Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/launcher/WriteScript.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import os |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import time |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 |
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4 class WriteScript(object): |
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5 |
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6 def __init__(self, job = None, jobdb = None, cdir = "", tmpdir = "", chooseTemplateWithCopy = False, chooseTemplateLight = False): |
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7 self._iJob = job |
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8 self._iJobdb = jobdb |
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9 self._cDir = cdir |
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10 self._tmpDir = tmpdir |
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11 self._chooseTemplateWithCopy = chooseTemplateWithCopy |
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12 self._chooseTemplateLight = chooseTemplateLight |
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13 |
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14 def run(self, cmdStart, cmdFinish, pyFileName, cmdSize = "", cmdCopy = ""): |
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15 if self._chooseTemplateLight: |
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16 d = self.createJobScriptLightDict(cmdStart, cmdFinish, cmdSize, cmdCopy) |
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17 else: |
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18 d = self.createJobScriptDict(cmdStart, cmdFinish, cmdSize, cmdCopy) |
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19 self.fillTemplate(pyFileName, d) |
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20 |
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21 def fillTemplate(self, outputFileName, dict): |
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22 if self._chooseTemplateWithCopy: |
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23 inputFileName = "%s/commons/core/launcher/JobScriptWithFilesCopyTemplate.py" % os.environ["REPET_PATH"] |
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24 else: |
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25 inputFileName = "%s/commons/core/launcher/JobScriptTemplate.py" % os.environ["REPET_PATH"] |
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26 |
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27 if self._chooseTemplateLight: |
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28 inputFileName = "%s/commons/core/launcher/JobScriptTemplateLight.py" % os.environ["REPET_PATH"] |
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29 |
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30 input = open(inputFileName, "r") |
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31 data = input.read() |
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32 input.close() |
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33 for key, value in dict.items(): |
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34 data = data.replace("@@%s@@" % key, value) |
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35 output = open(outputFileName, "w") |
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36 output.write(data) |
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37 output.close() |
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38 |
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39 def createJobScriptDict(self, cmdStart, cmdFinish, cmdSize, cmdCopy): |
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40 dict = { |
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41 "tmpDir" : self._tmpDir, |
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42 "jobTableName" : self._iJobdb._table, |
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43 "groupId" : self._iJob.groupid, |
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44 "jobName" : self._iJob.jobname, |
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45 "launcher" : self._iJob.launcher, |
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46 "time" : time.strftime("%Y%m%d-%H%M%S"), |
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47 "repet_path" : os.environ["REPET_PATH"], |
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48 "repet_host" : os.environ["REPET_HOST"], |
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49 "repet_user" : os.environ["REPET_USER"], |
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50 "repet_pw" : os.environ["REPET_PW"], |
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51 "repet_db" : os.environ["REPET_DB"], |
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52 "repet_port" : os.environ["REPET_PORT"], |
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53 "cmdStart" : cmdStart, |
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54 "cmdFinish" : cmdFinish, |
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55 "cDir" : self._cDir, |
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56 "cmdSize" : cmdSize, |
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57 "cmdCopy" : cmdCopy |
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58 } |
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59 return dict |
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60 |
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61 def createJobScriptLightDict(self, cmdStart, cmdFinish, cmdSize, cmdCopy): |
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62 dict = { |
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63 "tmpDir" : self._tmpDir, |
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64 "jobTableName" : self._iJobdb._table, |
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65 "groupId" : self._iJob.groupid, |
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66 "jobName" : self._iJob.jobname, |
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67 "launcher" : self._iJob.launcher, |
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68 "time" : time.strftime("%Y%m%d-%H%M%S"), |
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69 "repet_path" : os.environ["REPET_PATH"], |
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70 "cmdStart" : cmdStart, |
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71 "cmdFinish" : cmdFinish, |
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72 "cDir" : self._cDir, |
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73 "cmdSize" : cmdSize, |
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74 "cmdCopy" : cmdCopy |
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75 } |
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76 return dict |