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Commit bf950eee authored by Ian Longden's avatar Ian Longden
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added descriptions

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misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+ 35
− 31
View file @ bf950eee
......@@ -523,43 +523,44 @@ FSQL
#
# get the OFDN (HGNC/MGI) xrefs in the xrefs and add the synonyms, plus create hash to get id from the display name
# get the OFDN (HGNC/MGI) xrefs in the xrefs and add the synonyms, plus create hash to get id from the display name and desc
# This is becouse not all MGI.HGNC's are loaded as these are priority xrefs.
#
my %display_label_to_id;
my %display_label_to_desc;
$sql = 'select x.accession, sy.synonym from synonym sy, xref x, source so where x.xref_id = sy.xref_id and so.source_id = x.source_id and so.name like "'.$dbname.'"';
$sql = 'select x.accession, sy.synonym, x.description from synonym sy, xref x, source so where x.xref_id = sy.xref_id and so.source_id = x.source_id and so.name like "'.$dbname.'"';
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
my ($display_label, $acc, $syn,);
$sth->bind_columns(\$acc,\$display_label);
my ($display_label, $acc, $syn, $desc);
$sth->bind_columns(\$acc,\$display_label, \$desc);
while($sth->fetch){
$display_label_to_id{$display_label} = $acc;
$display_label_to_desc{$display_label} = $desc;
}
$sth->finish;
# get label to id from xref database to start with.
$sql = 'select x.accession, x.label from xref x, source s where s.source_id = x.source_id and s.name like "'.$dbname.'"';
$sql = 'select x.accession, x.label, x.description from xref x, source s where s.source_id = x.source_id and s.name like "'.$dbname.'"';
$sth = $self->xref->dbc->prepare($sql);
$sth->execute();
$sth->bind_columns(\$acc,\$display_label);
$sth->bind_columns(\$acc,\$display_label, \$desc);
while($sth->fetch){
$display_label_to_id{$display_label} = $acc;
$display_label_to_desc{$display_label} = $desc;
}
$sth->finish;
my %synonym;
$sth = $self->xref->dbc->prepare('select es.synonym, x.label from synonym es, xref x, source s where x.xref_id = es.xref_id and x.source_id = s.source_id and
s.name = "'.$dbname.'"' );
......@@ -755,17 +756,17 @@ FSQL
$sql = "insert into xref (xref_id, source_id, accession, label, version, species_id, info_type, info_text) values (?, ?, ?, ?, 0, ".$self->species_id.", 'MISC', ? )";
$sql = "insert into xref (xref_id, source_id, accession, label, version, species_id, info_type, info_text, description) values (?, ?, ?, ?, 0, ".$self->species_id.", 'MISC', ?, ? )";
my $ins_xref_sth = $self->xref->dbc->prepare($sql);
$sql = "insert into xref (xref_id, source_id, accession, label, version, species_id, info_type, info_text) values (?, ?, ?, ?, ?, ".$self->species_id.", 'MISC', ? )";
$sql = "insert into xref (xref_id, source_id, accession, label, version, species_id, info_type, info_text, description) values (?, ?, ?, ?, ?, ".$self->species_id.", 'MISC', ?, ? )";
my $ins_xref_ver_sth = $self->xref->dbc->prepare($sql);
# important or will crash and burn!!!
my %xref_added; # store those added already $xref_added{$accession:$source_id} = $xref_id;
my $get_xref_info_sth = $self->xref->dbc->prepare("select x.label, x.accession, s.priority_description from xref x, source s where xref_id = ? and s.source_id = x.source_id");
my $get_xref_info_sth = $self->xref->dbc->prepare("select x.label, x.accession, s.priority_description, x.description from xref x, source s where xref_id = ? and s.source_id = x.source_id");
#
# Okay we assign unused_priority to be the number of time a vega transcript is attached to make sure
......@@ -863,9 +864,9 @@ FSQL
if(defined($VEGA) and scalar(@ODN)){
my $found = 0;
foreach my $xref_id (@ODN){
my ($display, $acc, $text);
my ($display, $acc, $text, $desc);
$get_xref_info_sth->execute($xref_id);
$get_xref_info_sth->bind_columns(\$display, \$acc, \$text);
$get_xref_info_sth->bind_columns(\$display, \$acc, \$text, \$desc);
$get_xref_info_sth->fetch();
if(uc($VEGA) eq uc($display)){
$found = 1;
......@@ -908,14 +909,15 @@ FSQL
foreach my $name (keys %name_count){
my $id = $display_label_to_id{$name};
my $id = $display_label_to_id{$name};
my $desc = $display_label_to_desc{$name};
if(!defined($id)){
$id = $name;
print STDERR "Warning Could not find id for $name\n";
}
if(!defined($xref_added{$id.":".$odn_curated_gene_id})){
$max_xref_id++;
$ins_xref_sth->execute($max_xref_id, $odn_curated_gene_id, $id, $name, "via havana");
$ins_xref_sth->execute($max_xref_id, $odn_curated_gene_id, $id, $name, "via havana", $desc);
$xref_added{$id.":".$odn_curated_gene_id} = $max_xref_id;
......@@ -932,12 +934,13 @@ FSQL
}
$name = $v_name;
my $desc = $display_label_to_desc{$v_name} || undef;
my $tran_name_ext = 201;
foreach my $tran (sort keys %no_vega){
my $id = $name."-".$tran_name_ext;
if(!defined($xref_added{$id.":".$odn_automatic_tran_id})){
$max_xref_id++;
$ins_xref_sth->execute($max_xref_id, $odn_automatic_tran_id, $id, $id, "via havana");
$ins_xref_sth->execute($max_xref_id, $odn_automatic_tran_id, $id, $id, "via havana", $desc);
$xref_added{$id.":".$odn_automatic_tran_id} = $max_xref_id;
}
$max_object_xref_id++;
