Annotating Orthogroups: Blasting against set of known genes

[ViriatoII]

Hey,

Many people are asking about orthogroup annotation (https://github.com/davidemms/OrthoFinder/issues/373 , https://github.com/davidemms/OrthoFinder/issues/411 , https://github.com/davidemms/OrthoFinder/issues/440 ) so I'm sharing my scripts.

I have finished a script that picks up the resulting N0 of Orthofinder and blasts a gene of each orthogroup against a reference set of well annotated genes (this is a tblastn, so it blasts against DNA genes, not proteins). It outputs the orthogroups and the best hit names, as well as identity, length and coordinates of alignment.

The script is here: (the download will come as .txt, please change that to .py) annotate_ogroups_vs_ref.py

You run it like this: annotate_ogroups_vs_ref.py N0.tsv ortho_dir/ ref_genes.fasta

• ortho_dir contains fastas for all species in N0. It's the input dir of the Orthofinder run.
• ref_genes.fasta is a set of well annotated genes. For example all the arabidopsis genes

Also, do this first: makeblastdb -dbtype nucl -in reference_genes.fasta

We have a script that extrapolates the annotations of the genes in each orthogroup to that orthogroup annotation, in case you have many well studied proteins in your Orthofinder run

Happy annotating, Ricardo

[davidemms]

Hi Ricardo

Thanks, that's really great! I will put together a page on the tutorials site soon so will mention it there. It'd be great to hear from people here who are finding Ricardo's tool useful too.

All the best David

[guo-cheng]

Hey,

Many people are asking about orthogroup annotation (#373 , #411 , #440 ) so I'm sharing my scripts.

I have finished a script that picks up the resulting N0 of Orthofinder and blasts a gene of each orthogroup against a reference set of well annotated genes (this is a tblastn, so it blasts against DNA genes, not proteins). It outputs the orthogroups and the best hit names, as well as identity, length and coordinates of alignment.

The script is here: (the download will come as .txt, please change that to .py) annotate_ogroups_vs_ref.py

You run it like this: annotate_ogroups_vs_ref.py N0.tsv ortho_dir/ ref_genes.fasta

• ortho_dir contains fastas for all species in N0. It's the input dir of the Orthofinder run.
• ref_genes.fasta is a set of well annotated genes. For example all the arabidopsis genes

Also, do this first: makeblastdb -dbtype nucl -in reference_genes.fasta

We have a script that extrapolates the annotations of the genes in each orthogroup to that orthogroup annotation, in case you have many well studied proteins in your Orthofinder run

Happy annotating, Ricardo

Hi Ricardo,

Thank you for your scripts. When i used it, i find the running speed is too low. Do you have any idea to speed up the annotation steps?

All the best, Guo-Cheng

[ViriatoII]

Dear @guo-cheng;

I wrote this several years ago and wasn't such a good python programmer back then. I don't have time to rewrite this, but I think it is possible to make it better, yes. I'll say how:

This for loop is unnecessary:

for seq_record in SeqIO.parse(infasta, "fasta"):
                if seq_record.id == gene:

I would rather replace it by having a look_up dictionary prepared before any loop. Probably also have the SeqIO parser outside:

parser = SeqIO.parse(infasta, "fasta") 
lookup_dic = {seq.id : i for i,seq in enumerate(parser)}                      # dict should look like this: {"gene1": 0, "gene2":1 .......}

for row in range(0, len(df)):                 
   (......)
  # and directly extract the correct SeqIO object 
   seq_record =    parser [lookup_dic [gene]]
  (.....)

Hope this helps! :)

Kind regards, Ricardo

[guo-cheng]

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OK, I get it!Thanks for your immediately response.Best regardsGuo-Cheng

                            guochengli666

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          Re: [davidemms/OrthoFinder] Annotating Orthogroups: Blasting against set of known genes (#451)

Dear @guo-cheng; I wrote this several years ago and wasn't such a good python programmer back then. I don't have time to rewrite this, but I think it is possible to make it better, yes. I'll say how: This for loop is unnecessary: if seq_record.id == gene:

I would rather replace it by having a look_up dictionary prepared before any loop. Probably also have the SeqIO parser outside: parser = SeqIO.parse(infasta, "fasta") lookup = {seq.id : i for i,seq in enumerate(parser)} # dict should look like this: {"gene1": 0, "gene2":1 .......} for row in range(0, len(df)): ......... and directly extract the correct SeqIO object seq_record = parser [lookup_dic[gene]] ... Hope this helps! :) Kind regards, Ricardo

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