diff segcall.py @ 5:b7f3854e08f8

Adding all tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segcall.py	Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,62 @@
+import os
+import sys
+import subprocess
+import zipfile
+
+
+def main():
+
+    input_file=sys.argv[2]
+    tmp_dir=sys.argv[4]
+    settingsType=sys.argv[6]
+    zip_file=sys.argv[9]
+    tumorcsv=sys.argv[10]
+    cellularity=sys.argv[11]
+    outputlog=sys.argv[12]
+    log=sys.argv[13]
+    user=sys.argv[14]
+    method=sys.argv[15]
+    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 settingsType=="dataset":
+        settingsType=dataset
+
+    if (outputlog=="TRUE"):
+        errfile=open(log,'w')
+    else:
+        errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
+    
+    fig_dir=os.path.join("mpagenomics",user,"figures",dataset,"segmentation/CN")
+
+    abs_fig_dir=os.path.join(tmp_dir,fig_dir)
+    if (os.path.isdir(abs_fig_dir)) and (sys.argv[7]=="TRUE"):
+        old_files=os.listdir(abs_fig_dir)
+        for ifile in old_files:
+            os.remove(os.path.join(abs_fig_dir,ifile))
+           
+        
+    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)
+    
+    errfile.close()
+     
+    if (retcode == 0):
+        if (os.path.isdir(abs_fig_dir)) and (sys.argv[7]=="TRUE"):
+        
+            new_files=os.listdir(abs_fig_dir)
+            zipbuf = zipfile.ZipFile(os.path.join(abs_fig_dir,zip_file), 'w', zipfile.ZIP_DEFLATED)
+            for current_file in new_files:
+                fn = os.path.join(abs_fig_dir,current_file)
+                relfn=fn[len(abs_fig_dir)+len(os.sep):]
+                zipbuf.write(fn,relfn)
+        sys.exit(retcode)
+    else:
+        sys.exit(retcode)
+
+if __name__ == "__main__":
+    main()