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Could we maintain the functional annotation when use agat_sp_extract_sequences.pl #246

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zmz1988 opened this issue Apr 29, 2022 · 4 comments
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Could we maintain the functional annotation when use agat_sp_extract_sequences.pl #246

zmz1988 opened this issue Apr 29, 2022 · 4 comments

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@zmz1988
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zmz1988 commented Apr 29, 2022 •
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Hello, thanks for the very nice tool of agat! It's very helpful!

I'm now at the last step to generate the protein sequence fasta file with the annotations in the headline. What I have in hand is the gff file with functional annotation information, which was generated by agat_sp_manage_functional_annotation.pl with interproscan results. Now I would like to generate the protein fasta file with annotation info for my college to do protein search. I had tried agat_sp_extract_sequences.pl but the resulted fasta file has no functional annotation info. Do you know whether we could do this with agat? Thanks a lot!
@Juke34
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Juke34 commented Apr 29, 2022

Hi, sorry it is not currently possible.
We could add a parameter to keep all gff attributes from mRNA within the header of the generated fasta file.

@zmz1988
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zmz1988 commented May 3, 2022 •
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If the option could be added, that would be great!! Thanks!!

Juke34 added a commit that referenced this issue May 12, 2022
@Juke34
fix #246 - Remove name from header (now use --keep_attributes and the…
607f495 
… original attribute tag will be use instead ). Add --keep_attributes and --keep_parent_attributes to keep information fromm GFF into the fasta. Update test accordingly
@Juke34
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Juke34 commented May 12, 2022

I made an update. Could you try it using the branch 246 (https://agat.readthedocs.io/en/latest/troubleshooting.html#how-to-use-a-version-of-agat-from-a-specific-branch)

you will have to use the option --keep_parent_attributes.
I wanted to make it simple, so all attributes from GFF are stored within the fasta header.

@zmz1988
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zmz1988 commented May 13, 2022 •
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Thank you! It seems working fine! Really appreciated!

@Juke34 Juke34 closed this as completed in 8bdfbbb May 13, 2022
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@Juke34 @zmz1988