[maker-devel] tRNAscan and map_gff_ids

[Fields, Christopher J]

Thanks Carson!

chris

On Jun 2, 2014, at 10:23 AM, Carson Holt <carsonhh at gmail.com> wrote:

> 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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> 
>