Mercurial > repos > md-anderson-bioinformatics > matrix_manipulation

comparison Test_input_into_file.py @ 1:f1bcd79cd923 draft default tip

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author insilico-bob
date Tue, 27 Nov 2018 14:20:40 -0500
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0:7f12c81e2083 1:f1bcd79cd923
1 #!/usr/bin/env python
2
3 #Created on Jule 23, 2018
4
5 # @author: Bob Brown
6
7 import sys
8 import os
9
10 def main():
11
12 # Grab the inputs from the Galaxy xml interface and write to a file that is passed to the program
13 # Not each of the parameters as separate command line variables.
14 # ab_gene_name_for_header={}
15 # ab_rrid_for_header={}
16 dir= "/Users/bobbrown/Desktop/junk/"
17 accepted_extensions = ["csv", "tsv"]
18 filenames = [fn for fn in os.listdir(dir) if fn.split(".")[-1] in accepted_extensions]
19 for f in filenames:
20 print("filename= "+f)
21 os.remove(dir+f)
22
23 sys.exit(0)
24
25 ab_gene_name_for_header={'abc':'geneName'}
26 ab_rrid_for_header={'abc':'rrid123'}
27 line= 'abc,123\n'
28
29 pos= line.find(",")
30 ABname= line[0:pos]
31 ABnewName= ABname+ "|"+ab_gene_name_for_header[ABname]+"|"+ab_rrid_for_header[ABname]
32 line= ABnewName+line[pos:]
33 line= line.replace(',','\t')
34 sys.exit(0)
35 # try:
36 print(' \n starting Test program read params from file stored in tools dir. Arguments=')
37 print(str(sys.argv[1:])+'\n')
38
39 if False:
40 infileName = sys.argv[1]
41 # directory = sys.argv[2]
42 directory = '/Users/bobbrown/Desktop/'
43 outfileName = sys.argv[3] #use later
44 # outfile = sys.argv[6]
45
46 #sys.stdout.write
47
48 # ifile= open(directory+"/"+infileName,'rU')
49 ifile= open(directory+infileName,'rU')
50 ofile= open(directory+outfileName,'w')
51 # ofile= open('/Users/bobbrown/Desktop/TestOutFileVarParams.txt','w')
52
53 cnt= 0
54 # for param in range(2,len(sys.argv)):
55 # cnt +=1
56 # ofile.write("param "+str(cnt)+"= "+param+"\n")
57
58
59 for param in ifile:
60 cnt +=1
61 ofile.write("param "+str(cnt)+"= "+param)
62
63 ifile.close()
64
65 ofile.close()
66
67 print('Fini -- rows read = '+str(cnt)+'\n')
68
69 # except :
70 # print('Error>>> ')
71
72 return
73 ##
74 ##
75
76 if __name__ == '__main__': main()
77 #sys.exit(0)