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mgalardini / pyseer

SEER, reimplemented in python 🐍🔮
http://pyseer.readthedocs.io
Apache License 2.0
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Annotating Kmers in RNA regions #253

Closed idolawoye closed 7 months ago

idolawoye commented 7 months ago

Hi @mgalardini. I am trying to annotate kmers that are associated with drug resistance and some of the regions with high p-values are in the 16S rRNA which is visible from the Manhanttan plot. However, when I proceed to annotate the kmers, it doesn't show this region as it only annotates regions in genes. Is there a way we can include RNA annotation in this output?

mgalardini commented 7 months ago

Thanks for bringing this up; I have created a branch with a new option for the annotate_hits_pyseer script. If you are able to download it locally you can test it by adding the --feature-type rRNA --feature-type tRNA options. I have tested it on our own test data but would be good to have an external validation.

idolawoye commented 7 months ago

Thanks for your quick response. I tried that with the 253 branch but I have the unrecognized error message:

usage: annotate_hits [-h] [--bwa BWA] [--tmp-prefix TMP_PREFIX] kmers references output annotate_hits: error: unrecognized arguments: --feature-type annotated_kmers3.txt

mgalardini commented 7 months ago

that tells me that you are still using the version you have installed. to test this new script you can follow the link, download the source, cd into it and then run python3 annotate_hits_pyseer-runner.py followed by your arguments. that should force python to use the locally downloaded version

idolawoye commented 7 months ago

Thanks a lot. It worked. I now have the rRNA annotated in the output :)