def pare(file, prediction_code=None):
# Gunzip, parse, cut down to 25% best, bzip2 -9 pared file, delete old file
if not prediction_code:
prediction_code = get_prediction_code(file, hpf2=True)
print "\tParing results for {0}".format(prediction_code)
# Gunzip given file (cut '.gz' off the filename)
if subprocess.call(["gunzip", file]) != 0:
raise Exception("Gunzipping file '{0}' failed".format(file))
decompressed_file = file.rstrip('.gz')
# Open, parse, and pare file, storing in new file. Via denovo_results.denovoResultFile obj
drf = denovoResultFile(decompressed_file, prediction_code)
pared_file = decompressed_file + ".reduced"
drf.write_to_file(outfile=pared_file, percent=PERCENT_TO_KEEP)
# Bzip2 -9 new pared file
if subprocess.call(["bzip2", "-9", pared_file]) != 0:
raise Exception("Bzip2 -9'ing file '{0}' failed".format(pared_file))
recompressed_file = pared_file + ".bz2"
# Delete old file (NOTE: DO NOT DELETE FOR NOW)
if subprocess.call(["rm", decompressed_file]) != 0:
raise Exception("Deleting old file '{0}' failed".format(decompressed_file))
#print "Would delete old file '{0}' here..".format(decompressed_file)
print "\tParing '{0}' complete".format(file)
def test_parse(file, prediction_code=None):
# Test the denovo result file parsing without doing any other processing
if not prediction_code:
prediction_code = get_prediction_code(file, hpf2=True)
print "\tTesting results for {0}".format(prediction_code)
# Gunzip given file (cut '.gz' off the filename)
if subprocess.call(["gunzip", file]) != 0:
raise Exception("Gunzipping file '{0}' failed".format(file))
decompressed_file = file.rstrip('.gz')
# Open, parse, and pare file, storing in new file. Via denovo_results.denovoResultFile obj
drf = denovoResultFile(decompressed_file, prediction_code)
# Re-Gzip file
if subprocess.call(["gzip", decompressed_file]) != 0:
raise Exception("Re-Gzipping file '{0}' failed".format(decompressed_file))
print "\tTesting result {0} completed".format(prediction_code)
