import os import sys #subrates = [100.0, 10.0, 1.0, 0.0, 0.1, 0.01, 0.001, 0.0001, 0.00001, 0.000001] #dirc = "/pool/Kevin/LemmonLab/AncestralRecombinationGraphGeneTree/Data/14_2_2020/PopSize/" dirc = sys.argv[1] subrates = sys.argv[2] subrates = subrates.split(",") nameOfFiles = ".newick" listOfFiles = os.listdir(dirc) #subrates = "" #listOfFiles = ["Standard_Sample_10_Pop_0.0625_Recomb_8.0_Rep_18.newick"] for i in range(0, len(listOfFiles)): if nameOfFiles in listOfFiles[i]: f = open(dirc+listOfFiles[i], 'r') ancestralSeq = f.readline() ancestralSeq = f.readline() tailOfFile = listOfFiles[i][:-7] print(listOfFiles[i]) for item in subrates: existingPhyFile = tailOfFile + "_s_" + str(item) + ".phy" tempFile = [] f.close() print(dirc+existingPhyFile) f = open(dirc+existingPhyFile, 'r') for line in f: tempFile.append(line) f.close() f = open(dirc+existingPhyFile+"_m", 'w') for i in range(0, len(tempFile)): if i == 0: sline = tempFile[i].split() firstline = " " + str(int(sline[0])+1) + " " +sline[1] + "\n" secondline = ancestralSeq f.write(firstline) f.write(secondline) else: f.write(tempFile[i]) f.close() #os.system("rm " + dirc + existingPhyFile)