from django.template import Context
import StringIO
+import logging
+import os
#from django.db.models import base
+LANE_LIST = [1,2,3,4,5,6,7,8]
+
+def create_library_list():
+ """
+ Create a list of libraries that includes how many lanes were run
+ """
+ library_list = []
+ for lib in Library.objects.all():
+ summary = {}
+ summary['library_id'] = lib.library_id
+ summary['library_name'] = lib.library_name
+ summary['species_name' ] = lib.library_species.scientific_name
+ lanes_run = 0
+ for lane_id in LANE_LIST:
+ lane = getattr(lib, 'lane_%d_library' % (lane_id,))
+ lanes_run += len( lane.all() )
+ summary['lanes_run'] = lanes_run
+ library_list.append(summary)
+ return library_list
def library(request):
- library_list = Library.objects.all() #.order_by('-pub_date')
- rep_string = '<a href="/library/%s/">%s - %s (%s)</a>'
- output = '<br />\n'.join([rep_string \
- % (l.library_id,
- l.library_id,
- l.library_name,
- l.library_species.scientific_name) for l in library_list])
- return HttpResponse(output)
+ library_list = create_library_list()
+ t = get_template('library.html')
+ c = Context({'library_list': library_list })
+ return HttpResponse( t.render(c) )
def library_to_flowcells(request, lib_id):
"""
flowcell_list.extend([ (fc.flowcell_id, 8) for fc in lib.lane_8_library.all() ])
flowcell_list.sort()
- output.append('<br />')
-
- data_dict_list = []
+ lane_summary_list = []
for fc, lane in flowcell_list:
- dicts, err_list, summary_list = _summary_stats(fc, lane)
+ lane_summary, err_list = _summary_stats(fc, lane)
- data_dict_list.extend(dicts)
+ lane_summary_list.extend(lane_summary)
for err in err_list:
output.append(err)
-
- for summary in summary_list:
- output.append(summary.replace('\n', '<br />\n'))
- html = t.render(Context({'data_dict_list': data_dict_list}))
- output.append('<br />')
- output.append('<br />')
- output.append(html)
+
+ logging.error("len lane summary %d" % (len(lane_summary_list)))
output.append('<br />')
+ output.append(t.render(Context({'lane_summary_list': lane_summary_list})))
output.append('<br />')
if record_count == 0:
return HttpResponse(bedgen, mimetype="application/x-bedfile")
-def _summary_stats(flowcell_id, lane):
+def _summary_stats(flowcell_id, lane_id):
+ """
+ Return the summary statistics for a given flowcell, lane, and end.
+ """
+ fc_id = flowcellIdStrip(flowcell_id)
+ fc_result_dict = get_flowcell_result_dict(fc_id)
+
+ summary_list = []
+ err_list = []
+
+ if fc_result_dict is None:
+ err_list.append('Results for Flowcell %s not found.' % (fc_id))
+ return (summary_list, err_list)
+
+ for cycle_width in fc_result_dict:
+ xmlpath = fc_result_dict[cycle_width]['run_xml']
+
+ if xmlpath is None:
+ err_list.append('Run xml for Flowcell %s(%s) not found.' % (fc_id, cnm))
+ continue
+
+ tree = ElementTree.parse(xmlpath).getroot()
+ try:
+ runs = runfolder.PipelineRun(pathname='', xml=tree)
+ gerald_summary = runs.gerald.summary.lane_results
+ for end in range(len(gerald_summary)):
+ eland_summary = runs.gerald.eland_results.results[end][lane_id]
+ # add information to lane_summary
+ eland_summary.flowcell_id = flowcell_id
+ eland_summary.clusters = gerald_summary[end][lane_id].cluster
+ eland_summary.cycle_width = cycle_width
+ eland_summary.summarized_reads = runfolder.summarize_mapped_reads(eland_summary.mapped_reads)
+ summary_list.append(eland_summary)
+
+ except Exception, e:
+ summary_list.append("Summary report needs to be updated.")
+ logging.error("Exception: " + str(e))
+
+ return (summary_list, err_list)
+
+def _summary_stats_old(flowcell_id, lane):
"""
return a dictionary of summary stats for a given flowcell_id & lane.
"""
tree = ElementTree.parse(xmlpath).getroot()
results = runfolder.PipelineRun(pathname='', xml=tree)
try:
- summary_list.append(runfolder.summary_report([results]))
- except:
+ lane_report = runfolder.summarize_lane(results.gerald, lane)
+ summary_list.append(os.linesep.join(lane_report))
+ except Exception, e:
summary_list.append("Summary report needs to be updated.")
-
+ logging.error("Exception: " + str(e))
+
+ print "----------------------------------"
+ print "-- DOES NOT SUPPORT PAIRED END ---"
+ print "----------------------------------"
lane_results = results.gerald.summary[0][lane]
lrs = lane_results
return ''
return '(' + '|'.join(output) + ')'
-
+
return self._match_codes
match_codes = property(_get_match_codes)
+ def _get_no_match(self):
+ if self._mapped_reads is None:
+ self._update()
+ return self._match_codes['NM']
+ no_match = property(_get_no_match,
+ doc="total reads that didn't match the target genome.")
