Question: Blast2GO (csv output)
0
gravatar for jomaco
6.0 years ago by
jomaco190
European Union
jomaco190 wrote:

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.

 

ahrd blast2go csv dat annot • 2.7k views
ADD COMMENTlink modified 5.2 years ago by Stefan30 • written 6.0 years ago by jomaco190
1
gravatar for Prakki Rama
6.0 years ago by
Prakki Rama2.4k
Singapore
Prakki Rama2.4k wrote:

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

 

 

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Prakki Rama2.4k
1
gravatar for Stefan
5.2 years ago by
Stefan30
Spain
Stefan30 wrote:

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 ... 

 

 

ADD COMMENTlink written 5.2 years ago by Stefan30
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