diff validator.py @ 2:cf258ca024ff draft

planemo upload commit ca69686dfafcabb815c93fd46d3c4dfe57459e39-dirty

--- a/validator.py	Mon Dec 19 13:21:56 2016 -0500
+++ b/validator.py	Mon Dec 19 14:49:37 2016 -0500
@@ -7,6 +7,7 @@
 def checkAndFixBed(bedfile, revised_file):
 # Store the lines that have been removed
     removedLines = []
+    scoreLines = []
 # Remove the lines with invalid strand, create a score column to store the original scores and change scores in the original score column all to 1000
     with open(revised_file, 'w') as tmp:
         with open(bedfile, 'r') as f:
@@ -16,8 +17,9 @@
                 fields = line.split()
                 strand = fields[5]
                 score = fields[4]
-                fields[4] = '1000'  
-                fields.append(score)
+                if (int(fields[4]) > 1000):
+                    scoreLines.append("line" + str(i) + ":" + line) 
+                    fields[4] = '1000' 
                 if (strand == '+' or strand == '-'):
                     tmp.write('\t'.join(map(str, fields)))
                     tmp.write("\n")
@@ -25,15 +27,18 @@
                     removedLines.append("line" + str(i) + ": " + line)
                 i = i+1
 
-    return removedLines 
+    return removedLines, scoreLines 
 
 def main():
     inputfile = str(sys.argv[1])
     outputfile = str(sys.argv[2])
-    removed = checkAndFixBed(inputfile, outputfile)
+    removed, changed = checkAndFixBed(inputfile, outputfile)
     if (removed != []):
         print "\nRemoved invalid lines: \n"
         print "\n".join(removed)
+    if (changed != []):
+        print "\nThe following lines have scores > 1000, so they are changed to 1000:\n"
+        print "\n".join(changed)
 
 if __name__ == "__main__":
     main()