next flow worked. All code added

workflow/scripts/__init__.py

+

workflow/scripts/process.py

+#!/usr/bin/python
+# programmer : bbc
+# usage: main function to call all the procedures for chip-seq analysis
+import sys
+import os
+import argparse as ap
+import logging
+import pandas as pd
+import glob
+import subprocess
+from multiprocessing import Pool
+import runDeepTools
+import runMemechip
+logging.basicConfig(level=10)
+
+
+def prepare_argparser():
+  description = "Make wig file for given bed using bam"
+  epilog = "For command line options of each command, type %(prog)% COMMAND -h"
+  argparser = ap.ArgumentParser(description=description, epilog = epilog)
+  argparser.add_argument("-i","--input",dest = "infile",type=str,required=True, help="input design file")
+  argparser.add_argument("-g","--genome",dest = "genome",type=str,required=True, help="genome", default="hg19")
+  argparser.add_argument("--top-peak",dest="toppeak",type=int, default=-1, help = "Only use top peaks for motif call")
+  #argparser.add_argument("-s","--strandtype",dest="stranded",type=str,default="none", choices=["none","reverse","yes"])
+  #argparser.add_argument("-n","--name",dest="trackName",type=str,default="UserTrack",help = "track name for bedgraph header")
+  return(argparser)
+
+def memechip_wrapper(args):
+  #print args  
+  runMemechip.run(*args)
+
+def main():
+  argparser = prepare_argparser()
+  args = argparser.parse_args()
+  #dfile = pd.read_csv(args.infile)
+
+  #for testing, add testing path to all input files
+  test_path = "/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/"
+  designfile = pd.read_csv(args.infile)
+  designfile['Peaks'] = designfile['Peaks'].apply(lambda x: test_path+x)
+  designfile['bamReads'] = designfile['bamReads'].apply(lambda x: test_path+x)
+  designfile['bamControl'] = designfile['bamControl'].apply(lambda x: test_path+x)
+  designfile.to_csv(args.infile+"_new",index=False)
+  dfile = pd.read_csv(args.infile+"_new")
+  #call deeptools
+  runDeepTools.run(args.infile+"_new", args.genome) 
+  #call diffbind
+  this_script = os.path.abspath(__file__).split("/")
+  folder = "/".join(this_script[0:len(this_script)-1])
+  
+  diffbind_command = "Rscript "+folder+"/runDiffBind.R "+args.infile+"_new"
+  #logging.debug(diffbind_command)
+  p = subprocess.Popen(diffbind_command, shell=True)
+  p.communicate()
+  #call chipseeker on original peaks and overlapping peaks
+  chipseeker_command = "Rscript "+folder+"/runChipseeker.R "+",".join(dfile['Peaks'].tolist())+" "+",".join(dfile['SampleID'])
+#BC##  logging.debug(chipseeker_command)
+  p = subprocess.Popen(chipseeker_command, shell=True)
+  p.communicate()
+  overlapping_peaks = glob.glob('*diffbind.xls')
+  overlapping_peak_names = []
+  for pn in overlapping_peaks:
+    overlapping_peak_names.append(pn.split("_diffbind")[0].replace("!","non"))
+  chipseeker_overlap_command = "Rscript "+folder+"/runChipseeker.R "+",".join(overlapping_peaks)+" "+",".join(overlapping_peak_names)
+  p = subprocess.Popen(chipseeker_overlap_command, shell=True)
+  p.communicate()
+  #MEME-chip on all peaks
+  meme_arglist =  zip(dfile['Peaks'].tolist(),[test_path+"hg19.2bit"]*dfile.shape[0],[str(args.toppeak)]*dfile.shape[0],dfile['SampleID'].tolist())
+#BC#  #print meme_arglist
+  work_pool = Pool(min(12,dfile.shape[0]))
+  resultList = work_pool.map(memechip_wrapper, meme_arglist)
+  work_pool.close()
+  work_pool.join()
+ 
+
+if __name__=="__main__":
+  main()

workflow/scripts/runChipseeker.R

+args = commandArgs(trailingOnly=TRUE)
+#if (length(args)==0) {
+#  stop("At least one argument must be supplied (input file).n", call.=FALSE)
+#} else if (length(args)==1) {
+#  # default output file
+#  args[3] = "out.txt"
+#}
+
+library(ChIPseeker)
+library(TxDb.Hsapiens.UCSC.hg19.knownGene)
+txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
+#library(clusterProfiler)
+
+#files = list.files(".")
+files<-as.list(unlist(strsplit(args[1],",")))
+names(files)<-as.list(unlist(strsplit(args[2],",")))
+print(files)
+
+peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb, tssRegion=c(-3000, 3000), verbose=FALSE)
+for(index in c(1:length(peakAnnoList)))
+{
+  filename<-paste(names(files)[index],".chipseeker_annotation.xls",sep="")
+  write.table(as.data.frame(peakAnnoList[[index]]),filename,sep="\t",quote=F)
+  #draw individual plot
+  pie_name <- paste(names(files)[index],".chipseeker_pie.pdf",sep="") 
+  vennpie_name <- paste(names(files)[index],".chipseeker_vennpie.pdf",sep="") 
+  upsetplot_name <- paste(names(files)[index],".chipseeker_upsetplot.pdf",sep="")
+  pdf(pie_name)
+  plotAnnoPie(peakAnnoList[[index]])
+  dev.off()
+  pdf(vennpie_name)
+  vennpie(peakAnnoList[[index]])
+  dev.off()
+  pdf(upsetplot_name)
+  upsetplot(peakAnnoList[[index]])
+  dev.off()
+
+
+}
+#promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000)
+#tagMatrixList <- lapply(files, getTagMatrix, windows=promoter)
+
+#plotAvgProf(tagMatrixList, xlim=c(-3000, 3000), facet="row")
+
+#overlappeakfiles <- as.list(list.files("overlappeaks/"))
+