Bio-EnsEMBL
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lib/Bio/EnsEMBL/BaseAlignFeature.pm view on Meta::CPAN
-SEQNAME => $self->{'seqname'},
-START => $qstart,
-END => $qend,
-STRAND => $strand1,
-HSLICE => $self->{'hslice'},
-HSEQNAME => $self->{'hseqname'},
-HSTART => $hstart,
-HEND => $hend,
-HSTRAND => $strand2,
-SCORE => $self->{'score'},
-PERCENT_ID => $self->{'percent_id'},
-ANALYSIS => $self->{'analysis'},
-P_VALUE => $self->{'p_value'},
-EXTERNAL_DB_ID => $self->{'external_db_id'},
-HCOVERAGE => $self->{'hcoverage'},
-GROUP_ID => $self->{'group_id'},
-LEVEL_ID => $self->{'level_id'});
# end M cigar bits
} elsif( $piece =~ /I$/ ) {
lib/Bio/EnsEMBL/BaseAlignFeature.pm view on Meta::CPAN
} else {
@f = sort { $b->start <=> $a->start} @$features;
}
my $hstrand = $f[0]->hstrand;
my $slice = $f[0]->slice();
my $hslice = $f[0]->hslice();
my $name = $slice ? $slice->name() : undef;
my $hname = $f[0]->hseqname;
my $score = $f[0]->score;
my $percent = $f[0]->percent_id;
my $analysis = $f[0]->analysis;
my $pvalue = $f[0]->p_value();
my $external_db_id = $f[0]->external_db_id;
my $hcoverage = $f[0]->hcoverage;
my $group_id = $f[0]->group_id;
my $level_id = $f[0]->level_id;
my $seqname = $f[0]->seqname;
# implicit strand 1 for peptide sequences
$strand ||= 1;
lib/Bio/EnsEMBL/BaseAlignFeature.pm view on Meta::CPAN
$f->slice->name()."]");
}
if ( defined($hname) && $hname ne $f->hseqname) {
throw("Inconsistent hit names in feature array [$hname - ".
$f->hseqname . "]");
}
if ( defined($score) && $score ne $f->score) {
throw("Inconsisent scores in feature array [$score - " .
$f->score . "]");
}
if (defined($f->percent_id) && $percent ne $f->percent_id) {
throw("Inconsistent pids in feature array [$percent - " .
$f->percent_id . "]");
}
if(defined($pvalue) && $pvalue != $f->p_value()) {
throw("Inconsistant p_values in feature arraw [$pvalue " .
$f->p_value() . "]");
}
if($seqname && $seqname ne $f->seqname){
throw("Inconsistent seqname in feature array [$seqname - ".
$f->seqname . "]");
}
my $start1 = $f->start; #source sequence alignment start
lib/Bio/EnsEMBL/BaseAlignFeature.pm view on Meta::CPAN
$matchlength = "";
}
$string .= $matchlength."M";
}
$self->{'start'} = $f1start;
$self->{'end'} = $f1end;
$self->{'seqname'} = $seqname;
$self->{'strand'} = $strand;
$self->{'score'} = $score;
$self->{'percent_id'} = $percent;
$self->{'analysis'} = $analysis;
$self->{'slice'} = $slice;
$self->{'hslice'} = $hslice;
$self->{'hstart'} = $f2start;
$self->{'hend'} = $f2end;
$self->{'hstrand'} = $hstrand;
$self->{'hseqname'} = $hname;
$self->{'cigar_string'} = $string;
$self->{'p_value'} = $pvalue;
$self->{'external_db_id'} = $external_db_id;
lib/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm view on Meta::CPAN
return
$self->fetch_all_by_Slice_constraint( $slice, $constraint,
$logic_name );
} ## end sub fetch_all_by_Slice_and_external_db
=head2 fetch_all_by_Slice_and_pid
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice from which to obtain align features.
Arg [2] : (optional) float $pid
A lower bound for the percentage identity of features
to obtain.
Arg [3] : (optional) string $logic_name
The logic name of the type of features to obtain.
Example : @feats =
@{ $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 ) };
Description: Returns a listref of features created from the
database which are on the Slice $slice and with a
percentage identity greater than $pid. If logic name
is defined, only features with an analysis of type
$logic_name will be returned.
Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
in Slice coordinates
Exceptions : none
Caller : general
Status : Stable
=cut
lib/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm view on Meta::CPAN
prevent excessive interpolation of the database values.
Example : #interpolate:
$feats = $dfa->fetch_all_by_Slice($slice,'SNPDensity', 10, 1);
#do not interpoloate, get what is in the database:
$feats = $dfa->fetch_all_by_Slice($slice,'SNPDensity', 50);
#interpolate, but not too much
$feats = $dfa->fetch_all_by_Slice($slice,'SNPDensity',50,1,5.0);
Description: Retrieves a set of density features which overlap the region
of this slice. Density features are a discrete representation
of a continuous value along a sequence, such as a density or
percent coverage. Density Features may be stored in chunks of
different sizes in the database, and interpolated to fit the
desired size for the requested region. For example the database
may store a single density value for each 1KB and also for each
1MB. When fetching for an entire chromosome the 1MB density
chunks will be used if the requested number of blocks is not
very high.
Note that features which have been interpolated are not stored
in the database and as such will have no dbID or adaptor set.
Returntype : Bio::EnsEMBL::DensityFeature
Exceptions : warning on invalid $num_blocks argument
lib/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm view on Meta::CPAN
#what portion of this feature are we using to construct our new block?
$fstart = ($f->{'start'} < $start) ? $start : $f->{'start'};
$fend = ($f->{'end'} > $end ) ? $end : $f->{'end'};
$fend = $length if($fend > $length);
if($value_type eq 'sum') {
$portion = ($fend-$fstart+1)/$f->length();
#take a percentage of density value, depending on how much of the
#feature we overlapped
$density_value += $portion * $f->{'density_value'};
} elsif($value_type eq 'ratio') {
#maintain a running total of the length used from each feature
#and its value
push(@dvalues,[$fend-$fstart+1,$f->{'density_value'}]);
} else {
lib/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm view on Meta::CPAN
$sth->bind_param( 3, $feat->end, SQL_INTEGER );
$sth->bind_param( 4, $feat->strand, SQL_TINYINT );
$sth->bind_param( 5, $hstart, SQL_INTEGER );
$sth->bind_param( 6, $hend, SQL_INTEGER );
$sth->bind_param( 7, $hstrand, SQL_TINYINT );
$sth->bind_param( 8, $hseqname, SQL_VARCHAR );
$sth->bind_param( 9, $cigar_string, SQL_LONGVARCHAR );
$sth->bind_param( 10, $feat->analysis->dbID, SQL_INTEGER );
$sth->bind_param( 11, $feat->score, SQL_DOUBLE );
$sth->bind_param( 12, $feat->p_value, SQL_DOUBLE );
$sth->bind_param( 13, $feat->percent_id, SQL_FLOAT );
$sth->bind_param( 14, $feat->external_db_id, SQL_INTEGER );
$sth->bind_param( 15, $feat->hcoverage, SQL_DOUBLE );
$sth->bind_param( 16, $feat->align_type, SQL_VARCHAR);
$sth->execute();
my $dbId = $self->last_insert_id("${tablename}_id", undef, $tablename);
# store attributes if there are any
my $attr_adaptor = $db->get_AttributeAdaptor();
$attr_adaptor->store_on_DnaDnaAlignFeature($dbId, $feat->get_all_Attributes);
lib/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm view on Meta::CPAN
'slice' => $slice,
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'hseqname' => $hit_name,
'hstart' => $hit_start,
'hend' => $hit_end,
'hstrand' => $hit_strand,
'score' => $score,
'p_value' => $evalue,
'percent_id' => $perc_ident,
'cigar_string' => $cigar_line,
'analysis' => $analysis,
'adaptor' => $self,
'dbID' => $dna_align_feature_id,
'external_db_id' => $external_db_id,
'hcoverage' => $hcoverage,
'align_type' => $align_type,
'dbname' => $external_db_name,
'db_display_name' => $external_display_db_name
