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Manage_functional_annotation copy attributes from mRNA to CDS #162

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Juke34 opened this issue Aug 17, 2021 · 5 comments · Fixed by #167
Closed

Manage_functional_annotation copy attributes from mRNA to CDS #162

Juke34 opened this issue Aug 17, 2021 · 5 comments · Fixed by #167

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@Juke34
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Juke34 commented Aug 17, 2021

copy the Name, product, Ontology_term, Dbxref and uniprot_id attributes from mRNA to the CDS. It is necessary to have those information attach to the CDS to be kept by ENA submission pipeline (after being translated in the correct ENA attributes e.g. dbxref=>inference ).
@Juke34
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Juke34 commented Aug 23, 2021

@LucileSol Could you try the branch manage_function if you have what you need?
You must use --pcds

@LucileSol
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Yes! I am going to, thanks

@LucileSol
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LucileSol commented Aug 27, 2021 •
edited by Juke34
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Hi @Juke34 !
Sorry for the delay we had the retreat!

So here is the output I get :

LG1     maker   gene    15473   17296   .       +       .       ID=LEPHEG00000000001;Name=ak3;makerName=maker-LG1-augustus-gene-0.0
LG1     maker   mRNA    15473   17296   .       +       .       ID=LEPHEM00000000001;Parent=LEPHEG00000000001;Dbxref=**Gene3D:G3DSA:3.30.70.260**,Gene3D:G3DSA:3.40.1160.10,InterPro:IPR005260,InterPro:IPR001048,InterPro:IPR002912,InterPro:IPR036393,InterPro:IPR001341,KEGG:00260+2.7.2.4,KEGG:00261+2.7.2.4,KEGG:00270+2.7.2.4,KEGG:00300+2.7.2.4,MetaCyc:PWY-2941,MetaCyc:PWY-2942,MetaCyc:PWY-5097,MetaCyc:PWY-6160,MetaCyc:PWY-6559,MetaCyc:PWY-6562,MetaCyc:PWY-7153,MetaCyc:PWY-7977,MobiDBLite:mobidb-lite,PANTHER:PTHR21499:SF56,PANTHER:PTHR21499,PIRSF:PIRSF000726,Pfam:PF00696,ProSiteProfiles:PS51671,Reactome:R-HSA-8964539,SUPERFAMILY:SSF53633,SUPERFAMILY:SSF55021,TIGRFAM:TIGR00657;Name=ak3;Ontology_term=GO:0004072,GO:0009089,GO:0008652;_AED=0.23;_QI=0|0|0|1|1|1|9|0|370;_eAED=0.23;makerName=maker-LG1-augustus-gene-0.0-mRNA-1;product=Aspartokinase 3%2C chloroplastic;uniprot_id=Q9S702
LG1     maker   exon    15473   15721   .       +       .       ID=LEPHEE00000000001;Parent=LEPHEM00000000001;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:1
LG1     maker   exon    15796   15891   .       +       .       ID=LEPHEE00000000002;Parent=LEPHEM00000000001;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:2
LG1     maker   exon    15976   16092   .       +       .       ID=LEPHEE00000000003;Parent=LEPHEM00000000001;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:3
LG1     maker   exon    16171   16290   .       +       .       ID=LEPHEE00000000004;Parent=LEPHEM00000000001;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:4
LG1     maker   exon    16379   16471   .       +       .       ID=LEPHEE00000000005;Parent=LEPHEM00000000001;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:5
LG1     maker   exon    16540   16656   .       +       .       ID=LEPHEE00000000006;Parent=LEPHEM00000000001;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:6
LG1     maker   exon    16767   16880   .       +       .       ID=LEPHEE00000000007;Parent=LEPHEM00000000001;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:7
LG1     maker   exon    16965   17027   .       +       .       ID=LEPHEE00000000008;Parent=LEPHEM00000000001;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:8
LG1     maker   exon    17153   17296   .       +       .       ID=LEPHEE00000000009;Parent=LEPHEM00000000001;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:9
LG1     maker   CDS     15473   15721   .       +       0       ID=LEPHEC00000000001;Parent=LEPHEM00000000001;Dbxref=**Gene3D:G3DSA:3.30.70.260**,**Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260**;Name=ak3;Ontology_term=GO:0004072,GO:0004072,GO:0004072;makerName=maker-LG1-augustus-gene-0.0-mRNA-1:cds;product=Aspartokinase 3%2C chloroplastic;uniprot_id=Q9S702
LG1     maker   CDS     15796   15891   .       +       0       ID=LEPHEC00000000001;Parent=LEPHEM00000000001;Dbxref=Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260;Name=ak3;Ontology_term=GO:0004072,GO:0004072,GO:0004072;makerName=IDmodified-cds-4184;product=Aspartokinase 3%2C chloroplastic;uniprot_id=Q9S702
LG1     maker   CDS     15976   16092   .       +       0       ID=LEPHEC00000000001;Parent=LEPHEM00000000001;Dbxref=Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260,Gene3D:G3DSA:3.30.70.260;Name=ak3;Ontology_term=GO:0004072,GO:0004072,GO:0004072;makerName=IDmodified-cds-4185;product=Aspartokinase 3%2C chloroplastic;uniprot_id=Q9S702

