Report if the Summary.htm file is missing the Lane Results Summary block.

[htsworkflow.git] / htsworkflow / pipelines / summary.py

diff --git a/htsworkflow/pipelines/summary.py b/htsworkflow/pipelines/summary.py
index 72b3e5e058058e8e4715b0c033b314a8b25ff3ef..c5db2bc5e1bb04de24c99704174809a8b9634bac 100644 (file)
--- a/htsworkflow/pipelines/summary.py
+++ b/htsworkflow/pipelines/summary.py
@@ -1,11 +1,15 @@
 """
 Analyze the Summary.htm file produced by GERALD
 """
+import logging
 import types
+from pprint import pprint
 
 from htsworkflow.pipelines.runfolder import ElementTree
 from htsworkflow.util.ethelp import indent, flatten
 
+nan = float('nan')
+
 class Summary(object):
     """
     Extract some useful information from the Summary.htm file
@@ -51,7 +55,7 @@ class Summary(object):
 
         def set_elements_from_html(self, data):
             if not len(data) in (8,10):
-                raise RuntimeError("Summary.htm file format changed")
+                raise RuntimeError("Summary.htm file format changed, len(data)=%d" % (len(data),))
 
             # same in pre-0.3.0 Summary file and 0.3 summary file
             self.lane = int(data[0])
@@ -183,6 +187,8 @@ class Summary(object):
         for name, end in table_names:
           if tables.has_key(name):
             self._extract_lane_results_for_end(tables, name, end)
+        else:
+            logging.warning("No Lane Results Summary Found in %s" % (pathname,))
 
     def _extract_lane_results_for_end(self, tables, table_name, end):
         """
@@ -197,8 +203,9 @@ class Summary(object):
             # grab the lane by lane data
             lane_summary = lane_summary[1:]
 
-        # this is version 2 of the summary file
-        if len(lane_summary[-1]) == 10:
+        # len(lane_summary[-1] = 10 is version 2 of the summary file
+        #                      = 9  is version 3 of the Summary.htm file
+        elif len(lane_summary[-1]) in (9, 10):
             # lane_summary[0] is a different less specific header row
             headers = lane_summary[1]
             lane_summary = lane_summary[2:10]
@@ -230,7 +237,6 @@ class Summary(object):
         for element in list(tree):
             lrs = Summary.LaneResultSummary()
             lrs.set_elements(element)
-            print lrs.end, lrs.lane
             if len(self.lane_results) < (lrs.end + 1):
               self.lane_results.append({})
             self.lane_results[lrs.end][lrs.lane] = lrs
@@ -259,9 +265,16 @@ def parse_mean_range(value):
     Parse values like 123 +/- 4.5
     """
     if value.strip() == 'unknown':
-        return 0, 0
+        return nan, nan
+
+    values = value.split()
+    if len(values) == 1:
+        if values[0] == '+/-':
+            return nan,nan
+        else:
+            return tonumber(values[0])
 
-    average, pm, deviation = value.split()
+    average, pm, deviation = values
     if pm != '+/-':
         raise RuntimeError("Summary.htm file format changed")
     return tonumber(average), tonumber(deviation)