Script for downsampling of accurate mass data before peak alignment

lowResMass.py

# -*- coding: utf-8 -*-
"""
Created on 2016-03-05
@author: Martin Worm-Leonhard

----------------------------------------------------------------------------
"THE BEER-WARE LICENSE" (Revision 42):
<mwormleonhard@gmail.com> wrote this file. As long as you retain this notice you
can do whatever you want with this stuff. If we meet some day, and you think
this stuff is worth it, you can buy me a beer in return.   Martin Worm-Leonhard
----------------------------------------------------------------------------
"""
import csv
import sys
import re
import tkFileDialog
from os.path import dirname, basename, join

def downsampleFile(filename):

    outheader = 'Name\tR.T. (s)\tRetention Index\tCAS\tSample Concentration\tQuant Masses\tUniqueMass\tQuant S/N\tArea\tSimilarity\tWeight\tClassifications\tType\tSpectra\r\n'

    outfilename = join(dirname(filename), "LOWRES_" + basename(filename))

    with open(filename, 'rb') as infile:
        with open(outfilename, 'wb') as outfile:
            reader = csv.reader(infile, delimiter='\t')
            writer = csv.writer(outfile, delimiter='\t', quoting=csv.QUOTE_NONE, quotechar='~')  # Quotechar hack to avoid quoting quotes
            try:
                outfile.write(outheader)
                reader.next()  # Skip header line
                for row in reader:
                    rt1, rt2 = str.split(row[1], ',')  # Rounding of RT1
                    row[1] = '"' + str(round(float(rt1))) + ',' + rt2 + '"'  # Rounding of RT1
                    row[5] = 'T'  # Quant Masses replaced by the letter "T"
                    row[6] = str(round(float(row[6])))  # Rounding of Unique mass
                    if row[10] != '':   # If Weight fiels is empty, then leave it alone
                        row[10] = str(round(float(row[10])))  # Rounding of Weight
                    # Rounding of spectrum
                    spectrum = row[13]
                    speciter = re.finditer(r'(\d+\.\d+):(\d+\.\d+)', spectrum)
                    lowresspec = {}
                    for s in speciter:
                        mass, intensity = int(round(float(s.group(1)))), float(s.group(2))
                        if mass in lowresspec:
                            lowresspec[mass] += intensity
                        else:
                            lowresspec[mass] = intensity
                    lowresspecstring = ''
                    for k in sorted(lowresspec.keys()):
                        lowresspecstring += str(k) + ':' + str(int(round(lowresspec[k]))) + ' '  # Intentisies need to be integers as well
                    row[13] = lowresspecstring
                    writer.writerow(row)
            except csv.Error as e:
                sys.exit('file %s, line %d: %s' % (filename, reader.line_num, e))


infilenames = tkFileDialog.askopenfilenames(defaultextension='.txt',
                                          filetypes=[('TXT file', '.txt')],
                                          title='Select files to be downsampled')

if len(infilenames) > 0:
    for name in infilenames:
        downsampleFile(name)
        print "Done processing", name
else:
    sys.exit('No files selected. Exiting.')