From 1b43ab58f7e9b5a62fcf6e02b7f82b60e1c44de3 Mon Sep 17 00:00:00 2001
From: Dan Staines <dstaines@ebi.ac.uk>
Date: Mon, 5 Nov 2012 10:01:40 +0000
Subject: [PATCH] additional count methods to support gene density calculations
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 109 +++++++++++++++++++----
modules/t/gene.t | 14 +++
2 files changed, 108 insertions(+), 15 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 0919439709..93f5551f98 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -265,7 +265,26 @@ sub fetch_by_stable_id {
sub fetch_all_by_biotype {
my ($self, $biotype) = @_;
+ my @genes = @{$self->generic_fetch($self->biotype_constraint($biotype))};
+ return \@genes;
+}
+
+=head2 biotype_constraint
+
+ Arg [1] : String $biotype
+ listref of $biotypes
+ The biotype of the gene to retrieve. You can have as an argument a reference
+ to a list of biotypes
+ Description: Used internally to generate a SQL constraint to restrict a gene query by biotype
+ Returntype : String
+ Exceptions : If biotype is not supplied
+ Caller : general
+ Status : Stable
+
+=cut
+sub biotype_constraint {
+ my ($self, $biotype) = @_;
if (!defined $biotype) {
throw("Biotype or listref of biotypes expected");
}
@@ -283,13 +302,31 @@ sub fetch_all_by_biotype {
$constraint = "g.biotype = ? and g.is_current = 1";
$self->bind_param_generic_fetch($biotype, SQL_VARCHAR);
}
- my @genes = @{$self->generic_fetch($constraint)};
- return \@genes;
+ return $constraint;
}
-sub fetch_all {
- my ($self) = @_;
+=head2 count_all_by_biotype
+ Arg [1] : String $biotype
+ listref of $biotypes
+ The biotype of the gene to retrieve. You can have as an argument a reference
+ to a list of biotypes
+ Example : $cnt = $gene_adaptor->count_all_by_biotype('protein_coding');
+ $cnt = $gene_adaptor->count_all_by_biotypes(['protein_coding', 'sRNA', 'miRNA']);
+ Description : Retrieves count of gene objects from the database via its biotype or biotypes.
+ Returntype : integer
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub count_all_by_biotype {
+ my ($self, $biotype) = @_;
+ return $self->generic_count($self->biotype_constraint($biotype));
+}
+
+sub fetch_all {
+ my ($self) = @_;
my $constraint = 'g.biotype != "LRG_gene" and g.is_current = 1';
my @genes = @{$self->generic_fetch($constraint)};
return \@genes;
@@ -616,6 +653,36 @@ sub fetch_all_by_Slice {
return $genes;
} ## end sub fetch_all_by_Slice
+=head2 count_all_by_Slice
+
+ Arg [1] : Bio::EnsEMBL::Slice $slice
+ The slice to count genes on.
+ Arg [2] : (optional) biotype(s) string or arrayref of strings
+ the biotype of the features to count.
+ Arg [1] : (optional) string $source
+ the source name of the features to count.
+ Example : $cnt = $gene_adaptor->count_all_by_Slice();
+ Description: Method to count genes on a given slice, filtering by biotype and source
+ Returntype : integer
+ Exceptions : thrown if exon cannot be placed on transcript slice
+ Status : Stable
+ Caller : general
+=cut
+
+sub count_all_by_Slice {
+ my ($self, $slice, $biotype, $source) = @_;
+
+ my $constraint = 'g.is_current = 1';
+ if (defined($source)) {
+ $constraint .= " and g.source = '$source'";
+ }
+ if (defined($biotype)) {
+ $constraint .= " and " . $self->biotype_constraint($biotype);
+ }
+
+ return $self->count_by_Slice_constraint($slice, $constraint);
+}
+
=head2 fetch_by_transcript_id
Arg [1] : Int $trans_id
@@ -1562,7 +1629,9 @@ FEATURE: while ($sth->fetch()) {
#
if ($mapper) {
- if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper')) {
+ if (defined $dest_slice
+ && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper'))
+ {
($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand) = $mapper->map($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
@@ -1790,7 +1859,8 @@ sub fetch_all_by_exon_supporting_evidence {
}
my $anal_from = ", analysis a " if ($analysis);
- my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
+ my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? "
+ if ($analysis);
my $sql = qq(
SELECT DISTINCT(g.gene_id)
@@ -1854,7 +1924,8 @@ sub fetch_all_by_transcript_supporting_evidence {
}
my $anal_from = ", analysis a " if ($analysis);
- my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? " if ($analysis);
+ my $anal_where = "AND a.analysis_id = f.analysis_id AND a.analysis_id=? "
+ if ($analysis);
my $sql = qq(
SELECT DISTINCT(g.gene_id)
