Gene names/ids on annotated protein files
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22 months ago
nitinra ▴ 50

Hello all,

I have annotated around 276 protein files using EggNog. The protein files have the following headers (example from one of the species):

 head Spodoptera_frugiperda.fa

>file_1_file_1_g22553.t1 gene=file_1_file_1_g22553
MNRLGMIVDLSHVGENTTRAAIKLSRAPVVFTHSSVYSLCNHKRNVPDDIIHSLKENGGIIMVNFFPDFVKCAPNATISDVAEHFHYIKRMVGADYVGIGGDFDGVNRVPRGLEDVSRYPELFAELLRSGQWTVQELKNLAGLNMLRVMRQVEKVRDEMRTNGVEPEEHPDSPNDNGNCTSNAFYTEYV

The annotation file from EggNog has the following:

  head Spodoptera_frugiperda.softmasked.prot.fa.emapper.annotations

> file_1_file_1_g22553.t1   13037.EHJ66618  2.39e-121   357.0   COG2355@1|root,KOG4127@2759|Eukaryota,38D9H@33154|Opisthokonta,3BCAM@33208|Metazoa,3CRIG@33213|Bilateria,41U16@6656|Arthropoda,3SJQR@50557|Insecta,4488J@7088|Lepidoptera   6656|Arthropoda O   Membrane dipeptidase (Peptidase family M19) -   -   3.4.13.19   ko:K01273   -   -   ko00000,ko00537,ko01000,ko01002,ko04147 -   -   -   Peptidase_M19

How do I replace all the headers in the protein file with the gene names (in the case of the example,

gene=file_1_file_1_g22553  to Peptidase_M19.

Thank you!!

bash Protein GFF annotation • 437 views
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