Mercurial > repos > sblanck > mpagenomics_normalize

annotate segcall.py @ 6:7dc6ce39fb89 default tip

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add selection tool
author blanck
date Wed, 29 Apr 2015 10:08:52 +0200
parents b7f3854e08f8
children
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1 import os
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2 import sys
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3 import subprocess
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4 import zipfile
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5
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6
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7 def main():
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8
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9 input_file=sys.argv[2]
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10 tmp_dir=sys.argv[4]
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11 settingsType=sys.argv[6]
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12 zip_file=sys.argv[9]
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13 tumorcsv=sys.argv[10]
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14 cellularity=sys.argv[11]
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15 outputlog=sys.argv[12]
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16 log=sys.argv[13]
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17 user=sys.argv[14]
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18 method=sys.argv[15]
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19 script_dir=os.path.dirname(os.path.abspath(__file__))
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20
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21 iFile=open(input_file,'r')
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22 dataSetLine=iFile.readline()
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23 dataset=dataSetLine.split("\t")[1]
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24 iFile.close()
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25
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26
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27 if settingsType=="dataset":
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28 settingsType=dataset
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29
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30 if (outputlog=="TRUE"):
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31 errfile=open(log,'w')
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32 else:
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33 errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
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34
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35 fig_dir=os.path.join("mpagenomics",user,"figures",dataset,"segmentation/CN")
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36
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37 abs_fig_dir=os.path.join(tmp_dir,fig_dir)
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38 if (os.path.isdir(abs_fig_dir)) and (sys.argv[7]=="TRUE"):
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39 old_files=os.listdir(abs_fig_dir)
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40 for ifile in old_files:
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41 os.remove(os.path.join(abs_fig_dir,ifile))
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42
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43
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44 retcode=subprocess.call(["Rscript", os.path.join(script_dir,"segcall.R"), sys.argv[1], dataset, sys.argv[3], sys.argv[4], sys.argv[5], settingsType, sys.argv[7], sys.argv[8], tumorcsv, cellularity, user, method], stdout = errfile, stderr = errfile)
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45
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46 errfile.close()
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47
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48 if (retcode == 0):
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49 if (os.path.isdir(abs_fig_dir)) and (sys.argv[7]=="TRUE"):
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50
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51 new_files=os.listdir(abs_fig_dir)
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52 zipbuf = zipfile.ZipFile(os.path.join(abs_fig_dir,zip_file), 'w', zipfile.ZIP_DEFLATED)
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53 for current_file in new_files:
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54 fn = os.path.join(abs_fig_dir,current_file)
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55 relfn=fn[len(abs_fig_dir)+len(os.sep):]
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56 zipbuf.write(fn,relfn)
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57 sys.exit(retcode)
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58 else:
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59 sys.exit(retcode)
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60
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61 if __name__ == "__main__":
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62 main()