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1 #!/usr/bin/env python
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2
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3 #Created on Jule 23, 2018
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4
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5 # @author: Bob Brown
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6
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7 import sys
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8 import os
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9
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10 def main():
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11
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12 # Grab the inputs from the Galaxy xml interface and write to a file that is passed to the program
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13 # Not each of the parameters as separate command line variables.
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14 # ab_gene_name_for_header={}
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15 # ab_rrid_for_header={}
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16 dir= "/Users/bobbrown/Desktop/junk/"
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17 accepted_extensions = ["csv", "tsv"]
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18 filenames = [fn for fn in os.listdir(dir) if fn.split(".")[-1] in accepted_extensions]
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19 for f in filenames:
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20 print("filename= "+f)
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21 os.remove(dir+f)
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22
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23 sys.exit(0)
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24
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25 ab_gene_name_for_header={'abc':'geneName'}
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26 ab_rrid_for_header={'abc':'rrid123'}
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27 line= 'abc,123\n'
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28
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29 pos= line.find(",")
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30 ABname= line[0:pos]
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31 ABnewName= ABname+ "|"+ab_gene_name_for_header[ABname]+"|"+ab_rrid_for_header[ABname]
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32 line= ABnewName+line[pos:]
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33 line= line.replace(',','\t')
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34 sys.exit(0)
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35 # try:
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36 print(' \n starting Test program read params from file stored in tools dir. Arguments=')
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37 print(str(sys.argv[1:])+'\n')
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38
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39 if False:
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40 infileName = sys.argv[1]
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41 # directory = sys.argv[2]
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42 directory = '/Users/bobbrown/Desktop/'
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43 outfileName = sys.argv[3] #use later
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44 # outfile = sys.argv[6]
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45
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46 #sys.stdout.write
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47
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48 # ifile= open(directory+"/"+infileName,'rU')
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49 ifile= open(directory+infileName,'rU')
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50 ofile= open(directory+outfileName,'w')
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51 # ofile= open('/Users/bobbrown/Desktop/TestOutFileVarParams.txt','w')
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52
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53 cnt= 0
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54 # for param in range(2,len(sys.argv)):
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55 # cnt +=1
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56 # ofile.write("param "+str(cnt)+"= "+param+"\n")
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57
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58
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59 for param in ifile:
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60 cnt +=1
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61 ofile.write("param "+str(cnt)+"= "+param)
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62
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63 ifile.close()
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64
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65 ofile.close()
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66
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67 print('Fini -- rows read = '+str(cnt)+'\n')
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68
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69 # except :
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70 # print('Error>>> ')
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71
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72 return
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73 ##
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74 ##
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75
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76 if __name__ == '__main__': main()
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77 #sys.exit(0) |