......@@ -958,9 +961,9 @@ FSQL
# now store xref_id so get xref details from this.
# $get_xref_info_sth = $self->xref->dbc->prepare("select x.label, x.accession, x.info_text from xref x where xref_id = ?");
my ($display, $acc, $text);
my ($display, $acc, $text, $desc);
$get_xref_info_sth->execute($xref_id);
$get_xref_info_sth->bind_columns(\$display, \$acc, \$text);
$get_xref_info_sth->bind_columns(\$display, \$acc, \$text, \$desc);
$get_xref_info_sth->fetch();
my $id = $display_label_to_id{$display};
if(!defined($display)){
......@@ -971,10 +974,10 @@ FSQL
$max_xref_id++;
# "insert into xref (xref_id, source_id, accession, label, version, species_id , info_type, info_text)
# values (? , ? , ? , ? , 0 , ".$self->species_id.", 'MISC' , ? )";
$ins_xref_sth->execute($max_xref_id, $odn_automatic_gene_id, $acc, $display, "via ".$text);
$ins_xref_sth->execute($max_xref_id, $odn_automatic_gene_id, $acc, $display, "via ".$text, $desc);
$xref_added{$acc.":".$odn_automatic_gene_id} = $max_xref_id;
if(defined($syn_hash->{$name})){
foreach my $syn (@{$syn_hash->{$name}}){
if(defined($syn_hash->{$acc})){
foreach my $syn (@{$syn_hash->{$acc}}){
$add_syn_sth->execute($max_xref_id, $syn);
}
}
......@@ -987,9 +990,9 @@ FSQL
}
my $xref_id = $ODN[0];
my ($display, $acc, $text);
my ($display, $acc, $text, $desc);
$get_xref_info_sth->execute($xref_id);
$get_xref_info_sth->bind_columns(\$display, \$acc, \$text);
$get_xref_info_sth->bind_columns(\$display, \$acc, \$text, \$desc);
$get_xref_info_sth->fetch();
my $name = $display;
......@@ -1004,7 +1007,7 @@ FSQL
}
if(!defined($xref_added{$id.":".$odn_automatic_tran_id})){
$max_xref_id++;
$ins_xref_sth->execute($max_xref_id, $odn_automatic_tran_id, $id, $id, "via ".$text);
$ins_xref_sth->execute($max_xref_id, $odn_automatic_tran_id, $id, $id, "via ".$text, $desc);
$xref_added{$id.":".$odn_automatic_tran_id} = $max_xref_id;
}
else{
......@@ -1032,10 +1035,11 @@ FSQL
$gene_clone_name_count{$CLONE_NAME} = 1;
}
# $CLONE_NAME .= ".".$gene_clone_name_count{$CLONE_NAME};
my $id = $CLONE_NAME.".".$gene_clone_name_count{$CLONE_NAME};
# my $id = $CLONE_NAME.".".$gene_clone_name_count{$CLONE_NAME};
my $id = $CLONE_NAME; # vega clone names should have the gene number and not the version at the end.
if(!defined($xref_added{$id.":".$clone_based_vega_gene_id})){
$max_xref_id++;
$ins_xref_sth->execute($max_xref_id, $clone_based_vega_gene_id, $id, $id, "via Vega clonename");
$ins_xref_sth->execute($max_xref_id, $clone_based_vega_gene_id, $id, $id, "via Vega clonename",undef);
$xref_added{$id.":".$clone_based_vega_gene_id} = $max_xref_id;
}
......@@ -1050,7 +1054,7 @@ FSQL
my $id = $CLONE_NAME."-".$tran_name_ext;
if(!defined($xref_added{$id.":".$clone_based_vega_tran_id})){
$max_xref_id++;
$ins_xref_sth->execute($max_xref_id, $clone_based_vega_tran_id, $id, $id, "via Vega clonename");
$ins_xref_sth->execute($max_xref_id, $clone_based_vega_tran_id, $id, $id, "via Vega clonename",undef);
$xref_added{$id.":".$clone_based_vega_tran_id} = $max_xref_id;
}
......@@ -1119,7 +1123,7 @@ FSQL
# store the data
if(!defined($xref_added{$gene_name.":".$clone_based_ensembl_gene_id})){
$max_xref_id++;
$ins_xref_sth->execute($max_xref_id, $clone_based_ensembl_gene_id, $gene_name, $gene_name, "via clonename");
$ins_xref_sth->execute($max_xref_id, $clone_based_ensembl_gene_id, $gene_name, $gene_name, "via clonename", undef);
$xref_added{$gene_name.":".$clone_based_ensembl_gene_id} = $max_xref_id;
}
......@@ -1129,14 +1133,14 @@ FSQL
my $tran_name_ext = 201;
foreach my $tran (sort keys %no_vega){
my $id = $new_clone_name."-".$tran_name_ext;
my $id = $gene_name."-".$tran_name_ext;
while(defined($xref_added{$id.":".$clone_based_ensembl_tran_id})){
$tran_name_ext++;
$id = $new_clone_name."-".$tran_name_ext;
$id = $gene_name."-".$tran_name_ext;
}
$max_xref_id++;
$ins_xref_sth->execute($max_xref_id, $clone_based_ensembl_tran_id, $id, $id, "via clonename");
$ins_xref_sth->execute($max_xref_id, $clone_based_ensembl_tran_id, $id, $id, "via clonename", undef);
$xref_added{$id.":".$clone_based_ensembl_tran_id} = $max_xref_id;
$max_object_xref_id++;
......
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