ambitus_pno_annotatetips.py

#!/usr/bin/env python3

import csv # To process tab-delimited files
import numpy # Used for random sampling 
import sys # To process arguments
import subprocess
from ambitus_main import shell_call as shell_call

def AnnotateTips(process):
	binlist = [] # List of bins created by phyloclim
	weightlist = [] # List of probabilities matched to bins, used for weighted average
	midpointlist = [] # List of medians from pno distribution
	specieslabellist = {}
	specieslist = []
	counter = 1
	try:
		with open('specieslist.csv', 'r') as speciesfile:
			reader=csv.reader(speciesfile, delimiter='\t')
			for row in reader:
				specieslist.append(row[0])
	except:
		print("Could not open species list.")
	
	for species in specieslist:
		counter = 1
		while counter <= process:
			with open('./pnos/pno{0}_{1}.csv'.format(counter, species), 'r') as datafile:
				reader=csv.reader(datafile, delimiter=',')
				next(reader)
				for row in reader:
					binlist.append(float(row[1]))
					weightlist.append(float(row[2]))
			midpointlist.append('variable{0}={1}'.format(counter,numpy.average(binlist, weights = weightlist))) # Weighted average to get center of distribution
			binlist = []
			weightlist = []
			counter += 1
		
		label = ""
		for x in midpointlist:
			label += (x + ",")
		label = "[&" + label + "]"
	
		specieslabellist[species] = label
		midpointlist = []
	
	shell_call('cp tree_labels_midpoints_clean.tre tree_labels_midpointsandtips.tre')
	
	for species in specieslist:
		specieslabel = specieslabellist[species]
		command = 'sed "s/{0}:/{0}{1}:/g" tree_labels_midpointsandtips.tre > temp.txt'.format(species,specieslabel)
		command = command.replace("&","\&")
		shell_call(command)
		shell_call("mv temp.txt tree_labels_midpointsandtips.tre")