simplify summaryStats.py, change method to 20kb windows as used in ms

sanjaynagi / rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

https://sanjaynagi.github.io/rna-seq-pop/

MIT License

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simplify summaryStats.py, change method to 20kb windows as used in ms #44

Closed sanjaynagi closed 1 year ago

sanjaynagi commented 1 year ago

In this PR, I have:

Simplified SummaryStats.py, removing all plotting
Removed previous Pi and Theta calculations and replaced with functions in rnaseqpoptools which calculate the statistics in windows and then combine, getting CIs as done in Ag1000g phase 1 and as done in RNA-Seq-Pop ms
removed .travis.yml, as github actions is CI now
Turned GeneFamiliesHeatmap off in .test config, as required files are not present

sanjaynagi commented 1 year ago

New behaviour in conda 4.6.0 (strict channel priorities) means that a few conda envs that previously worked now do not. And therefore I am having to re-workout the conda envs, mainly pythonGenomics and variants.yaml