Functional annotation of BRAKER output

Question

[Szymon]

I'm trying to do a functional annotation of a BRAKER's output.

I didn't find any scripts inside BRAKER so I'm using maker_functional_fasta. However, using this:

!maker_functional_fasta $insect_swissprot $blast_out.blastp $path_to_proteins > $proteins_with_headers

gives this error:

Use of uninitialized value $mol_type in concatenation (.) or string at /home/cluster_user/scripts/maker-functional/maker_functional_fasta line 65, <$IN> line 1. Use of uninitialized value $mol_type in concatenation (.) or string at /home/cluster_user/scripts/maker-functional/maker_functional_fasta line 65, <$IN> line 8. (...)

And each header in the output file is just: >gene_id.transcript_id Name:"Protein of unknown function"

Do "all.maker.proteins.fasta" files contain something in the headers that makes the script impossible to run with the BRAKER's output? Is there an alternative script for outputs of BRAKER?

Thanks

[biofalconch]

From looking at the script, it expects different IDs from those you have. The line that is causing trouble:

my $header = ">$id $mol_type ";

So basically, it needs to look like

>PYU1_T015316 transcript offset:0 AED:0.0476397966594044
ATCGCCACACACAGCAGT......