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Commit dd85bd37 authored by Ian Longden's avatar Ian Longden
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set info types correctly, plus general fixes

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misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+ 45
− 17
View file @ dd85bd37
......@@ -1114,7 +1114,7 @@ sub parse_mappings {
$failed_xref_mappings{$query_id} = $reason;
}
else{
$priority_failed{$priority_xref_source_id{$query_id}.":".$query_id} = $reason;
$priority_failed{$priority_xref_source_id{$query_id}.":".$priority_xref_acc{$query_id}} = $reason;
print PRIORITY_FILE $priority_xref_acc{$query_id}."\tFailed cutoff $reason\n";
}
next;
......@@ -1139,6 +1139,7 @@ sub parse_mappings {
$target_start+1, $target_end,
$cigar_line, $score, "\\N", $analysis_id)) . "\n";
$priority_xref_state{$key} = "primary";
$priority_xref_extra_bit{$query_id} = "\tSEQUENCE_MATCH\t" . "Relationship generated from exonerate mapping" . "\n";
next;
}
if($priority_xref_priority{$key}
......@@ -1154,6 +1155,7 @@ sub parse_mappings {
$target_start+1, $target_end,
$cigar_line, $score, "\\N", $analysis_id)) . "\n";
$priority_xref_state{$key} = "primary";
$priority_xref_extra_bit{$query_id} = "\tSEQUENCE_MATCH\t" . "Relationship generated from exonerate mapping" . "\n";
}
else{
print PRIORITY_FILE $priority_xref_acc{$query_id}."\t".$source_id." has less priority (PRIMARY) so left as is\n";
......@@ -1582,6 +1584,8 @@ PSQL
my %triage_dumped=(); # dump only once for each accession
if(defined($priority_source_id{$source})){ # cannot do triage at the moment for priority type xrefs.
# oh yes we can!! but not yet
next;
}
my $sql = "select x.xref_id, x.accession, x.version, x.label, x.description, x.source_id, ".
......@@ -1599,7 +1603,7 @@ PSQL
$self->cleanup_sources_file($external_db_id);
}
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession .
"\t" . $label . "\t" . $version . "\t" . $description . "\n";
"\t" . $label . "\t" . $version . "\t" . $description . "\tMISC\tNo match\n";
#dump out dependencies aswell
......@@ -1708,7 +1712,7 @@ sub dump_orphan_xrefs() {
$self->cleanup_sources_file($external_db_id);
}
if(!defined($priority_xref_source_id{$xref_id})){
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\tMISC\tNo match\n";
$xrefs_written{$xref_id} = 1;
$count++;
}
......@@ -1774,8 +1778,11 @@ sub dump_direct_xrefs {
$xref_sth->bind_columns(\$xref_id, \$ensembl_stable_id, \$type, \$linkage_xref,\ $accession, \$version, \$label, \$description, \$source_id, \$species_id);
open(PRIORITY_FILE,">>priority_xref.out") || die "Could not open priority_xref.out\n";
my %error_count;
my %error_example;
open(PRIORITY_FILE,">>priority_xref.out") || die "Could not open priority_xref.out\n";
my $ccds_source = get_source_id_from_source_name($self->xref(), "CCDS");
while ($xref_sth->fetch()) {
my $external_db_id = $source_to_external_db{$source_id};
......@@ -1789,12 +1796,23 @@ sub dump_direct_xrefs {
# In the case of CCDS xrefs, direct_xref is to transcript but we want
# the mapping in the core db to be to the *translation*
if ($source_id == get_source_id_from_source_name($self->xref(), "CCDS")) {
if ($source_id == $ccds_source) {
$type = 'translation';
my $tmp_esid = $ensembl_stable_id;
$ensembl_stable_id = $transcript_stable_id_to_translation_stable_id{$tmp_esid};
