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annotate init.py @ 0:256cc0e17454 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
author galaxyp
date Sat, 20 Jul 2019 04:53:23 -0400
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256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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1 #!/usr/bin/env python3
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2 """Initialize MaxQuant tool for use with a new version of
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3 modifications/enzymes.xml.
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4
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5 TODO: Append function: only add modifications that are not
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6 already present, add modification entries to conda maxquant
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7
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8 Authors: Damian Glaetzer <d.glaetzer@mailbox.org>
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10 Usage: init.py [-a] [-m MODS_FILE] [-e ENZYMES_FILE]
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11 FILES are the modifications/enzymes.xml of MaxQuant, located at
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12 <ANACONDA_DIR>/pkgs/maxquant-<VERSION>/bin/conf/.
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13 (for conda installations)
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15 Updates modification parameters in macros.xml.
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16 """
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18 import argparse
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19 import re
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20 import xml.etree.ElementTree as ET
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21 from xml.dom import minidom
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24 def build_list(node, name, mod_list, append=False):
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25 """Build the modifications list in macros.xml"""
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26 node.clear()
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27 node.tag = 'xml'
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28 node.set('name', name)
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29 for m in mod_list:
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30 ET.SubElement(node, 'expand', attrib={'macro': 'mod_option',
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31 'value': m})
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34 parser = argparse.ArgumentParser()
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35 parser.add_argument("-m", "--modifications",
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36 help="modifications.xml of maxquant")
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37 parser.add_argument("-e", "--enzymes",
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38 help="enzymes.xml of maxquant")
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39 args = parser.parse_args()
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40
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41 if args.modifications:
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42 mods_root = ET.parse(args.modifications).getroot()
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43
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44 mods = mods_root.findall('modification')
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45 standard_mods = []
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46 label_mods = []
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47 for m in mods:
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48 if (m.findtext('type') == 'Standard'
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49 or m.findtext('type') == 'AaSubstitution'):
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50 standard_mods.append(m.get('title'))
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51 elif m.findtext('type') == 'Label':
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52 label_mods.append(m.get('title'))
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53
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54 if args.enzymes:
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55 enzymes_root = ET.parse(args.enzymes).getroot()
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56
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57 enzymes = enzymes_root.findall('enzyme')
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58 enzymes_list = [e.get('title') for e in enzymes]
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59
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60 macros_root = ET.parse('./macros.xml').getroot()
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61 for child in macros_root:
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62 if child.get('name') == 'modification' and args.modifications:
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63 build_list(child, 'modification', standard_mods)
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64 elif child.get('name') == 'label' and args.modifications:
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65 build_list(child, 'label', label_mods)
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66 elif child.get('name') == 'proteases' and args.enzymes:
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67 build_list(child, 'proteases', enzymes_list)
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68
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69 rough_string = ET.tostring(macros_root, 'utf-8')
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70 reparsed = minidom.parseString(rough_string)
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71 pretty = reparsed.toprettyxml(indent=" ")
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72 even_prettier = re.sub(r"\n\s+\n", r"\n", pretty)
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73 with open('./macros.xml', 'w') as f:
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74 print(even_prettier, file=f)