[maker-devel] tRNAscan and map_gff_ids

[Fields, Christopher J]

I found a problem with some tRNAscan output using MAKER 2.31.5.  I had a full MAKER data set (run initially using MAKER 2.31.5) that I mapped IDs for.  This was then run as follows, with the requisite error:

-system-specific-4.1$ map_gff_ids id.map Zalbi.all.gff3
Nested quantifiers in regex; marked by <-- HERE in m/trnascan-KB913038.1-noncoding-Undet_??? <-- HERE -gene-79.0/ at /home/groups/hpcbio/apps/maker/maker-2.31.5/bin/map_gff_ids line 111, <$IN> line 3067590.

The problematic lines:

----------------------------------------------
-system-specific-4.1$ grep "???" Zalbi.all.gff3
KB913038.1	maker	gene	23847890	23847958	.	-	.	ID=trnascan-KB913038.1-noncoding-Undet_???-gene-79.0;Name=trnascan-KB913038.1-noncoding-Undet_???-gene-79.0
KB913038.1	maker	tRNA	23847890	23847958	.	-	.	ID=trnascan-KB913038.1-noncoding-Undet_???-gene-79.0-tRNA-1;Parent=trnascan-KB913038.1-noncoding-Undet_???-gene-79.0;Name=trnascan-KB913038.1-noncoding-Undet_???-gene-79.0-tRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|70|0
KB913038.1	maker	exon	23847890	23847958	.	-	.	ID=trnascan-KB913038.1-noncoding-Undet_???-gene-79.0-tRNA-1:exon:2193;Parent=trnascan-KB913038.1-noncoding-Undet_???-gene-79.0-tRNA-1
KB913039.1	maker	gene	21710152	21710224	.	-	.	ID=trnascan-KB913039.1-noncoding-Undet_???-gene-72.0;Name=trnascan-KB913039.1-noncoding-Undet_???-gene-72.0
KB913039.1	maker	tRNA	21710152	21710224	.	-	.	ID=trnascan-KB913039.1-noncoding-Undet_???-gene-72.0-tRNA-1;Parent=trnascan-KB913039.1-noncoding-Undet_???-gene-72.0;Name=trnascan-KB913039.1-noncoding-Undet_???-gene-72.0-tRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|74|0
KB913039.1	maker	exon	21710152	21710224	.	-	.	ID=trnascan-KB913039.1-noncoding-Undet_???-gene-72.0-tRNA-1:exon:4036;Parent=trnascan-KB913039.1-noncoding-Undet_???-gene-72.0-tRNA-1
----------------------------------------------

I managed to get it going by using the following modifications (regex quotemeta) in map_gff_ids (lines 107-112):

	for my $id (@map_ids) {
		# Only if the value (or the portion preceding
		# the first colon) is equal to the map key.
		next unless ($value eq $id || $value =~ /^\Q$id\E:/);
		$value =~ s/\Q$id\E/$map{$id}/ unless($tag eq 'Name' && $id !~ /\-gene\-\d+\.\d+|^CG\:|^....\:|^[^\:]+\:temp\d+\:/);
	}

I’m guessing there may be a similar problem with map_fasta_ids?

chris