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

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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

Christopher Keeling
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.


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

Professeur associé
Département de biochimie, de microbiologie et de bio-informatique
Université Laval
https://www.researchgate.net/profile/Christopher_Keeling
https://scholar.google.ca/citations?user=KtGr86UAAAAJ

 


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Re: 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-2
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 <[hidden email]> 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.


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

Professeur associé
Département de biochimie, de microbiologie et de bio-informatique
Université Laval
https://www.researchgate.net/profile/Christopher_Keeling
https://scholar.google.ca/citations?user=KtGr86UAAAAJ

 

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maker-devel mailing list
[hidden email]
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[hidden email]
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