warn "Can't find translation for transcript $tmp_esid" if (!$ensembl_stable_id);
if(defined($error_count{$source_id})and defined(!$ensembl_stable_id)){
$error_count{$source_id}++;
if($error_count{$source_id} < 6){
$error_example{$source_id} .= ", $tmp_esid - $accession";
}
}
elsif(!$ensembl_stable_id){
$error_count{$source_id} = 1;
$error_example{$source_id} = "$tmp_esid - $accession";
}
# warn "Can't find translation for transcript $tmp_esid" if (!$ensembl_stable_id);
#print "CCDS: transcript $tmp_esid -> translation $ensembl_stable_id\n";
next;
}
my $ensembl_internal_id;
......@@ -1862,7 +1880,7 @@ sub dump_direct_xrefs {
$object_xref_id++;
$count++;
} else {
} else { ##ahh
if(!defined($worm_pep_source_id)){
$worm_pep_source_id = get_source_id_from_source_name($self->xref(), "wormpep_id");
$worm_locus_source_id = get_source_id_from_source_name($self->xref(), "wormbase_locus");
......@@ -1903,17 +1921,28 @@ sub dump_direct_xrefs {
} # foreach stable_id
} # if source_id
# if we haven't changed $object_xref_id, nothing was written
print STDERR "Can't find $type corresponding to stable ID $ensembl_stable_id in ${type}_stable_id, not writing record for xref $accession\n" if ($object_xref_id == $old_object_xref_id);
# print STDERR "Can't find $type corresponding to stable ID $ensembl_stable_id in ${type}_stable_id, not writing record for xref $accession\n" if ($object_xref_id == $old_object_xref_id);
if(defined($error_count{$source_id})){
$error_count{$source_id}++;
if($error_count{$source_id} < 6){
$error_example{$source_id} .= ", $ensembl_stable_id - $accession";
}
}
else{
$error_count{$source_id} = 1;
$error_example{$source_id} = "$ensembl_stable_id - $accession";
}
}
}
foreach my $key (keys %error_count){
print STDERR "Problems with ".$error_count{$key}." Direct Xrefs for source $key\n";
print STDERR "\te.g. ".$error_example{$key}."\n";
}
close(OBJECT_XREF);
close(XREF);
close(GO_XREF);
......@@ -2165,7 +2194,7 @@ sub dump_core_xrefs {
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\t" . "MISC\t" . "Relationship generated from exonerate mapping" . "\n";
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\t" . "SEQUENCE_MATCH\t" . "Relationship generated from exonerate mapping" . "\n";
$xrefs_written{$xref_id} = 1;
$source_ids{$source_id} = $source_id;
}
......@@ -3474,7 +3503,7 @@ EOS
$count++;
print XREF2 ($xref_id+$xref_id_offset)."\t". $source_to_external_db{$source_id}.
"\t$acc\t$label\t$ver\t$desc";
print XREF2 "\tDEPENDENT\tGenerated via its Pair ".$priority_seenit{$acc}."\n";
print XREF2 "\tINFERRED_PAIR\tGenerated via its Pair ".$priority_seenit{$acc}."\n";
$xrefs_written{$xref_id}
}
......@@ -3551,7 +3580,6 @@ EOS
print OBJECT_XREF2 $dep_xref+$xref_id_offset;
print OBJECT_XREF2 "\n";
}
print TRIAGE_UPDATE "DELETE unmapped_object FROM unmapped_object ";
print TRIAGE_UPDATE "WHERE identifier = '".$good2missed_acc{$goodxref}."' ";
print TRIAGE_UPDATE "AND external_db_id = $ex_db_id ;\n";
......@@ -3829,7 +3857,7 @@ PSQL
}
if(!defined($priority_xref_source_id{$xref_id})){
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession .
"\t" . $label . "\t" . $version . "\t" . $description . "\n";
"\t" . $label . "\t" . $version . "\t" . $description . "\tMISC\tNo match\n";
#dump out dependencies aswell
......
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