[maker-devel] How do I make maker combine interproscan and functional_gff results

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Emmanuel Nnadi

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Nov 11, 2020, 12:12:15 PM11/11/20
to Carson Holt, maker...@yandell-lab.org, maker-de...@yandell-lab.org
Hi Carson,
Please I will like to know how to combine the gff results obtained using  ipr_update_gff and the gff obtained using maker_functional_gff?  
For example the ipr_update_gff adds the following to the gff 

scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;       ID=CR513scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;Dbxref=InterPro:IPR000719,Pfam:PF00069;Ontology_term=GO:0004672,GO:0005524,GO:0006468;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1; 

While 
maker_functional_gff

scaffold_252    maker   gene    22873   47327   .       -       .       ID=CR513_001491;Name=CR513_001491;Alias=augustus_masked-scaffold_252-processed-gene-0.0;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652);scaffold_252    maker   mRNA    22873   47327   .       -       .       ID=CR513_001491-RA;Parent=CR513_001491;Name=CR513_001491-RA;Alias=augustus_masked-scaffold_252-processed-gene-0.0-mRNA-1;_AED=0.50;_QI=0|0.08|0.04|0.16|1|1|25|0|927;_eAED=0.50;_merge_warning=1;Note=Similar to IREH1: Putative serine/threonine protein kinase IREH1 (Fragment) (Mucuna pruriens OX%3D157652); (Fragment) (Mucuna pruriens OX%3D157652);


Is there a way of making maker reflect the GO and pfam alongside the functional names?



Also, how can this be reflected in the corresponding protein and transcript fastas?


Thanks for your support.



Nnaemeka Emmanuel Nnadi,Ph.D
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
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