#!/usr/bin/env python
#David Depierre,Taris Raphael
"""
From a depth text file produced with samtools, create contig and give in return:
chromosome name, Start and end of the contig, start and end from the most represented locus seperated by tabulation and output a text file
version: 0.1.0
"""

import os
import re
import subprocess
import sys
import tempfile


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit()


def Contig_locus_count(infile,fname):
    """Read a .txt file and find contig and loci.
    """
    in_handle = open(infile)#read the file in input
    out_handle = open(fname, "w")#right a file in output
    bestNbRead=[0,0,0,0] #start,end,numberOfReads,length
    inContig=False
    inLoci=False
    tmpLength=0
    tmpStart=0
    lastPos=0
    contigInf=["",0,0] #namecontig,start,end
    for line in in_handle:
		splitline=line.split("\t")
		if inContig==False:#Initiate the contig
			if int(splitline[2])>0:
				inContig=True
				bestNbRead=[int(splitline[1]),0,int(splitline[2]),1]
				contigInf=[splitline[0],int(splitline[1]),0]
				inLoci=True
				tmpLength=1
		else:#When we enter in a contig
			if int(splitline[1])==lastPos+1:#Verify that the current position is equal to the last +1
				if inLoci==True:#construct the best Loci
					if int(splitline[2])>bestNbRead[2]:
						bestNbRead=[int(splitline[1]),int(splitline[1]),int(splitline[2]),1]
						tmpLength=1
					elif int(splitline[2])==bestNbRead[2]:
						tmpLength+=1
						bestNbRead[1]=int(splitline[1])
					elif int(splitline[2])<bestNbRead[2]:
						bestNbRead[3]=tmpLength
						tmpLength=0
						inLoci=False
						tmpStart=0
				else:
					if int(splitline[2])>bestNbRead[2]:#read in the contig if a loci is more represented. 
						bestNbRead=[int(splitline[1]),int(splitline[1]),int(splitline[2]),1]
						tmpLength=1
						inLoci=True
					elif int(splitline[2])==bestNbRead[2]:
						tmpLength+=1
						if tmpLength==1:
							tmpStart=int(splitline[1])
						elif tmpLength>bestNbRead[3]:
							bestNbRead=[tmpStart,int(splitline[1]),int(splitline[2]),tmpLength]
							inLoci=True
							tmpStart=0
					elif int(splitline[2])<bestNbRead[2]:
						tmpLength=0
						tmpStart=0
			else: #THe position is'nt equal to the last one +1, then  we are out of a contig and write in the file.
				out_handle.write(str(contigInf[0])+"\t"+str(contigInf[1])+"\t"+str(lastPos)+"\t"+str(bestNbRead[0])+"\t"+str(bestNbRead[1])+"\t"+str(bestNbRead[2])+"\n")
				tmpStart=0
				bestNbRead=[int(splitline[1]),0,int(splitline[2]),1]
				contigInf=[splitline[0],int(splitline[1]),0]
				tmpLength=1
		lastPos=int(splitline[1])#Save the last position
    if inContig==True:#write the last contig.
		out_handle.write(str(contigInf[0])+"\t"+str(contigInf[1])+"\t"+str(lastPos)+"\t"+str(bestNbRead[0])+"\t"+str(bestNbRead[1])+"\t"+str(bestNbRead[2])+"\n")
    in_handle.close()
    out_handle.close()
    return fname


if len( sys.argv ) < 3:
    stop_err( "USAGE: prog input out_file" )
    
infile = sys.argv[1]
outfile = sys.argv[2]
contig= Contig_locus_count(infile,outfile)#Execution of our program