EvolutionModels/read_absrel_output.py at master · leanngward/EvolutionModels · GitHub

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import os
import re
import sys
import json
# pattern search for outfile:

def read_null(filename):
	#set default values
	mg94LNL = "NA"
	fulladptLNL = "NA"
	ngtrLNL = "NA"
	pvalue = "NA"
	Posresults = "NA"

	#load .json file and create a python dictionary
	with open(filename, 'r+') as file:
		data = json.load(file)

	#MG94XREV
	mg94LNL = str(data["fits"]["Baseline MG94xREV"]["Log Likelihood"])
	#Full adaptive model
	fulladptLNL = str(data["fits"]["Full adaptive model"]["Log Likelihood"])
	#Nucleotide GTR
	ngtrLNL = str(data["fits"]["Nucleotide GTR"]["Log Likelihood"])

	#P-value corrected Hon-Bonferroni
	pvalue = str(data["test results"]["P-value threshold"])
	#Positive test results
	Posresults = str(data["test results"]["positive test results"])


	return mg94LNL,fulladptLNL,ngtrLNL,pvalue,Posresults; #this is tuple and should be stored as such

#testin = sys.argv[1]
#values = read_null(testin)
#print(values)

#initializes the tuples to store output from function

values = ()

#Value will be set for true if an outfile is found.
nullflag = False
groupname = "NA"

unfinished = []

outputname = sys.argv[2]
outfile = open(outputname,'w+')

#write the headers for outfile
outfile.write("Group\t Baseline MG94xREV Log Likelihood \t Full adaptive model Log Likelihood \t Nucleotide GTR Log Likelihood \t P-vale \t Num. of Positive Results\n")
# Create a section to loop through a directory of group names that are subdirectories.
# Null and Alt out files will be within the subdirectories

filedir = sys.argv[1]

#Loops through every files in the given directory
for file in os.listdir(filedir):
	subdir = os.path.join(filedir,file)
	#Check if the file is subdirectory
	if os.path.isdir(subdir):
		#subdir is the path to the subdirectory WITHOUT THE FILE SLASH
		#Loops through the subdirectory to look for out files
		for subfile in os.listdir(subdir+"/"):
			fullpathsubfile = os.path.join(subdir+"/"+subfile)
			if os.path.isfile(fullpathsubfile):
#				print(subfile)
				if re.search(".treefile",subfile):
					groupname = subfile[4:-23]
				if re.search("absrel.json",subfile):
					nullflag = True
					nullfile = fullpathsubfile
					values = read_null(nullfile)

		if nullflag == True:
			outfile.write(groupname+"\t"+values[0]+"\t"+values[1]+"\t"+values[2]+"\t"+values[3]+"\t"+values[4]+"\n")
		else:
			outfile.write(groupname+"\t NA \t NA \t NA \t NA \t NA \n")
###		#Done with subdirectory and flagging if there were not outfiles
		if nullflag == False:
			print("No null file for"+subdir)
			unfinished.append(groupname)
		nullflag = False
		groupname = ""
		nullvalues = ()
##OPTIONAL: the feature can be edited to auto run any unrun files
#not used because unrun files either 1. didn't exist or 2. the nodes are working properly with job submission
#name = "undonelist.txt"
#todolist = open(name,"w+")
#for items in unfinishednull:
#	todolist.write("qsub "+items+"_null_runcod.sh \n")
#todolist.close()
outfile.close()