#!/usr/bin/env python
import os, sys, string


class Seq:
    def __init__(self):
        self.ID=0
        self.data=""

class DPSeq:
    def __init__(self):
        self.ID=0
        self.data=0


# DloopExcluded flag variable
# if non-zero, exclude d-loop
DloopExcluded=0

# read entire file into a string
file_string=open(sys.argv[1]).read()

# split according to line-endings.  Note I'd usually use \n but for the
# sequences on mtDB they have \r's.
lines=file_string.split("\r")


NumSeq=int(lines[0].split()[0])
NumSites=int(lines[0].split()[1])
Sequences=[]

#print "Number of total sites:",NumSites

#Deal with first block
for i in lines[1:NumSeq+1]:
    NewSeq=Seq()
    NewSeq.ID=i.split()[0]
    for j in i.split()[1:]:
        NewSeq.data=NewSeq.data+j

    Sequences.append(NewSeq)

skipLines=0

#Deal with the rest of data
for i in range(NumSeq+1,len(lines)):

    if len(lines[i])<2:
        skipLines=skipLines+1
     #   print "Skipping:",lines[i]
        continue

    #print (i-skipLines-1)%NumSeq

    for j in lines[i].split():
        Sequences[(i-skipLines-1) % NumSeq].data=Sequences[(i-skipLines-1) % NumSeq].data+j 
    
    
#for i in Sequences:
#    print i.ID,i.data[150:160]

#Transfer IDs to DPSeqs
DPSeqs=[]
for i in range(0,NumSeq):
    NewSeq=DPSeq()
    NewSeq.ID=Sequences[i].ID
    NewSeq.data=[0]*NumSites
    DPSeqs.append(NewSeq)


#Identify segragating sites within a region and output to DPSeqs
SegSites=[]


if DloopExcluded:
    region=range(577,16023) # to exclude  D loop
else:
    region=range(0,len(Sequences[0].data)) #whole mtDNA



for i in region:
    A=0
    C=0
    G=0
    T=0
    gap=0
    first=''
    for j in range(0,NumSeq):
    
        if Sequences[j].data[i]=='A':
            if first=='':
                first='A'
                DPSeqs[j].data[i]=0
            elif first=='A':
                DPSeqs[j].data[i]=0
            else:
                DPSeqs[j].data[i]=1
            A=1
        if Sequences[j].data[i]=='C':

            if first=='':
                first='C'
                DPSeqs[j].data[i]=0
            elif first=='C':
                DPSeqs[j].data[i]=0
            else:
                DPSeqs[j].data[i]=1

            C=1

        if Sequences[j].data[i]=='G':
            if first=='':
                first='G'
                DPSeqs[j].data[i]=0
            elif first=='G':
                DPSeqs[j].data[i]=0
            else:
                DPSeqs[j].data[i]=1
            G=1
            
        if Sequences[j].data[i]=='T':

            if first=='':
                first='T'
                DPSeqs[j].data[i]=0
            elif first=='T':
                DPSeqs[j].data[i]=0
            else:
                DPSeqs[j].data[i]=1

            T=1
        if Sequences[j].data[i]=='-':
            gap=1

    #This line will exclude sequences with gaps from being considered segregating sites
    if gap:
        sum=0
    else:
        sum=A+C+G+T

    #Note this line limits us to taking only segregating sites that are biallelic
    if sum==2:
        SegSites.append(i)

#print "Segregating Sites and corresponding original positions:",
#for i in range(0,len(SegSites)):
#    print i,"(", SegSites[i],")",
    
print
print "Seqs:",NumSeq
print "Markers:",len(SegSites)

#Output the sequences in the format for Eric and I's MDBlocks program
for i in DPSeqs:
    print i.ID,
    count=6
    for j in SegSites:
        print i.data[j],
        count=count+1
        if(count==60):
            print
            count=0
    print