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MGXlab / social_niche_breadth_SNB

Calculate the Social Niche Breadth (SNB) score of all taxonomic lineages in a set of microbiomes.
MIT License
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Nan produced #4

Open susheelbhanu opened 1 month ago

susheelbhanu commented 1 month ago

Hi,

I'm trying to run the attached file and despite several combinations of c1 and c2 values, only Nans are produced. Any thoughts on why this might be the case? output_table.csv

Thanks, Susheel

bastiaanvonmeijenfeldt commented 1 month ago

Hi @susheelbhanu,

The input file should be tab separated instead of comma separated. Could you try again with a tab separated file? For reference, converting a comma separated file into a tab separated file can be done with sed:

sed 's/,/\t/g' output_table.csv > output_table.tsv

Please keep me updated! :)

Best wishes,

Bastiaan

susheelbhanu commented 1 month ago

Hi @bastiaanvonmeijenfeldt,

Yeah I realised it after I posted the issue, based on your example in the readme. Seems to be working alright now. Any suggestions on what is a good way to identify cutoffs when using the --c1 and --c2 flags?

I've found that this is a little arbitrary at the moment and depending on the values, the SNB values change quite a bit.

Thank you!