes any entity that controls, is
controlled by, or is under common control with you. For purposes of this
definition, "control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or otherwise,
or (ii) ownership of fifty percent (50%) or more of the outstanding shares,
or (iii) beneficial ownership of such entity.
15) Right to Use. You may use the Original Work in all ways not otherwise
restricted or conditioned by this License or by law, and Licensor promises
not to interfere with or be responsible for such uses by You.
Bio-Roary
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lib/Bio/Roary/AccessoryBinaryFasta.pm view on Meta::CPAN
has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'annotate_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnnotateGroups', required => 1 );
has 'analyse_groups_obj' => ( is => 'ro', isa => 'Bio::Roary::AnalyseGroups', required => 1 );
has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'accessory_binary_genes.fa' );
has 'lower_bound_percentage' => ( is => 'ro', isa => 'Int', default => 5 );
has 'upper_bound_percentage' => ( is => 'ro', isa => 'Int', default => 5 );
has 'max_accessory_to_include' => ( is => 'ro', isa => 'Int', default => 4000 );
has 'groups_to_files' => ( is => 'ro', isa => 'HashRef', lazy => 1, builder => '_build__groups_to_files' );
has '_lower_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__lower_bound_value' );
has '_upper_bound_value' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build__upper_bound_value' );
lib/Bio/Roary/AccessoryBinaryFasta.pm view on Meta::CPAN
}
sub _build__lower_bound_value {
my ($self) = @_;
my $num_files = @{ $self->input_files };
return ceil( $num_files * ( $self->lower_bound_percentage / 100 ) );
}
sub _build__upper_bound_value {
my ($self) = @_;
my $num_files = @{ $self->input_files };
return $num_files - ceil( $num_files * ( $self->upper_bound_percentage / 100 ) );
}
sub create_accessory_binary_fasta {
my ($self) = @_;
my $out_seq_io = Bio::SeqIO->new( -file => ">" . $self->output_filename, -format => 'Fasta' );
Bio-SamTools
view release on metacpan or search on metacpan
"Legal Entity" shall mean the union of the acting entity and all other
entities that control, are controlled by, or are under common control
with that entity. For the purposes of this definition, "control" means
(i) the power, direct or indirect, to cause the direction or
management of such entity, whether by contract or otherwise, or (ii)
ownership of fifty percent (50%) or more of the outstanding shares, or
(iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity exercising
permissions granted by this License.
Bio-SearchIO-blastxml
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t/SearchIO/blastxml.t view on Meta::CPAN
is($hsp->query->end,815);
is($hsp->hit->start, 3);
is($hsp->hit->end, 310);
is($hsp->query->frame,0);
is($hsp->hit->frame,0);
is(sprintf("%.2f", $hsp->percent_identity), 37.73);
is(sprintf("%.4f", $hsp->frac_identical('hit')), 0.3994);
is(sprintf("%.4f", $hsp->frac_identical('query')), 0.3868);
is(sprintf("%.4f",$hsp->query->frac_identical), 0.3868);
is(sprintf("%.4f",$hsp->frac_conserved('total')),0.5245);
t/SearchIO/blastxml.t view on Meta::CPAN
is($hsp->end('query'), $hsp->query->end);
is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
float_is($hsp->evalue, 0.000286309);
is($hsp->score, 86);
is($hsp->bits, 37.7354);
is(sprintf("%.1f",$hsp->percent_identity), 20.9);
is(sprintf("%.4f",$hsp->frac_identical('query')), 0.2105);
is(sprintf("%.3f",$hsp->frac_identical('hit')), 0.224);
is($hsp->gaps('total'), 11);
$hsps_left--;
}
t/SearchIO/blastxml.t view on Meta::CPAN
is($hsp->end('query'), $hsp->query->end);
is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
float_is($hsp->evalue, 0.0242028);
is($hsp->score, 73);
is($hsp->bits, 32.7278);
is(sprintf("%.1f",$hsp->percent_identity), '24.0');
is(sprintf("%.4f",$hsp->frac_identical('query')), '0.2605');
is(sprintf("%.3f",$hsp->frac_identical('hit')), '0.240');
is($hsp->gaps, 10);
$hsps_left--;
}
Bio-SearchIO-hmmer
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lib/Bio/Search/HSP/HMMERHSP.pm view on Meta::CPAN
default = 'total'
arg 2: [optional] integer length value to set for specific type
=cut
=head2 percent_identity
Title : percent_identity
Usage : my $percentid = $hsp->percent_identity()
Function: Returns the calculated percent identity for an HSP
Returns : floating point between 0 and 100
Args : none
=cut
Bio-ToolBox
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lib/Bio/ToolBox/Data.pm view on Meta::CPAN
# add column
my $i = $summed_data->add_column($data_name);
$summed_data->metadata( $i, 'dataset', $datasets[$d] );
# tag for remembering we're working with percentile bins
my $do_percentile = 0;
# remember the row
my $row = 1;
# Collect summarized data
lib/Bio/ToolBox/Data.pm view on Meta::CPAN
);
# convert midpoint to fraction of 1000 for plotting if necessary
if ( substr( $self->name($column), -1 ) eq '%' ) {
$midpoint *= 10; # midpoint * 0.01 * 1000 bp
$do_percentile++;
}
if ( $do_percentile and substr( $self->name($column), -2 ) eq 'bp' ) {
# working on the extension after the percentile bins
$midpoint += 1000;
}
# collect the values in the column
my @values;
lib/Bio/ToolBox/Data.pm view on Meta::CPAN
header becomes a row identifier (i.e. the table is transposed). The
best use of this is to summarize the mean profile of windowed data
collected across a feature. See the L<Bio::ToolBox> scripts
L<get_relative_data.pl> and L<get_binned_data.pl> as examples.