@@ -1938,8 +2009,10 @@ sub fetch_nearest_Gene_by_Feature {
# MAYBE set the result of prepare to be static in case lots of calls.
#
my $sql1_sth = $self->prepare($sql1) || die "Could not prepare $sql1";
- $sql1_sth->execute($start, $seq_region_id, $start) || die "Could not execute sql";
- $sql1_sth->bind_columns(\$gene_id, \$min_dist) || die "Could mot bin columns";
+ $sql1_sth->execute($start, $seq_region_id, $start)
+ || die "Could not execute sql";
+ $sql1_sth->bind_columns(\$gene_id, \$min_dist)
+ || die "Could mot bin columns";
my $last_dist = 99999999999999999;
while ($sql1_sth->fetch()) {
@@ -1959,8 +2032,10 @@ sub fetch_nearest_Gene_by_Feature {
my $sql2_sth = $self->prepare($sql2) || die "could not prepare $sql2";
my ($tmp_min_dist, $tmp_gene_id);
- $sql2_sth->execute($end, $seq_region_id, $end) || die "Could not execute sql";
- $sql2_sth->bind_columns(\$tmp_gene_id, \$tmp_min_dist) || die "Could mot bin columns";
+ $sql2_sth->execute($end, $seq_region_id, $end)
+ || die "Could not execute sql";
+ $sql2_sth->bind_columns(\$tmp_gene_id, \$tmp_min_dist)
+ || die "Could mot bin columns";
my $first = 1;
while ($sql2_sth->fetch()) {
if ($tmp_min_dist <= $last_dist) {
@@ -1987,8 +2062,10 @@ sub fetch_nearest_Gene_by_Feature {
# MAYBE set the result of prepare to be static in case lots of calls.
#
my $sql1_sth = $self->prepare($sql1) || die "Could not prepare $sql1";
- $sql1_sth->execute($start, $seq_region_id, $start) || die "Could not execute sql";
- $sql1_sth->bind_columns(\$gene_id, \$min_dist) || die "Could mot bin columns";
+ $sql1_sth->execute($start, $seq_region_id, $start)
+ || die "Could not execute sql";
+ $sql1_sth->bind_columns(\$gene_id, \$min_dist)
+ || die "Could mot bin columns";
my $last_dist;
my $first = 1;
@@ -2013,8 +2090,10 @@ sub fetch_nearest_Gene_by_Feature {
my $sql2_sth = $self->prepare($sql2) || die "could not prepare $sql2";
my ($tmp_min_dist, $tmp_gene_id);
- $sql2_sth->execute($end, $seq_region_id, $end) || die "Could not execute sql";
- $sql2_sth->bind_columns(\$tmp_gene_id, \$tmp_min_dist) || die "Could mot bin columns";
+ $sql2_sth->execute($end, $seq_region_id, $end)
+ || die "Could not execute sql";
+ $sql2_sth->bind_columns(\$tmp_gene_id, \$tmp_min_dist)
+ || die "Could mot bin columns";
my $first = 1;
my $last_dist;
while ($sql2_sth->fetch()) {
diff --git a/modules/t/gene.t b/modules/t/gene.t
index 37b4c7848b..cdff69f47e 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -369,6 +369,16 @@ for my $gene (@$genes) {
}
}
+# try and count the genes on the slice
+my $geneCount = $ga->count_all_by_Slice($slice);
+ok(scalar(@$genes) == $geneCount);
+$geneCount = $ga->count_all_by_Slice($slice, 'protein_coding');
+ok(scalar(@$genes) == $geneCount);
+$geneCount = $ga->count_all_by_Slice($slice, 'banana');
+ok($geneCount == 0);
+$geneCount = $ga->count_all_by_Slice($slice, ['banana', 'protein_coding']);
+ok($geneCount == scalar(@$genes));
+
debug("known: $known Unknown: $unknown\n");
ok($known == 17);
@@ -478,6 +488,10 @@ debug("Test fetch_all_by_biotype");
ok(@genes == 20);
@genes = @{$ga->fetch_all_by_biotype(['protein_coding', 'sRNA'])};
ok(@genes == 20);
+$geneCount = $ga->count_all_by_biotype('protein_coding');
+ok($geneCount == 20);
+$geneCount = $ga->count_all_by_biotype(['protein_coding', 'sRNA']);
+ok($geneCount == 20);
#
# test Gene: get_all_alt_alleles
--
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