diff extractCN.py @ 5:b7f3854e08f8

Adding all tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractCN.py	Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,78 @@
+import os
+import sys
+import subprocess
+import getopt
+
+def main(argv):
+    
+    symmetrize="False"
+    
+    try:
+        opts, args = getopt.getopt(argv,"hc:i:o:f:s:y:t:p:l:g:n:u:",["chrom=","input=","output=","new_file_path=","settings_type=","settings_tumor=","symmetrize=","outputlog=","log=","settings_signal=","settings_snp=","userid="])
+    except getopt.GetoptError as err:
+        print str(err)
+        sys.exit(2)
+    for opt, arg in opts:
+        if opt == '-h':
+            print 'extractCN.py'
+            sys.exit()
+        elif opt in ("-c", "--chrom"):
+            chromosome = arg
+        elif opt in ("-i", "--input"):
+            input_file = arg
+        elif opt in ("-o", "--output"):
+            output_file = arg
+        elif opt in ("-f", "--new_file_path"):
+            tmp_dir = arg
+        elif opt in ("-s", "--settings_type"):
+            input_type = arg
+        elif opt in ("-t", "--settings_tumor"):
+            settings_tumor = arg
+        elif opt in ("-y", "--symmetrize"):
+            symmetrize = arg
+        elif opt in ("-p", "--outputlog"):
+            outputlog = arg
+        elif opt in ("-l", "--log"):
+            log = arg
+        elif opt in ("-g", "--settings_signal"):
+            signal = arg
+        elif opt in ("-n", "--settings_snp"):
+            snp = arg
+        elif opt in ("-u", "--userid"):
+            user_id = arg
+        
+            
+      
+    #===========================================================================
+    #chromosome=sys.argv[1]
+    #input_file=sys.argv[2]
+    # output_file=sys.argv[3]
+    # tmp_dir=sys.argv[4]
+    # input_type=sys.argv[5]
+    # settings_tumor=sys.argv[6]
+    # outputlog=sys.argv[7]
+    # log=sys.argv[8]
+    # signal=sys.argv[9]
+    # snp=sys.argv[10]
+    # user_id=sys.argv[11]
+    #===========================================================================
+    script_dir=os.path.dirname(os.path.abspath(__file__))
+    
+    iFile=open(input_file,'r')
+    dataSetLine=iFile.readline()
+    dataset=dataSetLine.split("\t")[1]
+    iFile.close()
+    
+    if (outputlog=="TRUE"):
+        errfile=open(log,'w')
+    else:
+        errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
+    
+    retcode=subprocess.call(["Rscript", os.path.join(script_dir,"extractCN.R"), chromosome, dataset, output_file, tmp_dir, input_type, settings_tumor, signal,snp,user_id, symmetrize], stdout = errfile, stderr = errfile)
+    
+    errfile.close()
+     
+    sys.exit(retcode)
+
+if __name__ == "__main__":
+    main(main(sys.argv[1:]))