Updated per-read report.

nanoporetech · Nov 14, 2019 · f998fe4 · f998fe4
1 parent 86b1e1d
commit f998fe4
Showing 1 changed file with 4 additions and 6 deletions.
diff --git a/scripts/cdna_classifier.py b/scripts/cdna_classifier.py
@@ -79,23 +79,21 @@ def _update_stats(st, d_fh,  segments, hits, usable_len, read):
         st["Classification"]["Unclassified"] += 1
         st["UnclassHitNr"][len(hits)] += 1
         if d_fh is not None:
-            d_fh.write("{}\t{}\t{}\t{}\t{}\n".format(read.Id, ".", ".", ".", "."))
+            d_fh.write("{}\t{}\t0\t{}\t{}\t{}\n".format(read.Id, len(read.Seq), -1, -1, "."))
     elif len(segments) == 1:
         st["Classification"]["Classified"] += 1
         st["Strand"][segments[0].Strand] += 1
         st["Unusable"][int(segments[0].Len / len(read.Seq) * 100)] += 1
         if d_fh is not None:
             rs = segments[0]
-            sr_id = "{}:{}|{}".format(rs.Start, rs.End, read.Id)
-            d_fh.write("{}\t{}\t{}\t{}\t{}\n".format(read.Id, sr_id, rs.Start, rs.End, rs.Strand))
+            d_fh.write("{}\t{}\t1\t{}\t{}\t{}\n".format(read.Id, len(read.Seq), rs.Start, rs.End, rs.Strand))
     else:
         for rs in segments:
             st["Classification"]["Rescue"] += 1
             st["RescueStrand"][rs.Strand] += 1
             st["RescueHitNr"][len(hits)] += 1
             if d_fh is not None:
-                sr_id = "{}:{}|{}".format(rs.Start, rs.End, read.Id)
-                d_fh.write("{}\t{}\t{}\t{}\t{}\n".format(read.Id, sr_id, rs.Start, rs.End, rs.Strand))
+                d_fh.write("{}\t{}\t{}\t{}\t{}\t{}\n".format(read.Id, len(read.Seq), len(segments), rs.Start, rs.End, rs.Strand))
         st["Unusable"][len(read.Seq) - int(sum([s.Len for s in segments]))] += 1
         st["RescueSegmentNr"][len(segments)] += 1
 
@@ -228,7 +226,7 @@ def _plot_stats(st, pdf):
     d_fh = None
     if args.D is not None:
         d_fh = open(args.D, "w")
-        d_fh.write("Read\tSegment\tStart\tEnd\tStrand\n")
+        d_fh.write("Read\tLength\tClassified\tStart\tEnd\tStrand\n")
 
     st = _new_stats()
     input_size = None