gene_prab and accessory_pca scripts

salvadorlab / mbovpan

Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.

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gene_prab and accessory_pca scripts #24

Closed noahaus closed 7 months ago

noahaus commented 9 months ago

[x] Check that the DSL2 scripts work properly when called
[x] Update their help page messages
[x] test on UK data and re analyze the outputs

noahaus commented 9 months ago

So the scripts run, but I am unable to generate the figures because the test case is too small to have accessory genes present - necessitates re-analyzing the UK data

noahaus commented 8 months ago

Results of the Accessory PCA

The separation between cattle and badger are still present - but the percent variation is way lower than before. probably because the effect of erroneous genes are mitigated + btb slow evolution.

noahaus commented 8 months ago

Results of the gene prab:

I feel like something here is not fully registering, I think I need to revisit the way a virulent gene is found, because I feel like there has to be more to show

noahaus commented 8 months ago

I did make some substantial changes to the code that makes this, but berceuse panaroo is more stringent, it appears that the virulent genes are the only ones that are found between 15 and 99% of isolates. might require a major rewrite!

noahaus commented 7 months ago

Decided to just include the gene prab hierarchical cluster as its own output

It's nice but it would be nice to see which genes are most responsible for the clustering pattern

noahaus commented 7 months ago

help messages added for each script

noahaus commented 7 months ago

I wonder which Liliana will prefer