Commit 17205473 authored by Monika Komorowska's avatar Monika Komorowska
Browse files

load core data before mapping stage

parent 92d109fe
......@@ -87,7 +87,8 @@ my $mapper = XrefMapper::BasicMapper->process_file($file, !$notverbose, $no_xref
if(defined($recalc_display_xrefs)){
$mapper->official_naming();
my $official_naming = XrefMapper::OfficialNaming->new($mapper);
$official_naming->run();
my $display = XrefMapper::DisplayXrefs->new($mapper);
# $display->set_display_xrefs_from_stable_table();
$display->genes_and_transcripts_attributes_set($no_xref);
......@@ -149,17 +150,17 @@ else{
$submitter->no_dump_xref()
}
$status = $mapper->xref_latest_status();
if($status eq "core_fasta_dumped"){# load core data needed
my $core_info = XrefMapper::CoreInfo->new($mapper);
$core_info->get_core_data();
}
$status = $mapper->xref_latest_status();
if($status eq "core_fasta_dumped"){
if($status eq "core_data_loaded") {
$submitter->build_list_and_map();
$status = $mapper->xref_latest_status();
}
else{
}
$status = $mapper->xref_latest_status();
if($status eq "mapping_started"){
......@@ -171,13 +172,7 @@ elsif($status eq "mapping_finished"){
}
$status = $mapper->xref_latest_status();
if($status eq "mapping_processed"){ # load core data needed
my $core_info = XrefMapper::CoreInfo->new($mapper);
$core_info->get_core_data();
}
$status = $mapper->xref_latest_status();
if($status eq "core_data_loaded"){ # add direct xrefs to the object_xref etctables
if($status eq "mapping_processed"){ # add direct xrefs to the object_xref etctables
my $direct_mappings = XrefMapper::DirectXrefs->new($mapper);
$direct_mappings->process();
}
......
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