mzXML.parse_file(f)
neg_pos_mz_sets_temp = XML_process(mzXML, threshold=threshold)
neg_pos_mz_sets[0] = neg_pos_mz_sets[0] + neg_pos_mz_sets_temp[0]
neg_pos_mz_sets[1] = neg_pos_mz_sets[1] + neg_pos_mz_sets_temp[1]
elif ".mzML" in f:
# Use ML processing
print "Reading %s ..." % f
neg_pos_mz_sets_temp = ML_process(f, threshold=threshold)
neg_pos_mz_sets[0] = neg_pos_mz_sets[0] + neg_pos_mz_sets_temp[0]
neg_pos_mz_sets[1] = neg_pos_mz_sets[1] + neg_pos_mz_sets_temp[1]
# Removes all duplicates from both neg and pos lists
neg_pos_mz_sets[0] = list(set(neg_pos_mz_sets[0]))
neg_pos_mz_sets[1] = list(set(neg_pos_mz_sets[1]))
# Fix for how writeTxt works - ugly code
name = outputName + "xxxxxx"
# Patch for bug when writing one file. Probably a better way to do this but this works.
if len(neg_pos_mz_sets[0]) > len(files):
writeTxt(neg_pos_mz_sets[0], name, 0)
if len(neg_pos_mz_sets[1]) > len(files):
writeTxt(neg_pos_mz_sets[1], name, 1)
# Automatically opens the web browser with the calculator page open
webbrowser.open('http://www.bmrb.wisc.edu/metabolomics/mass_query.php', new=1)
print('done')
# Checks to make sure two and only two arguments were entered into the command line
if len(sys.argv) != 2:
print usage_mesg
sys.exit(1)
# Gets the filename from the second argument passed in and makes sure the file can be found
filename_mzXML = sys.argv[1]
if not os.access(filename_mzXML, os.R_OK):
print "%s is not accessible." % filename_mzXML
print usage_mesg
sys.exit(1)
# Creates an MzXML object from the file provided
mzXML = MzXML()
mzXML.parse_file(filename_mzXML)
# Takes in the mzXML object and processes all the data to extract a list with both the positive and
# negative mz values extracted. Then writes those to two .txt files.
neg_pos_mz_sets = process_mzs(mzXML)
if neg_pos_mz_sets[0]:
writeTxt(neg_pos_mz_sets[0], filename_mzXML, 0)
if neg_pos_mz_sets[1]:
writeTxt(neg_pos_mz_sets[1], filename_mzXML, 1)
# Automatically opens the web browser with the calculator page open
webbrowser.open('http://www.bmrb.wisc.edu/metabolomics/mass_query.php', new=1)
print('done')
