Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/launcher/WriteScript.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import time
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 self._iJob = job
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8 self._iJobdb = jobdb
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 self._cDir = cdir
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 self._tmpDir = tmpdir
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 d = self.createJobScriptDict(cmdStart, cmdFinish, cmdSize, cmdCopy)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 self.fillTemplate(pyFileName, d)
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20
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 def fillTemplate(self, outputFileName, dict):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 if self._chooseTemplateWithCopy:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 inputFileName = "%s/commons/core/launcher/JobScriptWithFilesCopyTemplate.py" % os.environ["REPET_PATH"]
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24 else:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 input.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 for key, value in dict.items():
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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34 data = data.replace("@@%s@@" % key, value)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 output = open(outputFileName, "w")
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36 output.write(data)
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37 output.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 def createJobScriptDict(self, cmdStart, cmdFinish, cmdSize, cmdCopy):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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40 dict = {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 "tmpDir" : self._tmpDir,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 "jobTableName" : self._iJobdb._table,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 "groupId" : self._iJob.groupid,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 "jobName" : self._iJob.jobname,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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45 "launcher" : self._iJob.launcher,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 "time" : time.strftime("%Y%m%d-%H%M%S"),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 "repet_path" : os.environ["REPET_PATH"],
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 "repet_host" : os.environ["REPET_HOST"],
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 "repet_user" : os.environ["REPET_USER"],
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 "repet_pw" : os.environ["REPET_PW"],
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 "repet_db" : os.environ["REPET_DB"],
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 "repet_port" : os.environ["REPET_PORT"],
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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53 "cmdStart" : cmdStart,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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54 "cmdFinish" : cmdFinish,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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55 "cDir" : self._cDir,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 "cmdSize" : cmdSize,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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57 "cmdCopy" : cmdCopy
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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58 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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59 return dict
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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60
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61 def createJobScriptLightDict(self, cmdStart, cmdFinish, cmdSize, cmdCopy):
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62 dict = {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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63 "tmpDir" : self._tmpDir,
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64 "jobTableName" : self._iJobdb._table,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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"],
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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70 "cmdStart" : cmdStart,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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71 "cmdFinish" : cmdFinish,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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