Closed M-Zeeb closed 1 year ago
Dear @M-Zeeb
I've just updated the code which you can download from here. So it doesn't affect the read2tree installation. I tested the new version with the provided assembly and it is working. Please make sure that you remove the output from previous run and let me know whether it works for you. And I'm sorry for the inconvenience.
Regards, Sina
Dear Sina,
thanks for the quick response! It works now.
Best, Marius
Hi,
thanks for the great tool.
I stumbled upon a small issue when I was blindly following the instructions to gain viral marker genes (HIV in my case). It seems the "clean_fasta_cdnacds.py" file does not sufficiently clean the names as I had issues downstream due to underscores "". Resulting in "Keyerrors" at various steps. For example when generating the references. Although, it may be that I misunderstood the instructions, after manually removing all underscores it was resolved.
But this is an example of the error:
Example name: "02495|KC156214.1_AGF30950.1_2 [02495]"
Error at reference-generation (I actually could fix this with split "OG" instead of "" in lines 326-328 of "OGSet.py" but then I had errors at the final merging step):
Original files: https://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Human_immunodeficiency_virus_1/all_assembly_versions/GCA_003202495.1_ASM320249v1/GCA_003202495.1_ASM320249v1_translated_cds.faa.gz https://ftp.ncbi.nlm.nih.gov/genomes/genbank/viral/Human_immunodeficiency_virus_1/all_assembly_versions/GCA_003202495.1_ASM320249v1/GCA_003202495.1_ASM320249v1_cds_from_genomic.fna.gz