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Don't die if Summary.htm isn't present
author
Diane Trout
<diane@caltech.edu>
Fri, 28 Mar 2008 23:32:12 +0000
(23:32 +0000)
committer
Diane Trout
<diane@caltech.edu>
Fri, 28 Mar 2008 23:32:12 +0000
(23:32 +0000)
scripts/runfolder.py
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diff --git
a/scripts/runfolder.py
b/scripts/runfolder.py
index 9e45ea8c2ff8e6f23f4d6c13f4d092c9b8cb8033..4a2549aeb869bd623aee0700b1547bf9297c51bc 100644
(file)
--- a/
scripts/runfolder.py
+++ b/
scripts/runfolder.py
@@
-529,8
+529,11
@@
def get_runs(runfolder):
b = Bustard(bustard_pathname)
gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
for gerald_pathname in glob(gerald_glob):
b = Bustard(bustard_pathname)
gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
for gerald_pathname in glob(gerald_glob):
- g = GERALD(gerald_pathname)
- runs.append(PipelineRun(runfolder, f, b, g))
+ try:
+ g = GERALD(gerald_pathname)
+ runs.append(PipelineRun(runfolder, f, b, g))
+ except IOError, e:
+ print "Ignoring", str(e)
return runs
return runs
@@
-565,7
+568,7
@@
def summary_report(runs):
"""
for run in runs:
# print a run name?
"""
for run in runs:
# print a run name?
- logging.info('Summarizing ' + run.name)
+ print 'Summary for', run.name
for lane in run.gerald.summary.lane_results:
print 'lane', lane.lane, 'clusters', lane.cluster[0], '+/-',
print lane.cluster[1]
for lane in run.gerald.summary.lane_results:
print 'lane', lane.lane, 'clusters', lane.cluster[0], '+/-',
print lane.cluster[1]