From 63010ae9d2863af061d8bebf6593f86b43afd7ea Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 9 Jan 2012 15:38:47 +0000
Subject: [PATCH] update get_set_list to use ExonerateGappedBest5 method for
RefSeq_mRNA and ncRNA (predicted) xrefs
---
.../xref_mapping/XrefMapper/SubmitMapper.pm | 32 +++++++++++++++++--
.../XrefMapper/caenorhabditis_elegans.pm | 6 +++-
.../XrefMapper/canis_familiaris.pm | 6 +++-
.../XrefMapper/ciona_intestinalis.pm | 6 +++-
.../xref_mapping/XrefMapper/danio_rerio.pm | 6 +++-
.../XrefMapper/drosophila_ananassae.pm | 6 +++-
.../XrefMapper/drosophila_erecta.pm | 6 +++-
.../XrefMapper/drosophila_grimshawi.pm | 6 +++-
.../XrefMapper/drosophila_melanogaster.pm | 6 +++-
.../XrefMapper/drosophila_mojavensis.pm | 6 +++-
.../XrefMapper/drosophila_persimilis.pm | 6 +++-
.../XrefMapper/drosophila_pseudoobscura.pm | 6 +++-
.../XrefMapper/drosophila_sechellia.pm | 6 +++-
.../XrefMapper/drosophila_simulans.pm | 6 +++-
.../XrefMapper/drosophila_virilis.pm | 6 +++-
.../XrefMapper/drosophila_yakuba.pm | 6 +++-
.../xref_mapping/XrefMapper/fugu_rubripes.pm | 6 +++-
.../xref_mapping/XrefMapper/macaca_mulatta.pm | 6 +++-
.../XrefMapper/monodelphis_domestica.pm | 6 +++-
.../XrefMapper/neurospora_crassa.pm | 6 +++-
.../XrefMapper/saccharomyces_cerevisiae.pm | 6 +++-
.../XrefMapper/schizosaccharomyces_pombe.pm | 6 +++-
.../XrefMapper/xenopus_tropicalis.pm | 6 +++-
23 files changed, 139 insertions(+), 25 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm b/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
index 88aaffcecb..b3d4eb5528 100644
--- a/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
@@ -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{
+}
###################################################################################################
diff --git a/misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm b/misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm
index d7cdb15402..38c9289b9c 100644
--- a/misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/canis_familiaris.pm b/misc-scripts/xref_mapping/XrefMapper/canis_familiaris.pm
index 217142cc7f..5da53dc043 100644
--- a/misc-scripts/xref_mapping/XrefMapper/canis_familiaris.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/canis_familiaris.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/ciona_intestinalis.pm b/misc-scripts/xref_mapping/XrefMapper/ciona_intestinalis.pm
index 13c39ae0fb..7c38a048a1 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ciona_intestinalis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/ciona_intestinalis.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
index 24a424fb16..772e25d46d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_ananassae.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_ananassae.pm
index 10d77d0676..3a34ec9581 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_ananassae.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_ananassae.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_erecta.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_erecta.pm
index 312166de26..72177e0b17 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_erecta.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_erecta.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_grimshawi.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_grimshawi.pm
index 2af3545725..2cd4b17b19 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_grimshawi.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_grimshawi.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_melanogaster.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_melanogaster.pm
index c61e6ea7b5..78e3602a20 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_melanogaster.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_melanogaster.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_mojavensis.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_mojavensis.pm
index 414ad98bfc..153f6956de 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_mojavensis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_mojavensis.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_persimilis.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_persimilis.pm
index f47adb330f..a66224b625 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_persimilis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_persimilis.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_pseudoobscura.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_pseudoobscura.pm