} ) );
lib/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm view on Meta::CPAN
$sth->bind_param(2,$feat->start,SQL_INTEGER);
$sth->bind_param(3,$feat->end,SQL_INTEGER);
$sth->bind_param(4,$feat->strand,SQL_TINYINT);
$sth->bind_param(5,$feat->hstart,SQL_INTEGER);
$sth->bind_param(6,$feat->hend,SQL_INTEGER);
$sth->bind_param(7,$feat->hseqname,SQL_VARCHAR);
$sth->bind_param(8,$feat->cigar_string,SQL_LONGVARCHAR);
$sth->bind_param(9,$feat->analysis->dbID,SQL_INTEGER);
$sth->bind_param(10,$feat->score,SQL_DOUBLE);
$sth->bind_param(11,$feat->p_value,SQL_DOUBLE);
$sth->bind_param(12,$feat->percent_id,SQL_REAL);
$sth->bind_param(13,$feat->external_db_id,SQL_INTEGER);
$sth->bind_param(14,$feat->hcoverage,SQL_DOUBLE);
$sth->bind_param(15,$feat->align_type,SQL_VARCHAR);
$sth->execute();
my $dbId = $self->last_insert_id("${tablename}_id", undef, $tablename);
$original->dbID($dbId);
$original->adaptor($self);
}
lib/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm view on Meta::CPAN
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'hseqname' => $hit_name,
'hstart' => $hit_start,
'hend' => $hit_end,
'hstrand' => 1, # dna_pep_align features
# are always hstrand 1
'score' => $score,
'p_value' => $evalue,
'percent_id' => $perc_ident,
'cigar_string' => $cigar_line,
'analysis' => $analysis,
'adaptor' => $self,
'dbID' => $protein_align_feature_id,
'external_db_id' => $external_db_id,
'hcoverage' => $hcoverage,
'align_type' => $align_type,
'dbname' => $external_db_name,
'db_display_name' => $external_display_db_name
} ) );
lib/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm view on Meta::CPAN
my $i = 0;
$sth->bind_param(++$i, $translation_id, SQL_INTEGER);
$sth->bind_param(++$i, $feature->start, SQL_INTEGER);
$sth->bind_param(++$i, $feature->end, SQL_INTEGER);
$sth->bind_param(++$i, $feature->hstart, SQL_INTEGER);
$sth->bind_param(++$i, $feature->hend, SQL_INTEGER);
$sth->bind_param(++$i, $feature->hseqname, SQL_VARCHAR);
$sth->bind_param(++$i, $analysis->dbID, SQL_INTEGER);
$sth->bind_param(++$i, $feature->score, SQL_DOUBLE);
$sth->bind_param(++$i, $feature->p_value, SQL_DOUBLE);
$sth->bind_param(++$i, $feature->percent_id, SQL_FLOAT);
$sth->bind_param(++$i, $feature->external_data, SQL_VARCHAR);
$sth->bind_param(++$i, $feature->hdescription, SQL_LONGVARCHAR);
if ($self->schema_version > 92) {
$sth->bind_param(++$i, $feature->cigar_string, SQL_VARCHAR);
$sth->bind_param(++$i, $feature->align_type, SQL_VARCHAR);
}
$sth->execute();
lib/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm view on Meta::CPAN
}
=head2 fetch_by_Feature
Arg [1] : Bio::EnsEMBL::Feature $feat
The feature to fetch the slice around
Arg [2] : int size (optional)
The desired number of flanking basepairs around the feature.
The size may also be provided as a percentage of the feature
size such as 200% or 80.5%.
Example : $slice = $slice_adaptor->fetch_by_Feature($feat, 100);
Description: Retrieves a slice around a specific feature. All this really
does is return a resized version of the slice that the feature
is already on. Note that slices returned from this method
are always on the forward strand of the seq_region regardless of
the strandedness of the feature passed in.
Returntype : Bio::EnsEMBL::Slice
Exceptions : throw if the feature does not have an attached slice
throw if feature argument is not provided
lib/Bio/EnsEMBL/DensityFeature.pm view on Meta::CPAN
$feature = Bio::EnsEMBL::DensityFeature->new(
-seq_region => $region,
-start => 1,
-end => 1e6,
-density_type => $dt,
-density_value => 98.5
);
=head1 DESCRIPTION
A density feature represents a count, density, or percentage coverage,
etc. for a given region.
