compress.py

import os
from datetime import datetime
import sys
import tarfile
import shutil




genome_fastq_file = sys.argv[1]
genome_name = sys.argv[1][:-6]
t1 = datetime.now()

if not os.path.exists(genome_name):
    os.makedirs(genome_name)

Temp='temp'
if not os.path.exists(Temp):
    os.makedirs(Temp)



file = open(genome_fastq_file)
ID = open(os.path.join(genome_name, genome_name+'.ID'), "w")
Seq = open(os.path.join(genome_name, genome_name+'.Seq'), "w")
Qual = open(os.path.join(genome_name, genome_name+'.Qual'), "w")
Seq.write('>\n')
line = file.readline()

def tsplit(string, delimiters):
    """Behaves str.split but supports multiple delimiters."""
    
    delimiters = tuple(delimiters)
    stack = [string,]
    
    for delimiter in delimiters:
        for i, substring in enumerate(stack):
            substack = substring.split(delimiter)
            stack.pop(i)
            for j, _substring in enumerate(substack):
                stack.insert(i+j, _substring)
            
    return stack

Length= len(tsplit(line, (' ','.', '/', '-','_',':','=')))

sep=''

for i in line:
	if i == ' ' or i == '.' or i == '/' or i == '-' or i == '_' or i == ':' or i == '=':
		sep+=i

Sep = open(os.path.join(Temp,"sep.txt"), "w")
Sep.write(sep)
Sep.close()
file.seek(0)

while line:

    ID.write(file.readline())
    Seq.write(file.readline().strip())
    line = file.readline()
    Qual.write(file.readline())

file.readline().strip()
Qual.close()
ID.close()
Seq.close()
file.close()



cd='./MFcompress/MFCompressC -3 '+'-o'+' ' + os.path.join(Temp,genome_name+'.Seq') +' '+os.path.join(genome_name,genome_name+'.Seq') +' &' + './lpaq8/lpaq8 9 '+ os.path.join(genome_name,genome_name+'.Qual') +' '+os.path.join(Temp,genome_name+'.Qual') + '| grep Hello'
os.system(cd)

AWK= 'awk -F'
Delimter= "'[_ =:./-]'" 
cd2 = " '{print $"
	 
space= ' '
source= os.path.join(genome_name, genome_name+'.ID')
concat= ' > '


for h in range(1,Length+1):
	cd3= str(h)+"}'"
	dest= os.path.join(genome_name, str(h)+'.ID')#
	cd = AWK+ Delimter+cd2+cd3+space+source+concat+dest
	os.system(cd)



for x in range(1,Length+1):
    cd='./lpaq8/lpaq8 9 '+ os.path.join(genome_name,str(x)+'.ID') +' '+os.path.join(genome_name,str(x)+'.ID.lpaq8') + '| grep Hello'
    os.system(cd)
    os.remove(os.path.join(genome_name,str(x)+'.ID'))


IDtar = tarfile.open(os.path.join(Temp,genome_name+'.LFastqC'), mode='w')

try:
    
    for x in range(1,Length+1):
        IDtar.add(os.path.join(genome_name,str(x)+'.ID.lpaq8'))
        os.remove(os.path.join(genome_name,str(x)+'.ID.lpaq8'))
finally:
    IDtar.close()



out = tarfile.open(genome_name+'.LFastqC', mode='w')
try:
    out.add('temp')
finally:
    out.close()
shutil.rmtree('temp')
shutil.rmtree(genome_name)
print "Compression time in seconds = ", (datetime.now() - t1).seconds, "\n"