index 592cf2df5e..97eca001ee 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_pseudoobscura.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_pseudoobscura.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_sechellia.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_sechellia.pm
index 73754a6255..229e3c1287 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_sechellia.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_sechellia.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_simulans.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_simulans.pm
index 6f7fe5bc7f..54b7c1cf5d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_simulans.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_simulans.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_virilis.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_virilis.pm
index 15d984ecdf..8d593b54d9 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_virilis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_virilis.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/drosophila_yakuba.pm b/misc-scripts/xref_mapping/XrefMapper/drosophila_yakuba.pm
index 6384d9ca70..7880f96253 100644
--- a/misc-scripts/xref_mapping/XrefMapper/drosophila_yakuba.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/drosophila_yakuba.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/fugu_rubripes.pm b/misc-scripts/xref_mapping/XrefMapper/fugu_rubripes.pm
index 7b80418f05..2d7f535cb7 100644
--- a/misc-scripts/xref_mapping/XrefMapper/fugu_rubripes.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/fugu_rubripes.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/macaca_mulatta.pm b/misc-scripts/xref_mapping/XrefMapper/macaca_mulatta.pm
index 0928d37fd3..609fed4590 100644
--- a/misc-scripts/xref_mapping/XrefMapper/macaca_mulatta.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/macaca_mulatta.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/monodelphis_domestica.pm b/misc-scripts/xref_mapping/XrefMapper/monodelphis_domestica.pm
index 2b6b3178d6..98fc1d0138 100644
--- a/misc-scripts/xref_mapping/XrefMapper/monodelphis_domestica.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/monodelphis_domestica.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm b/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm
index f18a93762f..0498b27789 100644
--- a/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/neurospora_crassa.pm
@@ -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","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm b/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm
index b371716ed8..47545b7c7c 100644
--- a/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm
@@ -9,7 +9,11 @@ use vars qw(@ISA);
sub get_set_lists {
- return [["ExonerateGappedBest1", ["saccharomyces_cerevisiae","*"]]];
+ return [["ExonerateGappedBest5", ["saccharomyces_cerevisiae","RefSeq_mRNA"]],
+ ["ExonerateGappedBest5", ["saccharomyces_cerevisiae","RefSeq_mRNA_predicted"]],
+ ["ExonerateGappedBest5", ["saccharomyces_cerevisiae","RefSeq_ncRNA"]],
+ ["ExonerateGappedBest5", ["saccharomyces_cerevisiae","RefSeq_ncRNA_predicted"]],
+ ["ExonerateGappedBest1", ["saccharomyces_cerevisiae","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
index 353ddfffa7..1e22d0ffc5 100644
--- a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
@@ -8,7 +8,11 @@ use vars qw(@ISA);
sub get_set_lists {
- return [["ExonerateGappedBest1", ["schizosaccharomyces_pombe","*"]]];
+ return [["ExonerateGappedBest5", ["schizosaccharomyces_pombe","RefSeq_mRNA"]],
+ ["ExonerateGappedBest5", ["schizosaccharomyces_pombe","RefSeq_mRNA_predicted"]],
+ ["ExonerateGappedBest5", ["schizosaccharomyces_pombe","RefSeq_ncRNA"]],
+ ["ExonerateGappedBest5", ["schizosaccharomyces_pombe","RefSeq_ncRNA_predicted"]],
+ ["ExonerateGappedBest1", ["schizosaccharomyces_pombe","*"]]];
}
diff --git a/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm b/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm
index 31f966efbe..bc80e5a0fd 100644
--- a/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm
@@ -8,7 +8,11 @@ use vars '@ISA';
sub get_set_lists{
- return [["ExonerateGappedBest_90_perc_id", ["xenopus_tropicalis","*"]]];
+ return [["ExonerateGappedBest5", ["xenopus_tropicalis","RefSeq_mRNA"]],
+ ["ExonerateGappedBest5", ["xenopus_tropicalis","RefSeq_mRNA_predicted"]],
+ ["ExonerateGappedBest5", ["xenopus_tropicalis","RefSeq_ncRNA"]],
+ ["ExonerateGappedBest5", ["xenopus_tropicalis","RefSeq_ncRNA_predicted"]],
+ ["ExonerateGappedBest1", ["xenopus_tropicalis","*"]]];
}
--
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