[maker-devel] tRNAscan and map_gff_ids

[Carson Holt]

I've now patched the current download to fix this and a plus strand
spliced tRNA bug.

--Carson


On 5/20/14, 1:17 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>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-nonco
>ding-Undet_???-gene-79.0;Name=trnascan-KB913038.1-noncoding-Undet_???-gene
>-79.0
>KB913038.1	maker	tRNA	23847890	23847958	.	-	.	ID=trnascan-KB913038.1-nonco
>ding-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-nonco
>ding-Undet_???-gene-79.0-tRNA-1:exon:2193;Parent=trnascan-KB913038.1-nonco
>ding-Undet_???-gene-79.0-tRNA-1
>KB913039.1	maker	gene	21710152	21710224	.	-	.	ID=trnascan-KB913039.1-nonco
>ding-Undet_???-gene-72.0;Name=trnascan-KB913039.1-noncoding-Undet_???-gene
>-72.0
>KB913039.1	maker	tRNA	21710152	21710224	.	-	.	ID=trnascan-KB913039.1-nonco
>ding-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-nonco
>ding-Undet_???-gene-72.0-tRNA-1:exon:4036;Parent=trnascan-KB913039.1-nonco
>ding-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
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