Blast2GO (csv output)
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Entering edit mode
7.0 years ago
jomaco ▴ 190

Hi,

Is there a way to produce a .csv output from Blast2GO? I cannot find the option, all I can see is to output as .annot or .dat format.

Alternatively, does a tool exist which can convert .annot or .dat to .csv format?

I require a csv file as input for the functional annotation program I am using (AHRD -https://github.com/groupschoof/AHRD).

Thanks,

Jon.

blast2go csv annot dat ahrd • 3.1k views
1
Entering edit mode
7.0 years ago
Prakki Rama ★ 2.5k

Hi, you can actually export the .annot file and then convert into csv format.

Using Vi editor:

vi blast2go_file.annot -c '%s/\t/,/g | wq'

or by using sed:

sed -i 's/\t/,/g' blast2go_file.annot

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Entering edit mode
6.2 years ago
Stefan ▴ 30

In the latest version of Blast2GO (3.0+) there exist at least two option to generate comma separated value (csv) files. The "Export Annotations" functions has now a "Custom format" option which lets you, apart from the separator character, also choose in which format you want your functional annotation to be; for example: one Gene Ontology term per line or one sequence per line, with or without GO categories etc.

Another option is the "Generic Export" function which allows to choose and combine any kind of information from within a Blast2GO project be exported as csv, tab-separated, etc ...