Developed from an example provided by Marie Bolger at Forschungszentrum Juelich on 2019-14-01 That code is implemented on the plabi website.
There may be an issue in the way that code handled gene lists that resulted in inflated gene counts in a parent bin where a gene is present in multiple child bins. I fixed this by collecting genes into a set instead of a list.
I expanded the functionality by separating the up/down regulated targets for independent testing and reporting the raw counts, fold-changes and significant directional biases. These are all useful in interpreting and presenting the data.
This tool loads a Mercator4 mapping file and a DEG file containing matching target IDs, p-values and fold-change values
in order to assess enrichment based on Fisher test (2 sided) for Up/Down/Differentially regulated targets.
It then performs Benjamini Hochberg correction for false discovery rate adjustment of p-values
and writes all this to a tsv file.
""" Usage:
Single file: python BinEnrichment/ sleuth mapping.txt "out_bins.tsv" "in.tsv"
Recursive on directories:
for i in find . -name *result.txt;
do python BinEnrichment/ sleuth mapping.txt "${i%_result.txt}_bins.tsv" "${i}";
done
Note for this if filenames have spaces then change the IFS IFS=$(echo -en "\n\b")
"""