Fixes to various tools: scatterplot, cor, grouping

tools/plotting/scatterplot.py

@@ -6,7 +6,7 @@ from rpy import *
 
 def fail( message ):
     print >> sys.stderr, message
-    return -1
+    sys.exit()
 
 def main():
 
@@ -20,30 +20,59 @@ def main():
     ylab = sys.argv[7]
 
     matrix = []
-    for i, line in enumerate( open( sys.argv[1] ) ):
-        # Skip comments
-        if line.startswith( '#' ): 
-            continue
-        # Extract values and convert to floats
-        row = []
-        for column in columns:
-            fields = line.split( "\t" )
-            if len( fields ) <= column:
-                return fail( "No column %d on line %d" % ( column+1, i ) )
-            val = fields[column]
-            if val.lower() == "na": 
-                row.append( float( "nan" ) )
-            else:
-                try:
-                    row.append( float( fields[column] ) )
-                except ValueError:
-                    return fail( "Value '%s' in column %d on line %d is not numeric" % ( fields[column], column+1, i ) )
-        matrix.append( row )
+    skipped_lines = 0
+    first_invalid_line = 0
+    invalid_value = ''
+    invalid_column = 0
+
+    for i, line in enumerate( file ( sys.argv[1] ) ):
+        valid = True
+        line = line.rstrip('\r\n')
+        if line and not line.startswith( '#' ): 
+            # Extract values and convert to floats
+            row = []
+            for column in columns:
+                if not valid:
+                    break
+                fields = line.split( "\t" )
+                if len( fields ) <= column:
+                    return fail( "Column %d on line %d missing, line: %s" % ( column+1, i, line ) )
+                val = fields[column]
+                if val.lower() == "na": 
+                    row.append( float( "nan" ) )
+                else:
+                    try:
+                        row.append( float( fields[column] ) )
+                    except:
+                        valid = False
+                        skipped_lines += 1
+                        if not first_invalid_line:
+                            first_invalid_line = i+1
+                            invalid_value = fields[column]
+                            invalid_column = column+1
+        else:
+            valid = False
+            skipped_lines += 1
+            if not first_invalid_line:
+                first_invalid_line = i+1
+
+        if valid:
+            matrix.append( row )
         
     r.pdf( out_fname, 8, 8 )
     r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
     r.dev_off()
+
+    msg = "--Scatter plot on "
+    for i,col in enumerate(columns):
+        col += 1
+        msg += "c%d, " %col
+    if skipped_lines > 0:
+        msg += " skipped %d lines starting with line #%d.  Value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column )
+
+    print msg
+
     r.quit( save="no" )
-    
+
 if __name__ == "__main__":
     main()