Update igv_files_to_session.py script

Author: drpatelh

bin/igv_files_to_session.py

@@ -26,6 +26,9 @@
 argParser.add_argument(
     "LIST_FILE", help="Tab-delimited file containing two columns i.e. file_name\tcolour. Header isnt required."
 )
+argParser.add_argument(
+    "REPLACE_FILE", help="Tab-delimited file containing two columns i.e. file_name\treplacement_file_name. Header isnt required."
+)
 argParser.add_argument(
     "GENOME", help="Full path to genome fasta file or shorthand for genome available in IGV e.g. hg19."
 )
@@ -65,10 +68,21 @@ def makedir(path):
 ############################################
 
 
-def igv_files_to_session(XMLOut, ListFile, Genome, PathPrefix=""):
+def igv_files_to_session(XMLOut, ListFile, ReplaceFile, Genome, PathPrefix=""):
 
     makedir(os.path.dirname(XMLOut))
 
+    replaceFileDict = {}
+    fin = open(ReplaceFile, "r")
+    while True:
+        line = fin.readline()
+        if line:
+            ofile, rfile = line.strip().split("\t")
+            replaceFileDict[ofile] = rfile
+        else:
+            break
+            fin.close()
+
     fileList = []
     fin = open(ListFile, "r")
     while True:
@@ -77,10 +91,18 @@ def igv_files_to_session(XMLOut, ListFile, Genome, PathPrefix=""):
             ifile, colour = line.strip().split("\t")
             if len(colour.strip()) == 0:
                 colour = "0,0,178"
+            for ofile,rfile in replaceFileDict.items():
+                if ofile in ifile:
+                    ifile = ifile.replace(ofile, rfile)
             fileList.append((PathPrefix.strip() + ifile, colour))
         else:
             break
-            fout.close()
+            fin.close()
+    
+    fout = open('igv_files.txt', "w")
+    for ifile, colour in fileList:
+        fout.write(ifile + '\n')
+    fout.close()
 
     ## ADD RESOURCES SECTION
     XMLStr = '<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n'
@@ -153,7 +175,7 @@ def igv_files_to_session(XMLOut, ListFile, Genome, PathPrefix=""):
 ############################################
 ############################################
 
-igv_files_to_session(XMLOut=args.XML_OUT, ListFile=args.LIST_FILE, Genome=args.GENOME, PathPrefix=args.PATH_PREFIX)
+igv_files_to_session(XMLOut=args.XML_OUT, ListFile=args.LIST_FILE, ReplaceFile=args.REPLACE_FILE, Genome=args.GENOME, PathPrefix=args.PATH_PREFIX)
 
 ############################################
 ############################################