plain2fq.py

import sys, os
import mimetypes

pos_path = "/home/qmtran/Indel_Analysis/Data_reads22_29/positions/"
perl_path = "/home/qmtran/Indel_Analysis/"

def get_filepaths(directory):
    """
    This function will generate the file names in a directory 
    tree by walking the tree either top-down or bottom-up. For each 
    directory in the tree rooted at directory top (including top itself), 
    it yields a 3-tuple (dirpath, dirnames, filenames).
    """
    file_paths = []  # List which will store all of the full filepaths.

    # Walk the tree.
    for root, directories, files in os.walk(directory):
        for filename in files:
            # Join the two strings in order to form the full filepath.
            filepath = os.path.join(root, filename)
            file_paths.append(filepath)  # Add it to the list.

    return file_paths  # Self-explanatory.



if __name__ == '__main__':

	
	#for f in get_filepaths(sys.argv[1]):
	#	if mimetypes.guess_type(f)[0] == 'text/plain':
	f = open(sys.argv[1])
	while True:
		fname = f.readline().strip()
		if fname == '':
			break

		#print(fname[:-2]+"txt")
		init = open(fname[:-2]+"txt")
		fpos = open(pos_path+fname[:-3])
		print ("Opening the file: " + fname[:-2]+"txt")
		target = open(fname[:-2]+"fa", 'w')
		i = 0
		while True:
			i += 1
			read = init.readline()
			pos = fpos.readline()				
			if read == '':
				break
			target.write(">" + str(i) + "##" + pos.strip())
			target.write("\n")
			target.write(read.strip())
			target.write("\n")
		target.close()
		init.close()
		fpos.close()
		os.system("perl " + perl_path + "fasta_to_fastq.pl " + fname[:-2]+"fa >" + fname[:-2]+"fq")

	os.system("../fq2fastq.sh")