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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Error in gene_fullxref.txt #65

Closed dietmarfdz closed 5 years ago

dietmarfdz commented 5 years ago

Hi, I am trying to annotate some samples and when reading the gene_fullxref.txt file the software crashes. I read the error but I do not understand it at all. Could you give me a clue?

This was my code:

table_annovar.pl ./109.avinput ~/software/annovar/humandb --buildver hg19 --out ./test/109.annovar --remove --otherinfo --protocol refGene,cytoBand,1000g2015aug_all,1000g2015aug_afr,1000g2015aug_eas,1000g2015aug_eur,snp138,exac03,gnomad_genome,gnomad_exome,kaviar_20150923,clinvar_20170905,dbnsfp33a --operation gx,r,f,f,f,f,f,f,f,f,f,f,f, --arg '-splicing 6',,,,,,,,,,,, --nastring . --thread 4 --xref ~/software/annovar/example/gene_fullxref.txt

and I get:

NOTICE: Processing operation=gx protocol=refGene
NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver hg19 -dbtype refGene -outfile........
....
....
NOTICE: Finished reading 836010 cross references (each with 22 fields) from /annovar/example/gene_fullxref.txt Unescaped left brace in regex is illegal here in regex; marked by <-- HERE in m/(^|;)FUNCTION: DNA-binding protein that specifically binds heat shock promoter elements (HSE) and activates transcription. In higher eukaryotes, HSF is unable to bind to the HSE unless the cells are heat shocked. { <-- HERE ECO:0000269|PubMed:11447121, ECO:0000269|PubMed:11583998, ECO:0000269|PubMed:12659875, ECO:0000269|PubMed:12665592, ECO:0000269|PubMed:16278218, ECO:0000269|PubMed:8946918, ECO:0000

Any clue about how to solve that?

Thanks in advance

kaichop commented 5 years ago

This was a problem that was raised a while ago and I updated script to handle it, but never had a chance to include it in the annovar release itself which was delayed a bit. It is attached table_annovar.txt