indexdata.py

import sys
import os
import struct
import xml.etree.ElementTree as ET

def parse_index_data(f):
    #read the header and file length
    try:
    	file = open(f + '/InterOp/IndexMetricsOut.bin', 'r')
    except IOError:
    	print '/InterOp/IndexMetricsOut.bin not found...'
    	sys.exit()

    print 'File version', struct.unpack('B', file.read(1))[0]
    file.seek(0, 2)
    length = file.tell() - 1
    print 'Length', length
    file.seek(1, 0)
    
    #get the run id
    tree = ET.parse(f + '/RunInfo.xml')
    root = tree.getroot()
    run_id = root[0].attrib['Id']
    print 'Parsing index data for run id', run_id

    #output all data
    output_dir = f + '/InterOp/Text/'
    output_path = f + '/InterOp/Text/IndexMetricsOut.txt'
    if not os.path.exists(output_dir):
    	os.makedirs(output_dir)
    with open(output_path, 'w') as outfile:
    	print >>outfile, ','.join(['RunId', 'Lane', 'Tile', 'Bool1', 'Bool2', 'Index1', 'Index2', 'Read count', 'Sample name', 'Project name'])
    	i = 0
    	while True:
    		lane = struct.unpack('B', file.read(1))[0] #Lane
    		swath = struct.unpack('B', file.read(1))[0] #Swath
    		tile = struct.unpack('H', file.read(2))[0] #Tile
    		bool1 = struct.unpack('?', file.read(1))[0] #?
    		bool2 = struct.unpack('?', file.read(1))[0] #?
    		indexlen = struct.unpack('H', file.read(2))[0]
    		index1, index2 = struct.unpack('%ss' %(indexlen), file.read(indexlen))[0].split('-')
    		readcount = struct.unpack('i', file.read(4))[0]
    		samplelen = struct.unpack('H', file.read(2))[0]
    		sample = struct.unpack('%ss' %(samplelen), file.read(samplelen))[0]
    		projectlen = struct.unpack('H', file.read(2))[0]
    		project = struct.unpack('%ss' %(projectlen), file.read(projectlen))[0]
    		print >>outfile, '%s,%i,%i,%s,%s,%s,%s,%i,%s,%s' %(run_id, lane, tile, bool1, bool2, index1, index2, readcount, sample, project)
    		i += (16 + indexlen + samplelen + projectlen)
    		if i == length:
    			break
                
if __name__ == '__main__':
    parse_index_data(sys.argv[1])