Mercurial > repos > tomnl > deconrank
annotate dma-filelist-generation.py @ 14:5b0eceae2d6c draft
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 2864a500a25e87f292f185872b92ecfe5800dea1
author | tomnl |
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date | Fri, 04 May 2018 12:49:30 -0400 |
parents | defa57c7775e |
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rev | line source |
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defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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1 import argparse |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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2 import textwrap |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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3 import os |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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4 import re |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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5 import collections |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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6 import csv |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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7 from operator import itemgetter |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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8 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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9 def check_folder(in_dir, reg_string): |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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10 filelist = [] |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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11 for f in os.listdir(in_dir): |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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12 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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13 if re.match(reg_string, f, re.IGNORECASE): |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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14 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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15 fn, fe = os.path.splitext(f) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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16 fnl = fn.split("_") |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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17 filename = fn |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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18 fullpth = os.path.join(in_dir, f) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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19 wells = fnl[0] |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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20 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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21 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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22 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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23 if re.match("^.*pos.*", f, re.IGNORECASE): |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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24 polarity = "pos" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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25 elif re.match("^.*neg.*", f, re.IGNORECASE): |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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26 polarity = "neg" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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27 else: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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28 error_message = "Files need to have either 'pos' or 'neg' in the file name" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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29 print error_message |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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30 return 1, error_message, "", "" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
diff
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31 if re.match("^.*blank.*", f, re.IGNORECASE): |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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32 sample_type = "blank" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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33 else: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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34 sample_type = "sample" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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35 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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36 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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37 filelist.append([wells, sample_type, polarity, filename, fullpth]) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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38 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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39 return filelist |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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40 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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41 def get_filelist(filesin, o, file_type='mzML', create_filelist=True): |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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42 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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43 filedict = collections.OrderedDict() |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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44 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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45 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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46 if file_type=="mzML": |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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47 reg_string = "^.*mzML$" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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48 else: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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49 reg_string = "^.*raw$" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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50 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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51 if isinstance(filesin, list): |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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52 filelist = [] |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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53 for f in filesin: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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54 filelist.extend(check_folder(f, reg_string)) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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55 else: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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56 filelist = check_folder(filesin, reg_string) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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57 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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58 # Turn filelist into a dictionary |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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59 for f1 in filelist: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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60 well = f1[0] |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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61 filedict[well] = [] |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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62 for f2 in filelist: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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63 if well == f2[0]: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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64 filedict[well].append(f2[1:len(f2)+1]) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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65 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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66 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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67 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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68 filelist = sorted(filelist, key=itemgetter(0, 1)) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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69 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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70 for k, v in filedict.iteritems(): |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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71 classes = [i[0] for i in v] |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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72 classes.sort() |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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73 if not classes == ['blank', 'sample']: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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74 error_message = "!!!!ERROR!!!! Blank and sample required for each well, file type {}".format(file_type) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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75 print error_message |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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76 return 1, error_message, "", "" |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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77 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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78 print 'files of type {} checked, files OK'.format(file_type) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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79 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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80 if create_filelist: |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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81 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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82 outname = write_filedict(filedict, o, file_type) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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83 print 'filelist created in folder {}, using file type {}, full path {}'.format(o, file_type, outname) |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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84 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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85 return 0, "files OK", filedict, filelist |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
parents:
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86 |
defa57c7775e
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
tomnl
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87 def write_filedict(filedict, out_dir, file_type, file_spacing='tsv'): |
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88 |
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89 outname = os.path.join(out_dir,'filelist_{}.{}'.format(file_type, file_spacing)) |
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90 |
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91 if file_spacing=='tsv': |
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92 delim = '\t' |
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93 elif file_spacing=='csv': |
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94 delim = ',' |
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95 else: |
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96 delim = ',' |
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97 |
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98 |
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99 with open(outname, 'wb') as csvfile: |
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100 w = csv.writer(csvfile, delimiter=delim) |
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101 |
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102 w.writerow(['filename','classLabel', 'multilist', 'multilistLabel']) |
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103 c = 1 |
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104 for k, v in filedict.iteritems(): |
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105 for i in v: |
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106 w.writerow([os.path.basename(i[3]), i[0], c, k]) |
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107 c +=1 |
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108 |
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109 return outname |
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110 |
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111 |
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112 def main(): |
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113 |
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114 p = argparse.ArgumentParser(prog='PROG', |
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115 formatter_class=argparse.RawDescriptionHelpFormatter, |
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116 description='''Create filelist for DMA DIMS nearline workflow''', |
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117 epilog=textwrap.dedent(''' |
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118 ------------------------------------------------------------------------- |
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119 |
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120 Example Usage |
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121 |
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122 python dma-filelist-generation.py -i [dir with sample files], [dir with blank files] -o . |
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123 |
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124 ''')) |
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125 |
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126 p.add_argument('-i', dest='i', help='dir with sample files', nargs = '*', required=True) |
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127 p.add_argument('-o', dest='o', help='out dir', required=True) |
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128 p.add_argument('--check_mzml', dest='check_mzml', action='store_true') |
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129 p.add_argument('--check_raw', dest='check_raw', action='store_true') |
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130 p.add_argument('--create_filelist_mzml', dest='create_filelist_mzml', action='store_true') |
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131 p.add_argument('--create_filelist_raw', dest='create_filelist_raw', action='store_true') |
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132 |
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133 args = p.parse_args() |
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134 |
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135 if not os.path.exists(args.o): |
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136 os.makedirs(args.o) |
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137 print args.o |
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138 |
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139 if not args.check_mzml and not args.check_raw: |
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140 print '--check_mzml or --check_raw (or both) are required as inputs' |
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141 exit() |
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142 |
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143 if args.check_mzml: |
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144 get_filelist(args.i, args.o, file_type='mzML', create_filelist=args.create_filelist_mzml) |
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145 |
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146 if args.check_raw: |
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147 |
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148 get_filelist(args.i, args.o, file_type='raw', create_filelist=args.create_filelist_raw) |
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149 |
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150 |
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151 |
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152 if __name__ == '__main__': |
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153 main() |
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154 |