Commit 63010ae9 authored by Monika Komorowska's avatar Monika Komorowska
Browse files

update get_set_list to use ExonerateGappedBest5 method for RefSeq_mRNA and ncRNA (predicted) xrefs

parent 3a5eb382
......@@ -190,18 +190,33 @@ sub dump_xref{
my @exception_sql = ();
if($exception){
my $source_sth = $xref->dbc->prepare("select s.source_id from source s, species sp, source_url u where u.source_id = s.source_id and u.species_id = sp.species_id and sp.name like ? and s.name like ?");
my $source_sth = $xref->dbc->prepare("select s.source_id from source s, species sp, source_url u where u.source_id = s.source_id and u.species_id = sp.species_id and sp.name like ? and s.name like ?");
my $dep_source_sth = $xref->dbc->prepare("select distinct s2.source_id from source_url u, source s1, species sp, dependent_source d, source s2 where u.source_id = s1.source_id and u.species_id = sp.species_id and s1.name = d.dependent_name and s2.source_id = d.master_source_id and sp.name like ? and s2.name like ?");
$k = 0;
my @exception_list =();
while($k <= $number_of_sets){
my @tmp=();
if($k != $all){
$source_sth->execute($species[$k], $sources[$k]);
my $source_found = 0;
while(my @row = $source_sth->fetchrow_array()){
# print $row[0]."\t".$species[$k]."\t".$sources[$k]."\n";
push @tmp, $row[0];
push @exception_list, $row[0]
push @exception_list, $row[0];
$source_found = 1;
}
if (!$source_found) {
#if we haven't found the source in the source_url table try the dependent_source table
$dep_source_sth->execute($species[$k], $sources[$k]);
while(my @row = $dep_source_sth->fetchrow_array()){
push @tmp, $row[0];
push @exception_list, $row[0];
$source_found = 1;
}
}
if (!$source_found) {
die "unable to find source_id for source name ". $sources[$k] ."\n";
}
$exception_sql[$k] .= " AND x.source_id in (".join(', ',@tmp).") ";
}
......@@ -211,6 +226,8 @@ sub dump_xref{
$exception_sql[$all] = " AND x.source_id not in (".join(', ', @exception_list).")";
}
$source_sth->finish();
$dep_source_sth->finish();
}
else{
$exception_sql[0] = "";
......@@ -254,7 +271,7 @@ sub dump_xref{
my $sql = "SELECT p.xref_id, p.sequence, x.species_id , x.source_id ";
$sql .= " FROM primary_xref p, xref x ";
$sql .= " WHERE p.xref_id = x.xref_id AND ";
$sql .= " p.sequence_type ='$sequence_type' ";
$sql .= " p.sequence_type ='" . $sequence_type ."' ";
$sql .= $exception_sql[$i];
my $sth = $xref->dbc->prepare($sql);
......@@ -619,15 +636,24 @@ sub fetch_and_dump_seq_via_genes{
sub get_set_lists{
my ($self) = @_;
# format: [ method, [species (* - all species),source]]
return [["ExonerateGappedBest_100_perc_id", ["*","Uniprot/SWISSPROT"]],
["ExonerateGappedBest_100_perc_id", ["*","Uniprot/SPTREMBL"]],
["ExonerateGappedBest5", ["*","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["*","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["*","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["*","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["*","*"]] ];
# return [["ExonerateGappedBest1", ["*","*"]]];
}
# some external references are downloaded under one source and then split up into several
# different sources,
sub map_sources{
}
###################################################################################################
......
......@@ -9,7 +9,11 @@ use vars qw(@ISA);
sub get_set_lists {
return [["ExonerateGappedBest1", ["caenorhabditis_elegans","*"]]];
return [["ExonerateGappedBest5", ["caenorhabditis_elegans","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["caenorhabditis_elegans","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["caenorhabditis_elegans","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["caenorhabditis_elegans","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["caenorhabditis_elegans","*"]]];
}
......
......@@ -8,7 +8,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["canis_familiaris","*"]]];
return [["ExonerateGappedBest5", ["canis_familiaris","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["canis_familiaris","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["canis_familiaris","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["canis_familiaris","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["canis_familiaris","*"]]];
}
......
......@@ -8,7 +8,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["ciona_intestinalis","*"]]];
return [["ExonerateGappedBest5", ["ciona_intestinalis","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["ciona_intestinalis","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["ciona_intestinalis","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["ciona_intestinalis","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["ciona_intestinalis","*"]]];
}
......
