From e61981f31e0c4a8014d9cbf3d5c7eb7875f1b97d Mon Sep 17 00:00:00 2001 From: mueller Date: Mon, 14 Feb 2011 21:52:52 -0500 Subject: [PATCH] Only warn of missing protocols - set to protocol to "unknown" if missing --- bin/load_map_data.pl | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/bin/load_map_data.pl b/bin/load_map_data.pl index 94f010d2b..98a7c8ce0 100755 --- a/bin/load_map_data.pl +++ b/bin/load_map_data.pl @@ -170,6 +170,7 @@ eval { if ($inserts and @{$inserts}) { print"New marker inserted: $marker_name\n" } else { die "Oops, I thought I was inserting some new data" } $marker_id=$marker->marker_id(); + } print $marker->name_that_marker()."\n"; my $loc=$marker->new_location(); #create a new location object @@ -182,6 +183,10 @@ eval { #my ($chromosome,$position) = #CXGN::Marker::Tools::lg_name_and_position($pos); +# foreach my $me (@{$marker->current_mapping_experiments}) { +# print $me->{protocol}."\n"; +# } + my $chromosome=$ss->value_at($dirty_marker_name,'LINKAGE_GROUP') # get chromosome from spreadsheet or die"No chromosome found for $marker_name"; @@ -217,14 +222,17 @@ eval { if (@protocols) { print "Protocols found: ".CXGN::Tools::Text::list_to_string(@protocols)."\n"; } - else { die "Protocols not found for '$dirty_marker_name'" } + else { + print STDERR "Protocols not found for '$dirty_marker_name'"; + @protocols = ('unknown'); + } for my $protocol(@protocols) { $protocol =~ tr/[a-z]/[A-Z]/; unless ($protocol eq 'AFLP' or $protocol eq 'CAPS' or $protocol eq 'RAPD' or $protocol eq 'SNP' or $protocol eq 'SSR' or $protocol eq 'RFLP' or $protocol eq 'PCR' or $protocol eq 'DCAPS' or $protocol =~/DArt/i or $protocol =~ /OPA/i or $protocol =~ /INDEL/i or $protocol =~ /ASPE/i ) { - die "UNKNOWN protocol ($protocol)\n! "; + print STDERR "UNKNOWN protocol ($protocol)\n! "; $protocol = 'unknown'; } -- 2.11.4.GIT