You can see that for the CDS the first Gene3D has been duplicated several time, and this part : G3DSA:3.40.1160.10,InterPro:IPR005260,InterPro:IPR001048,InterPro:IPR002912,InterPro:IPR036393,InterPro:IPR001341,KEGG:00260+2.7.2.4,KEGG:00261+2.7.2.4,KEGG:00270+2.7.2.4,KEGG:00300+2.7.2.4,MetaCyc:PWY-2941,MetaCyc:PWY-2942,MetaCyc:PWY-5097,MetaCyc:PWY-6160,MetaCyc:PWY-6559,MetaCyc:PWY-6562,MetaCyc:PWY-7153,MetaCyc:PWY-7977,MobiDBLite:mobidb-lite,PANTHER:PTHR21499:SF56,PANTHER:PTHR21499,PIRSF:PIRSF000726,Pfam:PF00696,ProSiteProfiles:PS51671,Reactome:R-HSA-8964539,SUPERFAMILY:SSF53633,SUPERFAMILY:SSF55021,TIGRFAM:TIGR00657

Is missing

Thanks!

update :

I check different one and the first DBxref seems to be duplicated :

LG1 maker mRNA 36797 40614 76.68694 + . ID=LEPHEM00000000018;Parent=LEPHEG000
00000010;Dbxref=InterPro:IPR004709,InterPro:IPR006153,InterPro:IPR018422,PANTHER:PTHR10110:SF169,PANTHER:PTHR10110,PRINTS:PR01084,Pfam:PF00999,Reactome:R-HSA-425986,TIGRFAM:TIGR00840;Name=nhx5_iso2;Ontology_term=GO:0006814,GO:0006885,GO:0015385,GO:0016021,GO:0055085,GO:0006812,GO:0015299;_AED=0.11_QI=78|0.89|0.85|1|0|0|20|167|481;_eAED=0.11;makerName=maker-LG1-exonerate_protein2genome-gene-0.3-mRNA-2;product=Sodium/hydrogen exchanger 5;uniprot_id=Q8S396

LG1 maker CDS 39745 39854 . + 2 ID=LEPHEC00000000018;Parent=LEPHEM00000000018;Dbxref=InterPro:IPR004709,InterPro:IPR004709,InterPro:IPR004709,InterPro:IPR004709,InterPro:IPR004709,InterPro:IPR004709,InterPro:IPR004709,InterPro:IPR004709,InterPro:IPR004709;Name=nhx5_iso2;Ontology_term=GO:0006814,GO:0006814,GO:0006814,GO:0006814,GO:0006814,GO:0006814,GO:0006814;makerName=maker-LG1-exonerate_protein2genome-gene-0.3-mRNA-2:cds;product=Sodium/hydrogen exchanger 5;uniprot_id=Q8S396

@Juke34
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Juke34 commented Aug 27, 2021

Ok should be fine now, could you check?

@LucileSol
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Yes it seems good, I need to try the output with EMBLmyGGF3 now! thanks

@Juke34 Juke34 mentioned this issue Aug 27, 2021
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Manage function add info to CDS for ENA compliance NBISweden/AGAT
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@Juke34 @LucileSol