diff segmentFracB.py @ 5:af4f63f27c77 draft

planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 11d660a2de749dae548b2fae0dd81f9f2b2c4b4f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segmentFracB.py	Wed Apr 08 15:34:17 2020 +0000
@@ -0,0 +1,87 @@
+import os
+import sys
+import subprocess
+import zipfile
+import getopt
+
+
+def main(argv):
+       
+    try:
+        opts, args = getopt.getopt(argv,"hc:i:o:f:s:og:fig:t:p:l:u:m:",["chrom=","input=","output=","new_file_path=","settings_type=","output_graph=","zip_figures=","settings_tumor=","outputlog=","log=","userid=","method="])
+    except getopt.GetoptError as err:
+        print str(err)
+        sys.exit(2)
+    for opt, arg in opts:
+        if opt == '-h':
+            print 'extractCNopts.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 ("-og", "--output_graph"):
+            output_graph = arg
+        elif opt in ("-fig", "--zip_figures"):
+            zip_file = arg
+        elif opt in ("-t", "--settings_tumor"):
+            tumorcsv = arg
+        elif opt in ("-p", "--outputlog"):
+            outputlog = arg
+        elif opt in ("-l", "--log"):
+            log = arg
+        elif opt in ("-u", "--userid"):
+            user_id = arg
+        elif opt in ("-m", "--method"):
+            method = arg
+  
+    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 input_type=="dataset":
+        input_type=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_id,"figures",dataset,"segmentation/fracB")
+
+    abs_fig_dir=os.path.join(tmp_dir,fig_dir)
+    if (os.path.isdir(abs_fig_dir)) and (output_graph=="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,"segmentFracB.R"),  chromosome, dataset, output_file, tmp_dir, input_type, output_graph, tumorcsv, user_id, method], stdout = errfile, stderr = errfile)
+    
+    errfile.close()
+     
+    if (retcode == 0):
+        if (os.path.isdir(abs_fig_dir)) and (output_graph=="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(main(sys.argv[1:]))