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gff3 header delimiter space or a tab

Dear All,

I could not find a source which states the field delimiter to be used in gff3 header. Can it be a space or a tab or it should be a space only ? My hunch is a space. 

##gff-version 3 
##sequence-region 1 10

Many Thanks!

gff3
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updated by Carambakaracho Carambakaracho • written by microfuge microfuge

I don't think it even matters.

you could op en it in vi and then do :set list to show all 'invisible' chars ( ^I is tab )

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written by lieven.sterck lieven.sterck

Thanks so much! This was a fake gff entry I created, just wanted to know if the official specification says something about it. Did not know about the set list option in vi (quite nice :) ).

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written by microfuge microfuge

2 answers

This is a great question, and one why I 'love' the gff format so much. It is not explicitly defined. Period. See definition of directives in gff3 format - implicitly the documentation uses spaces, just as ATpoint illustrated, so I recommend spaces, too. Tabs are usually used for separation of the feature lines.

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written by Carambakaracho Carambakaracho

gff3 from gencode is tab.

edit: sorry, I didn't notice the post is talk about the header... Then it just regular sentences I think.

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written by shoujun.gu shoujun.gu

No, it isn't, it is space, at least in the mouse (v20) files I have on my machine.

gzcat gencode.vM20.annotation.gff3.gz | head
##gff-version 3
#description: evidence-based annotation of the mouse genome (GRCm38), version M20 (Ensembl 95)
#provider: GENCODE
#contact: gencode-help@ebi.ac.uk
#format: gff3
#date: 2018-11-30
##sequence-region chr1 1 195471971
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written by ATpoint ATpoint

Yes, I just realize the post is deal with the header only.

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written by shoujun.gu shoujun.gu

I guess the header line is simply more or less non-standardized at all, but for the actual file, yes it is tab, like in most bioinformatics formats.

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written by ATpoint ATpoint

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