......@@ -60,7 +60,11 @@ JSQL
sub get_set_lists {
return [["ExonerateGappedBest1", ["danio_rerio","*"]]];
return [["ExonerateGappedBest5", ["danio_rerio","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["danio_rerio","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["danio_rerio","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["danio_rerio","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["danio_rerio","*"]]];
}
......
......@@ -7,7 +7,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_ananassae","*"]]];
return [["ExonerateGappedBest5", ["drosophila_ananassae","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_ananassae","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_ananassae","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_ananassae","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_ananassae","*"]]];
}
......
......@@ -7,7 +7,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_erecta","*"]]];
return [["ExonerateGappedBest5", ["drosophila_erecta","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_erecta","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_erecta","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_erecta","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_erecta","*"]]];
}
......
......@@ -9,7 +9,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_grimshawi","*"]]];
return [["ExonerateGappedBest5", ["drosophila_grimshawi","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_grimshawi","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_grimshawi","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_grimshawi","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_grimshawi","*"]]];
}
......
......@@ -7,7 +7,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_melanogaster","*"]]];
return [["ExonerateGappedBest5", ["drosophila_melanogaster","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_melanogaster","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_melanogaster","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_melanogaster","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_melanogaster","*"]]];
}
......
......@@ -8,7 +8,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_mojavensis","*"]]];
return [["ExonerateGappedBest5", ["drosophila_mojavensis","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_mojavensis","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_mojavensis","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_mojavensis","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_mojavensis","*"]]];
}
......
......@@ -7,7 +7,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_persimilis","*"]]];
return [["ExonerateGappedBest5", ["drosophila_persimilis","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_persimilis","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_persimilis","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_persimilis","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_persimilis","*"]]];
}
......
......@@ -8,7 +8,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_pseudoobscura","*"]]];
return [["ExonerateGappedBest5", ["drosophila_pseudoobscura","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_pseudoobscura","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_pseudoobscura","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_pseudoobscura","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_pseudoobscura","*"]]];
}
......
......@@ -8,7 +8,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_sechellia","*"]]];
return [["ExonerateGappedBest5", ["drosophila_sechellia","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_sechellia","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_sechellia","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_sechellia","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_sechellia","*"]]];
}
......
......@@ -7,7 +7,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_simulans","*"]]];
return [["ExonerateGappedBest5", ["drosophila_simulans","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_simulans","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_simulans","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_simulans","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_simulans","*"]]];
}
......
......@@ -7,7 +7,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_virilis","*"]]];
return [["ExonerateGappedBest5", ["drosophila_virilis","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_virilis","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_virilis","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_virilis","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_virilis","*"]]];
}
......
......@@ -7,7 +7,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["drosophila_yakuba","*"]]];
return [["ExonerateGappedBest5", ["drosophila_yakuba","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["drosophila_yakuba","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["drosophila_yakuba","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["drosophila_yakuba","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["drosophila_yakuba","*"]]];
}
......
......@@ -8,7 +8,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["fugu_rubripes","*"]]];
return [["ExonerateGappedBest5", ["fugu_rubripes","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["fugu_rubripes","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["fugu_rubripes","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["fugu_rubripes","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["fugu_rubripes","*"]]];
}
......
......@@ -8,7 +8,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["macaca_mulatta","*"]]];
return [["ExonerateGappedBest5", ["macaca_mulatta","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["macaca_mulatta","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["macaca_mulatta","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["macaca_mulatta","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["macaca_mulatta","*"]]];
}
......
......@@ -8,7 +8,11 @@ use vars '@ISA';
sub get_set_lists {
return [["ExonerateGappedBest1", ["monodelphis_domestica","*"]]];
return [["ExonerateGappedBest5", ["monodelphis_domestica","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["monodelphis_domestica","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["monodelphis_domestica","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["monodelphis_domestica","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["monodelphis_domestica","*"]]];
}
......
......@@ -9,7 +9,11 @@ use vars qw(@ISA);
sub get_set_lists {
return [["ExonerateGappedBest1", ["neurospora_crassa","*"]]];
return [["ExonerateGappedBest5", ["neurospora_crassa","RefSeq_mRNA"]],
["ExonerateGappedBest5", ["neurospora_crassa","RefSeq_mRNA_predicted"]],
["ExonerateGappedBest5", ["neurospora_crassa","RefSeq_ncRNA"]],
["ExonerateGappedBest5", ["neurospora_crassa","RefSeq_ncRNA_predicted"]],
["ExonerateGappedBest1", ["neurospora_crassa","*"]]];
}
......
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