How To Convert CSV to GFF3?

Question

I want to convert a .csv file to a GFF3 file. The csv file contains annotation data. I know that I should parse the .csv file and then write the .gff file, but I dont know the complete code

There's very little information in your question. Can you provide more details about what the CSV file contains? What have you tried so far? — vkkodali, May 19 '19 at 12:00

score 0 · Answer 1 · answered May 22 '19 at 00:56

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In Libreoffice, merge all columns that need to be in column 9 of GFF3. They will end up being space separated. Then, export your file as tab-separated values. Resulting file will have 9 tab-delimited columns. Using sed replace spaces with semi colons. Also, if I remember correctly, ID should be the first attribute in GFF3 column 9, not Name.

answered May 22 '19 at 00:56

vkkodali

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Thankyou very much. Yes it works. I wrote an script and it was converted. – eli bio67 May 22 '19 at 09:21

How To Convert CSV to GFF3?

1 Answers1