+
+ def _get_no_match_percent(self):
+ return float(self.no_match)/self.reads * 100
+ no_match_percent = property(_get_no_match_percent,
+ doc="no match reads as percent of total")
+
+ def _get_qc_failed(self):
+ if self._mapped_reads is None:
+ self._update()
+ return self._match_codes['QC']
+ qc_failed = property(_get_qc_failed,
+ doc="total reads that didn't match the target genome.")
+
+ def _get_qc_failed_percent(self):
+ return float(self.qc_failed)/self.reads * 100
+ qc_failed_percent = property(_get_qc_failed_percent,
+ doc="QC failed reads as percent of total")
+
+ def _get_unique_reads(self):
+ if self._mapped_reads is None:
+ self._update()
+ sum = 0
+ for code in ['U0','U1','U2']:
+ sum += self._match_codes[code]
+ return sum
+ unique_reads = property(_get_unique_reads,
+ doc="total unique reads")
+
+ def _get_repeat_reads(self):
+ if self._mapped_reads is None:
+ self._update()
+ sum = 0
+ for code in ['R0','R1','R2']:
+ sum += self._match_codes[code]
+ return sum
+ repeat_reads = property(_get_repeat_reads,
+ doc="total repeat reads")
+
def get_elements(self):
lane = ElementTree.Element(ElandLane.LANE,
{'version':
+<hr/>
+<br/>
+<style type="text/css">
+ /* <![CDATA[ */
+ table, td {
+ border-style: solid;
+ }
+ table {
+ border-width: 0 0 1px 1px;
+ border-spacing: 0;
+ border-collapse: collapse;
+ }
+ td {
+ margin: 0;
+ padding: 4px;
+ border-width: 1px 1px 0 0;
+ }
+ thead {
+ text-align: center;
+ }
+ tbody {
+ text-align: right;
+ }
+ /* ]]> */
+</style>
{% block summary_stats %}
+<table>
+ <thead>
+ <tr>
+ <td colspan="6"></td>
+ <td colspan="2">No Match</td>
+ <td colspan="2">QC Failed</td>
+ <td colspan="4">Unique</td>
+ <td colspan="4">Repeat</td>
+ </tr>
+ <tr>
+ <td>Cycles</td>
+ <td>Flowcell</td>
+ <td>Lane</td>
+ <td>End</td>
+ <td>Clusters</td>
+ <td>Raw Reads</td>
+ <td>total</td>
+ <td>%</td>
+ <td>total</td>
+ <td>%</td>
+ <td>Total</td>
+ <td>0 mismatch</td>
+ <td>1 mismatch</td>
+ <td>2 mismatch</td>
+ <td>Total</td>
+ <td>0 mismatch</td>
+ <td>1 mismatch</td>
+ <td>2 mismatch</td>
+ </tr>
+ </thead>
+ <tbody>
-<table border="1">
-{% for d in data_dict_list %}
- {# Header row for table #}
- {% if forloop.first %}
- <tr>
- {% for key, value in d.items %}
- <td><b>{{ key }}</b></td>
- {% endfor %}
- </tr>
- {% endif %}
- {# Main contents of table #}
+ {% for lane in lane_summary_list %}
<tr>
- {% for key, value in d.items %}
- <td>{{ value }}</td>
- {% endfor %}
+ <td>{{ lane.cycle_width }}</td>
+ <td>{{ lane.flowcell_id }}</td>
+ <td>{{ lane.lane_id }}</td>
+ <td>{% if lane.end %}{{ lane.end }}{% endif %}</td>
+ <td>{{ lane.clusters.0 }} ± {{ lane.clusters.1 }}</td>
+ <td>{{ lane.reads }}</td>
+ <td>{{ lane.no_match }}</td>
+ <td>{{ lane.no_match_percent|stringformat:".2f" }}</td>
+ <td>{{ lane.qc_failed }}</td>
+ <td>{{ lane.qc_failed_percent|stringformat:".2f" }}</td>
+ <td>{{ lane.unique_reads }}</td>
+ <td>{{ lane.match_codes.U0 }}</td>
+ <td>{{ lane.match_codes.U1 }}</td>
+ <td>{{ lane.match_codes.U2 }}</td>
+ <td>{{ lane.repeat_reads }}</td>
+ <td>{{ lane.match_codes.R0 }}</td>
+ <td>{{ lane.match_codes.R1 }}</td>
+ <td>{{ lane.match_codes.R2 }}</td>
</tr>
-{% endfor %}
+ {% endfor %}
+ </tbody>
</table>
-
+<br/>
+<hr/>
+{% for lane in lane_summary_list %}
+<h2>{{lane.cycle_width}} {{ lane.flowcell_id }} {{ lane.lane_id }} {{ lane.end }}</h2>
+ <ul>
+ {% for name, counts in lane.summarized_reads.items %}
+ <li><b>{{ name }}</b>: {{ counts }}</li>
+ {% endfor %}
+ </ul>
+{% endfor %}
{% endblock %}
projects / htsworkflow.git / commitdiff