This module is part of the Ensembl project http://www.ensembl.org
=head1 METHODS
=cut
use strict;
lib/Bio/EnsEMBL/DensityFeature.pm view on Meta::CPAN
return 0;
}
=head2 density_value
Arg [1] : (optional) float $density_value
Example : $dv = $density_feature->density_value();
Description: Getter/Setter for the density value of this DensityFeature.
The density value may be a count, a percentage, or a coverage
of a feature type in the area defined by this feature.
Returntype : float
Exceptions : throw if a negative density value is provided
Caller : general
Status : Stable
=cut
sub density_value {
my $self = shift;
lib/Bio/EnsEMBL/DensityType.pm view on Meta::CPAN
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
=cut
=head1 NAME
Bio::EnsEMBL::DensityType - A type representing a density, or percentage
coverage etc. in a given region.
=head1 SYNOPSIS
use Bio::EnsEMBL::DensityType;
$type = Bio::EnsEMBL::DensityType->new(
-analysis => $analysis,
-blocksize => 1000000,
-value_type => $type
);
=head1 DESCRIPTION
A density type represents a density, or percentage coverage etc. in a
given region.
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::DensityType;
lib/Bio/EnsEMBL/FeaturePair.pm view on Meta::CPAN
my $feat = Bio::EnsEMBL::FeaturePair->new(
-start => 132_231,
-end => 132_321,
-strand => -1,
-slice => $slice,
-hstart => 10,
-hend => 100,
-hstrand => 1,
-score => 100,
-percent_id => 92.0,
-hseqname => 'ALUSX10.1',
-analysis => $analysis
);
my $hit_start = $feat->hstart();
my $hit_end = $feat->hend();
my $hit_strand = $feat->hstrand();
my $analysis = $feat->analysis();
=head1 DESCRIPTION
lib/Bio/EnsEMBL/FeaturePair.pm view on Meta::CPAN
$clone = $slice_adpator->fetch_by_region( 'clone', 'HS120G22' );
$fp = Bio::EnsEMBL::FeaturePair(
-start => 100,
-end => 220,
-strand => 1,
-slice => $clone,
-hstart => 1,
-hend => 40,
-hstrand => 1,
-percent_id => 92.0,
-score => 100,
-hseqname => 'SW:HBA_HUMAN',
-species => 'Homo sapiens',
-hspecies => 'Homo sapiens'
);
=head1 METHODS
=cut
lib/Bio/EnsEMBL/FeaturePair.pm view on Meta::CPAN
Arg [EXTRA_DATA]: HashRef - Additional data, specified as name, value attribute pairs (optional)
Arg [...] : Named superclass constructor args (Bio::EnsEMBL::Feature)
Example : $feat = Bio::EnsEMBL::FeaturePair->new(-start => 132_231,
-end => 132_321,
-strand => -1,
-slice => $slice,
-hstart => 10,
-hend => 100,
-hstrand => 1,
-score => 100,
-percent_id => 92.0,
-hseqname => 'ALUSX10.1',
-analysis => $analysis);
Description: Creates a new Bio::EnsEMBL::FeaturePair object
Returntype : Bio::EnsEMBL::FeaturePair
Exceptions : throw if start > end
throw if invalid strand is provided
Caller : general
Status : Stable
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($hstart, $hend, $hstrand, $percent_id, $score, $species, $hspecies, $p_value, $hseqname, $f1, $f2, $coverage, $hcoverage, $group_id, $level_id, $external_db_id, $extra_data, $external_db_name, $external_display_db_name, $hdescription) = rearran...
if (defined($hstart) && defined($hend) && ($hend < $hstart)) {
throw('HSTART must be less than or equal to HEND');
}
if (defined($hstrand) && $hstrand != 1 && $hstrand != -1 && $hstrand != 0) {
throw('HSTRAND must be one of (0,1,-1)');
}
$self->{'hstart'} = $hstart;
$self->{'hend'} = $hend;
$self->{'hstrand'} = $hstrand;
$self->{'score'} = $score;
$self->{'percent_id'} = $percent_id;
$self->{'species'} = $species;
$self->{'hspecies'} = $hspecies;
$self->{'hseqname'} = $hseqname;
$self->{'coverage'} = $coverage;
$self->{'hcoverage'} = $hcoverage;
$self->{'p_value'} = $p_value;
$self->{'group_id'} = $group_id;
$self->{'level_id'} = $level_id;
$self->{'external_db_id'} = $external_db_id;
$self->{'extra_data'} = $extra_data;
lib/Bio/EnsEMBL/FeaturePair.pm view on Meta::CPAN
Status : Stable
=cut
sub score {
my $self = shift;
$self->{'score'} = shift if (@_);
return $self->{'score'};
}
=head2 percent_id
Arg [1] : float $percent_id (optional)
Example : $percent_id = $fp->percent_id();
Description: Getter/Setter for the percentage identity of this feature pair
Returntype : float
Exceptions : none
Caller : general
Status : Stable
=cut
sub percent_id {
my $self = shift;
$self->{'percent_id'} = shift if (@_);
return $self->{'percent_id'};
}
=head2 species
Arg [1] : string $genus_species_name (optional)
e.g. Homo_sapiens or Mus_musculus
Example : $species = $fp->species();
Description: get/set on the species of feature1
Returntype : string
Execeptions: none
lib/Bio/EnsEMBL/FeaturePair.pm view on Meta::CPAN
=cut
sub hspecies {
my $self = shift;
$self->{'hspecies'} = shift if (@_);
return $self->{'hspecies'};
}
=head2 coverage
Arg [1] : number (percentage) $coverage (optional)
Example : $cov = $fp->coverage();
Description: Getter/Setter for the % of the query covered by the feature
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub coverage {
my $self = shift;
$self->{'coverage'} = shift if (@_);
return $self->{'coverage'};
}
=head2 hcoverage
Arg [1] : number (percentage) $hcoverage (optional)
Example : $hcov = $fp->hcoverage();
Description: Getter/Setter for the % of the target covered by the feature
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub hcoverage {
lib/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm view on Meta::CPAN
}
closedir($dumpdir);
# determine number of jobs to split task into
my $bytes_per_job = $self->conf->param('exonerate_bytes_per_job')
|| 250000;
my $num_jobs = $self->conf->param('exonerate_jobs');
$num_jobs ||= int( $source_size/$bytes_per_job + 1 );
my $percent =
int( ( $self->conf->param('exonerate_threshold') || 0.5 )*100 );
my $lsf_name = 'idmapping_exonerate_' . time;
my $exonerate_path = $self->conf->param('exonerate_path');
my $exonerate_extra_params =
$self->conf->param('exonerate_extra_params');
#
# run exonerate jobs using lsf
#
my $exonerate_job =
qq{$exonerate_path } .
qq{--query $source_file --target $target_file } .
q{--querychunkid $LSB_JOBINDEX } .
qq{--querychunktotal $num_jobs } .
q{--model ungapped -M 1000 -D 100 } .
q{--showalignment FALSE --subopt no } . qq{--percent $percent } .
$self->conf->param('exonerate_extra_params') . " " .
q{--ryo 'myinfo: %qi %ti %et %ql %tl\n' } .
qq{| grep '^myinfo:' > $dump_path/exonerate_map.\$LSB_JOBINDEX} .
"\n";
$self->logger->info("Submitting $num_jobs exonerate jobs to lsf.\n");
$self->logger->debug("$exonerate_job\n\n");
my $bsub_cmd = sprintf(
"|bsub -J '%s[1-%d]%%%d' -o %s/exonerate.%%I.out %s",
lib/Bio/EnsEMBL/SeqFeature.pm view on Meta::CPAN
} else {
bless $self, $caller;
}
$self->{'_gsf_tag_hash'} = {};
$self->{'_gsf_sub_array'} = [];
$self->{'_parse_h'} = {};
$self->{'_is_splittable'} = 0;
my ($start,$end,$strand,$frame,$score,$analysis,$seqname, $source_tag,
$primary_tag, $percent_id, $p_value, $phase, $end_phase) =
&rearrange([qw(START
END
STRAND
FRAME
SCORE
ANALYSIS
SEQNAME
SOURCE_TAG
PRIMARY_TAG
lib/Bio/EnsEMBL/SeqFeature.pm view on Meta::CPAN
# $gff_string && $self->_from_gff_string($gff_string);
if ( defined $analysis && $analysis ne "") { $self->analysis($analysis)};
if ( defined ($start) && $start ne "" ) { $self->start($start)};
if ( defined ($end ) && $end ne "" ) { $self->end($end)}
if ( defined $strand && $strand ne "") { $self->strand($strand)}
if ( defined $frame && $frame ne "") { $self->frame($frame)}
if ( defined $score && $score ne "") { $self->score($score)}
if ( defined $seqname && $seqname ne "") { $self->seqname($seqname)};
if ( defined $percent_id && $percent_id ne ""){ $self->percent_id($percent_id)};
if ( defined $p_value && $p_value ne "") { $self->p_value($p_value)};
if ( defined $phase && $phase ne "") { $self->phase($phase)};
if ( defined $end_phase && $end_phase ne "") { $self->end_phase($end_phase)};
return $self; # success - we hope!
}
lib/Bio/EnsEMBL/SeqFeature.pm view on Meta::CPAN
=cut
# Shouldn't this go as "validate" into Pro_SeqFeature?
sub validate_prot_feature{
my ($self,$num) = @_;
$self->throw("Seqname not defined in feature") unless defined($self->seqname);
$self->throw("start not defined in feature") unless defined($self->start);
$self->throw("end not defined in feature") unless defined($self->end);
if ($num == 1) {
$self->throw("score not defined in feature") unless defined($self->score);
$self->throw("percent_id not defined in feature") unless defined($self->percent_id);
$self->throw("evalue not defined in feature") unless defined($self->p_value);
}
$self->throw("analysis not defined in feature") unless defined($self->analysis);
}
# These methods are specified in the SeqFeatureI interface but we don't want
# people to store data in them. These are just here in order to keep
# existing code working
lib/Bio/EnsEMBL/SeqFeature.pm view on Meta::CPAN
my ($self,$value) = @_;
if (defined($value)) {
$self->{_id} = $value;
}
return $self->{_id};
}
=head2 percent_id
Title : percent_id
Usage : $pid = $feat->percent_id()
$feat->percent_id($pid)
Function: get/set on percentage identity information
Returns : float
Args : none if get, the new value if set
=cut
sub percent_id {
my ($self,$value) = @_;
if (defined($value))
{
$self->{_percent_id} = $value;
}
return $self->{_percent_id};
}
=head2 p_value
Title : p_value
Usage : $p_val = $feat->p_value()
$feat->p_value($p_val)
Function: get/set on p value information
Returns : float
Args : none if get, the new value if set
lib/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm view on Meta::CPAN
}
my $bio_ens_seqFeature_converter = $self->_bio_ens_seqFeature_converter;
my $ens_feature1 = $bio_ens_seqFeature_converter->_convert_single(
$hsp->feature1);
my $ens_feature2 = $bio_ens_seqFeature_converter->_convert_single(
$hsp->feature2);
$ens_feature1->p_value($hsp->evalue);
$ens_feature1->score($hsp->score);
$ens_feature1->percent_id($hsp->percent_identity);
$ens_feature2->p_value($hsp->evalue);
$ens_feature2->score($hsp->score);
$ens_feature2->percent_id($hsp->percent_identity);
my $cigar_string = $hsp->cigar_string;
my @args = (
-feature1 => $ens_feature1,
-feature2 => $ens_feature2,
-cigar_string => $cigar_string
);
my $contig = $self->contig;
# choose the AlignFeature based on the blast program
lib/Bio/EnsEMBL/Utils/Converter/bio_ens_hsp.pm view on Meta::CPAN
my ($self, $hsp) = @_;
my $bio_ens_seqFeature_converter = $self->_bio_ens_seqFeature_converter;
my $ens_feature1 = $bio_ens_seqFeature_converter->_convert_single(
$hsp->feature1);
my $ens_feature2 = $bio_ens_seqFeature_converter->_convert_single(
$hsp->feature2);
$ens_feature1->p_value($hsp->evalue);
$ens_feature1->score($hsp->score);
$ens_feature1->percent_id($hsp->percent_identity);
$ens_feature2->p_value($hsp->evalue);
$ens_feature2->score($hsp->score);
$ens_feature2->percent_id($hsp->percent_identity);
my $featurePair = Bio::EnsEMBL::FeaturePair->new(
-feature1 => $ens_feature1,
-feature2 => $ens_feature2
);
return $featurePair;
}
sub _convert_single_to_proteinFeature {
lib/Bio/EnsEMBL/Utils/Converter/bio_ens_seqFeature.pm view on Meta::CPAN
$self->throw("a Bio::SeqFeature::Generic object needed");
}
my $seqFeature = $in;
my $seq_id = $seqFeature->seq_id;
unless(defined($seq_id) && $seq_id){
$self->warn("No seq_id value. EnsEMBL SeqFeature will validate it");
$seq_id = 'Unknown';
