Mercurial > repos > guerler > springsuite

annotate spring_package/Utilities.py @ 39:172398348efd draft

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"planemo upload commit 26b4018c88041ee0ca7c2976e0a012015173d7b6-dirty"
author guerler
date Fri, 22 Jan 2021 15:50:27 +0000
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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39
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1 from os.path import isfile
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2
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3
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4 def validateIdentifier(identifier):
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5 if len(identifier) < 6 or identifier[4:5] != "_":
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6 raise Exception("Invalid list entry (`PDB_CHAIN`): %s." % identifier)
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7
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8
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9 def getId(identifier):
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10 identifier = identifier.strip()
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11 validateIdentifier(identifier)
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12 return identifier[:4].upper() + identifier[4:6]
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13
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14
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15 def getChain(identifier):
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16 validateIdentifier(identifier)
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17 pdbChain = identifier[5:6]
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18 return pdbChain
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19
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20
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21 def getName(identifier):
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22 pdb = identifier[:4].lower()
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23 return pdb
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24
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25
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26 def getCrossReference(crossReferenceFile, allPartners=False):
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27 crossReference = dict()
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28 crossCount = 0
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29 with open(crossReferenceFile) as file:
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30 for line in file:
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31 columns = line.split()
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32 if len(columns) < 2:
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33 raise Exception("Invalid Cross Reference Entry %s." % line)
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34 core = columns[0]
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35 partner = columns[1]
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36 if len(columns) < 4:
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37 templates = [core, partner]
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38 else:
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39 templates = [columns[2], columns[3]]
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40 if core not in crossReference:
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41 crossReference[core] = dict(partners=list(), templates=list())
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42 if allPartners or partner not in crossReference[core]["partners"]:
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43 crossReference[core]["partners"].append(partner)
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44 crossReference[core]["templates"].append(templates)
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45 crossCount = crossCount + 1
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46 print("Identified %s reference interactions." % crossCount)
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47 return crossReference
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48
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49
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50 def getTemplates(hhrFile, minScore=10):
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51 result = dict()
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52 topTemplate = None
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53 if isfile(hhrFile):
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54 with open(hhrFile) as file:
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55 for index, line in enumerate(file):
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56 if index > 8:
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57 if not line.strip():
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58 break
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59 templateId = line[4:10]
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60 templateScore = float(line[57:63])
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61 if templateScore > minScore:
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62 if topTemplate is None:
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63 topTemplate = templateId
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64 result[templateId] = templateScore
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65 return topTemplate, result