For data from L<get_binned_data.pl> where the columns are expressed
as percentile bins, the reported midpoint column is automatically
converted based on a length of 1000 bp.
You may pass these options. They are optional.
=over 4
Bio-Tools-CodonOptTable
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lib/Bio/Tools/CodonOptTable.pm view on Meta::CPAN
. "|%{color:red}G%|"
. $monomers->{G} . "|\n"
. "|%{color:red}C%|"
. $monomers->{C} . "|\n";
my $gc_percentage =
( ( $monomers->{G} + $monomers->{C} ) /
( $monomers->{A} + $monomers->{T} + $monomers->{G} + $monomers->{C} )
) * 100;
$gc_percentage = sprintf( "%.2f", $gc_percentage );
my $REPORT = <<EOT;
h1. Bio::Tools::CodonOptTable
%{color:green}Report for $sequence_id%
%{color:red}Codon Adaptation Index (CAI) for sequence% : $cai
%{color:red}GC percentage for sequence% : $gc_percentage%
%{color:red}GENETIC CODE USED% : $genetic_code "--more about genetic code--":http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
%{background:#336699;color:white;padding:5px}++**CODON USAGE**++%
Bio-Tools-Phylo-PAML
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lib/Bio/Tools/Phylo/PAML.pm view on Meta::CPAN
(\d+)\s+ # constant sites
\(\s*([\d\.]+)\s*\%\s*\)/x
)
{
$self->{'_summary'}->{'stats'}->{'constant_sites'} = $1;
$self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2;
}
elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/x) {
$self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1;
$done = 1; # done for sure
}
lib/Bio/Tools/Phylo/PAML.pm view on Meta::CPAN
(\d+)\s+ # constant sites
\(\s*([\d\.]+)\s*\%\s*\)/ox
)
{
$self->{'_summary'}->{'stats'}->{'constant_sites'} = $1;
$self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2;
}
elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/ox) {
$self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1;
$done = 1; # done for sure
}
Bio-Tools-Primer3Redux
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lib/Bio/Tools/Primer3Redux/Primer.pm view on Meta::CPAN
sub gc_content {
my ($self, $gc) = @_;
if (defined $gc) {
$self->remove_tag('gc_percent') if $self->has_tag('gc_percent');
$self->add_tag_value('gc_percent', $gc);
}
$self->has_tag('gc_percent') ? return ($self->get_tag_values('gc_percent'))[0] : return;
}
sub run_description {
my ($self, $desc) = @_;
lib/Bio/Tools/Primer3Redux/Primer.pm view on Meta::CPAN
=head2 gc_content
Title : gc
Usage : $obj->gc
Function : returns the GC content calculated for the primer via Primer3
Returns : float (percent)
Args : optional GC content (possibly calculated via other means)
=head2 run_description
Title : run_description
Bio-Tools-Run-Alignment-TCoffee
view release on metacpan or search on metacpan
t/TCoffee.t view on Meta::CPAN
my $seq_array_ref = \@seq_array;
$aln = $factory->align($seq_array_ref);
is $aln->num_sequences, 7;
my $s1_perid = $aln->average_percentage_identity;
my $profile1 = test_input_file("cysprot1a.msf");
my $profile2 = test_input_file("cysprot1b.msf");
# convert any warnings about program to an actual exception
t/TCoffee.t view on Meta::CPAN
$aln1 = $str1->next_aln();
$str2 = Bio::SeqIO->new(-file=> test_input_file("cysprot1b.fa"));
my $seq = $str2->next_seq();
is $aln1->num_sequences, 3;
is( int($aln1->average_percentage_identity), 39);
$aln = $factory->profile_align($aln1,$seq);
is( $aln->num_sequences, 4);
if( $version <= 1.22 ) {
cmp_ok( $aln->overall_percentage_identity, '>', 18);
is( int($aln->average_percentage_identity), 44);
} else {
my $overall = int($aln->overall_percentage_identity);
ok( $overall >=21 && $overall <= 23, 'expect 21 >= val >= 23');
my $avg = int($aln->average_percentage_identity);
ok( $avg == 47 || $avg ==48, 'expect 47 or 48');
}
# test new 'run' generic running of factory
$aln = $factory->run('-type' => 'align',
'-seq' => test_input_file("cysprot.fa"));
is ($aln->num_sequences, 7, 'simple generic run');
is ($aln->percentage_identity,$s1_perid); #calculated before
lives_ok{ $aln = $factory->run('-type' => 'profile',
'-profile' => $aln1,
'-seq' => test_input_file("cysprot1b.fa"))} ;
ok(! $@, "no T-COFFEE errors");
is( $aln->num_sequences, 7);
if( $version <= 1.22 ) {
cmp_ok( $aln->overall_percentage_identity, '>', 18);
is( int($aln->average_percentage_identity), 44);
} else {
my $overall = int $aln->overall_percentage_identity;
ok($overall == 14 || $overall == 13, 'expect 13 or 14');
my $avg = int($aln->average_percentage_identity);
ok($avg == 41 || $avg == 42, 'expect 41 or 42');
}
done_testing();
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