}
# Debated issue here. There are p_value and percent_id in EnsEMBL API and DB
# schema, but not in bioperl. If in bioperl there are tags called p_value or
# percent_id, then the values are passed, otherwise set the default 1.
#
# the problem arise when I try to converter the seqfeature for tmhmm to
# EnsEMBL seqFeature.
# -- Juguang, 11 July '03
my $score = $in->score || 0;
my $percent_id;
if($in->has_tag('percent_id')){
($percent_id) = $in->get_tag_values('percent_id');
}else{
$percent_id ||= 0;
}
my $p_value;
if($in->has_tag('p_value')){
($p_value) = $in->get_tag_values('p_value');
}elsif($in->has_tag('evalue')){
($p_value) = $in->get_tag_values('evalue');
}else{
$p_value ||= 1;
}
my $ens_seqFeature;
my %args = (
-start => $in->start,
-end => $in->end,
-strand => $in->strand,
-score => $score,
-analysis => $self->analysis,
-source_tag => $in->source_tag,
-seqname => $seq_id,
-percent_id => $percent_id,
-p_value => $p_value
);
my $output_module = $self->out;
if($output_module eq 'Bio::EnsEMBL::SeqFeature'){
$ens_seqFeature = new Bio::EnsEMBL::SeqFeature(%args);
}elsif($self->out eq 'Bio::EnsEMBL::SimpleFeature'){
$ens_seqFeature = new Bio::EnsEMBL::SimpleFeature(%args);
lib/Bio/EnsEMBL/Utils/Logger.pm view on Meta::CPAN
my $indent = shift;
throw("You must provide a name and the current value for your progress bar")
unless ($name and $curr);
# return if we haven't reached the next increment
return if ($curr < int($self->{'_progress'}->{$name}->{'next'}));
my $index = $self->{'_progress'}->{$name}->{'index'};
my $num_bins = $self->{'_progress'}->{$name}->{'numbins'};
my $percent = $index/$num_bins*100;
my $log_str;
$log_str .= ' 'x$indent if ($index == 0);
$log_str .= "\b"x4;
$log_str .= sprintf("%3s%%", $percent);
$log_str .= "\n" if ($curr == $self->{'_progress'}->{$name}->{'max_val'});
$self->info($log_str);
# increment counters
$self->{'_progress'}->{$name}->{'index'}++;
$self->{'_progress'}->{$name}->{'next'} += $self->{'_progress'}->{$name}->{'binsize'};
}
lib/Bio/EnsEMBL/Utils/Logger.pm view on Meta::CPAN
my $indent = shift;
throw("You must provide a name and the current value for your progress bar")
unless ($name and $curr);
# return if we haven't reached the next increment
return if ($curr < int($self->{'_progress'}->{$name}->{'next'}));
my $index = $self->{'_progress'}->{$name}->{'index'};
my $num_bins = $self->{'_progress'}->{$name}->{'numbins'};
my $percent = $index/$num_bins*100;
my $log_str = "\r".(' 'x$indent)."[".('='x$index).(' 'x($num_bins-$index))."] ${percent}\%";
$log_str .= "\n" if ($curr == $self->{'_progress'}->{$name}->{'max_val'});
$self->info($log_str);
# increment counters
$self->{'_progress'}->{$name}->{'index'}++;
$self->{'_progress'}->{$name}->{'next'} += $self->{'_progress'}->{$name}->{'binsize'};
}
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