[maker-devel] Maker 2.31.10: maker_functional_gff and maker_functional_fasta not parsing correctly, Can't use string ("") as a HASH ref while "strict refs" in use

[Carson Holt]

Thanks I’ll update the related scripts. In my tests the old regular expression still works, but ends up adding the OX= tag as part of the GFF3 entry and not throwing a hash ref error. So you still may have another issue if you are getting a hash ref error.

—Carson


> On Mar 14, 2020, at 11:24 AM, Christopher Keeling <christopher.keeling.1 at ulaval.ca> wrote:
> 
> Hello,
> 
> In sub parse_blast{, during parsing of uniprot fasta file:
> 
> if (/>(\S+)\s+(.*?)\s+OS=(.*?)\s+(GN=(.*?)\s+)?PE=/) {
> 
> should be changed to:
> 
> if (/>sp\|(\S+)\|\S+\s+(.*?)\s+OS=(.*?)\s+OX=\S+\s+(GN=(.*?)\s+)?PE=/) {
> 
> to avoid "Can't use string ("") as a HASH ref while "strict refs" in use at…" errors.
> 
> For UniProt release 2020_01: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz <ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz>
> 
> Cheers,
> Chris
> 
> 
> --
> Christopher I. Keeling
> Chercheur scientifique en génomique forestière/ Research Scientist in Forest Genomics
> 
> Ressources naturelles Canada / Natural Resources Canada
> Service canadien des forêts / Canadian Forest Service
> Centre de foresterie des Laurentides / Laurentian Forestry Centre
> 1055, rue du PEPS Québec, QC G1V 4C7 Canada
> https://cfs.nrcan.gc.ca/employees/read/ckeeling <https://cfs.nrcan.gc.ca/employees/read/ckeeling>
> 
> Professeur associé
> Département de biochimie, de microbiologie et de bio-informatique
> Université Laval
> https://www.researchgate.net/profile/Christopher_Keeling <https://www.researchgate.net/profile/Christopher_Keeling>
> https://scholar.google.ca/citations?user=KtGr86UAAAAJ <https://scholar.google.ca/citations?user=KtGr86UAAAAJ>
>  
> 
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