Last updated: 2018-09-06

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    File Version Author Date Message
    Rmd 46b7343 Briana Mittleman 2018-09-06 add overlap analysis with code to subset

I will use this to overlap my QTLs with the other molecular QTLs already identified in the same individuals. First pass I will subset my nuclear and total nomial qtls by the snps with pvals less than .05 in each of the sets and make a qqplot.

I want to create a python script that takes in which type of qtl and a pvalue and subsets the full file for snps that pass that filter.

subset_qtls.py


def main(inFile, outFile, qtl, cutoff):
    fout=open(outFile, "w")
    ifile=open(inFile, "r")
    cutoff=float(cutoff)
    qtl_types= ['4su_30', '4su_60', 'RNAseq', 'RNAseqGeuvadis', 'ribo', 'prot']
    if qtl not in qtl_types:
         raise NameError("QTL arg must be 4su_30, 4su_60, RNAseq, RNAseqGeuvadis, ribo, or prot") 
    elif qtl=="4su_30":
        target=4
    elif qtl=="4su60":
        target=5
    elif qtl=="RNAseq":
        target=6
    elif qtl=="RNAseqGeuvadis":
        target=7
    elif qtl=="ribo":
        target =8
    elif qtl=="prot":
        target=9
    for num,ln in enumerate(ifile):
        if num > 0 :
            line_list = ln.split()
            chrom=line_list[0]
            pos=line_list[1]
            rsid=line_list[2]
            geneID=line_list[3]
            val = float(line_list[target].split(":")[0])
            if val <= cutoff:
                fout.write("%s\t%s\t%s\t%s\t%f\n"%(chrom, pos, rsid, geneID,val))
    


if __name__ == "__main__":
    import sys

    qtl = sys.argv[1]
    cutoff= sys.argv[2]
    
    inFile = "/project2/gilad/briana/threeprimeseq/data/otherQTL/summary_betas_ste_100kb.txt"
    outFile = "/project2/gilad/briana/threeprimeseq/data/otherQTL/summary_betas_ste_100kb.%s%s.txt"%(qtl, cutoff)
    main(inFile, outFile, qtl, cutoff)

I can run this to subset by each qtl at .05

run_subsetQTLs05.sh

#!/bin/bash

#SBATCH --job-name=run_subsetqtl05
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_subsetqtl05.out
#SBATCH --error=run_subsetqtl05.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

module load Anaconda3
source activate three-prime-env

qtls=('4su_30', '4su_60', 'RNAseq', 'RNAseqGeuvadis', 'ribo', 'prot')  

for i in ${qtls[@]}; do
    python subset_qtls.py $i .05 
done

Session information

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_0.12.18      digest_0.6.16    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.23.0      magrittr_1.5      evaluate_0.11    
[10] stringi_1.2.4     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.7.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.3.1     yaml_2.2.0        compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20

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