Changeset 1586:4e44d29377e3

Timestamp:

10/30/08 14:46:57 (2 months ago)

Author:

Dan Blankenberg <dan@bx.psu.edu>

branch:

default

Message:

Annotation profiler: Better handling of the case where regions extend beyond known chromosome boundaries.

Files:

• tools/annotation_profiler/annotation_profiler_for_interval.py (modified) (2 diffs)

tools/annotation_profiler/annotation_profiler_for_interval.py

@@ -123 +123 @@
-        self.table_regions_overlaped_count = {} #total number of table regions overlaping user's input intervals (non unique)
-        self.interval_table_overlap_count = {} #total number of user input intervals which overlap table
+        self.region_size_errors = {} #dictionary of lists of invalid ranges by chromosome
-    def add_region( self, chrom, start, end ):
-
+
+
+
+
+
+
+
+
+
+
+
+
-        self.total_interval_count += 1
-        if chrom not in self.chromosome_coverage:
-
-
-
+
+
+
+
-            if table_name not in self.table_coverage:
-                self.table_coverage[table_name] = 0
@@ -215 +228 @@
-            out.write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( table_name, table_chromosome_size, table_chromosome_count, table_region_coverage, table_region_count, total_interval_count, total_interval_size, total_coverage, table_regions_overlaped_count, interval_region_overlap_count, nr_interval_count, nr_interval_size, nr_coverage, nr_table_regions_overlaped_count, nr_interval_table_overlap_count ) )
-    out.close()
+    
+    #report chrom size errors as needed:
+    if table_coverage_summary.region_size_errors:
+        print "Regions provided extended beyond known chromosome lengths, and have been truncated as necessary, for the following intervals:"
+        for chrom, regions in table_coverage_summary.region_size_errors.items():
+            if len( regions ) > 3:
+                extra_region_info = ", ... "
+            else:
+                extra_region_info = ""
+            print "%s has max length of %s, exceeded by %s%s." % ( chrom, chrom_lengths.get( chrom ), ", ".join( map( str, regions[:3] ) ), extra_region_info )
-
-class ChromosomeLengths: