scripts missing

[swutke]

Hi, first of all, thanks for providing such a detailed description of the pipeline used to estimate viral domestication. I have sequenced the genome of a sawfly (Diprion pini) and thought I check if there are traces of virus domestication in its genome. While going through your pipeline, I noticed that several python scripts mentioned in the description cannot be found on the GitHub page, namely:

• Filter_clusters.py
• Extract_loci.py
• Add_genomic_ontology.py
• Add_interproscan_and_ontology.py
• Extract_candidat_scaffolds.py
• Add_augustus_to_blast.py
• Filter_TEs.py
• Get_busco_scaff.py
• Add_genomic_env_last.py

as well as an R and bash script:

- Overlapping_sequences_BUSCO_Viral_loci.R
- Recover_loci_sequences2.sh

Would it be possible to provide those scripts? Best, Saskia

[BenjaminGuinet]

Dear Saskia, thanks for opening this issue.

I just added all these files into a directory named : Multiple_scripts

I also noticed that the file _FilterTEs.py should be named Filter_repeat_results.py instead.

[swutke]

Hi Benjamin, thank you! I am curious what I will find. Best, Saska