Commit b3b7108b authored by maxime mano's avatar maxime mano
Browse files

add L50 stats to the analysis

parent f38915c1
......@@ -70,6 +70,7 @@ class Run_stats (Analysis):
if parts[0] == "median_read_length": stats["median_read_length"] = parts[1]
if parts[0] == "mean_read_length": stats["mean_read_length"] = parts[1]
if parts[0] == "N50_read_length": stats["N50_read_length"] = parts[1]
if parts[0] == "L50_read_length": stats["L50_read_length"] = parts[1]
if parts[0] == "median_read_quality": stats["median_read_quality"] = parts[1]
if parts[0] == "mean_read_quality": stats["mean_read_quality"] = parts[1]
if parts[0] == "nb_read_Q>5": stats["nb_read_Q>5"] = parts[1]
......@@ -110,13 +111,14 @@ class Run_stats (Analysis):
group = 'basic'
metrics.append(group)
self._add_result_element("metrics", "headers", ','.join(["nb_reads", "total_bases", "median_read_length", "N50_read_length", "median_yield_per_sec", "nb_actif_channel"]), group)
self._add_result_element("metrics", "headers", ','.join(["nb_reads", "total_bases", "median_read_length", "N50_read_length", "L50_read_length", "median_yield_per_sec", "nb_actif_channel"]), group)
self._add_result_element(sample, "nb_reads", str(stat_info["nb_reads"]),group),
self._add_result_element(sample, "total_bases", str(stat_info["total_bases"]),group),
self._add_result_element(sample, "median_read_length", str(stat_info["median_read_length"]),group),
self._add_result_element(sample, "mean_read_length", str(stat_info["mean_read_length"]),group),
self._add_result_element(sample, "N50_read_length", str(stat_info["N50_read_length"]),group),
self._add_result_element(sample, "L50_read_length", str(stat_info["L50_read_length"]),group),
group = 'quality'
metrics.append(group)
self._add_result_element("metrics", "headers", ','.join(["median_read_quality", "nb_read_Q>5", "nb_read_Q>10", "total_bases_Q>10", "nb_read_Q>15"]), group)
......@@ -165,7 +167,7 @@ class Run_stats (Analysis):
#print (self.sequencing_summary_file)
self.add_shell_execution(self.get_exec_path("Rscript") +" /work/ng6-test/claire/test_ont_qc/graph_albacoresummary.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2',
self.add_shell_execution(self.get_exec_path("Rscript") +" /save/sbsuser/trunk/ont/graph_albacoresummary.R " +' -f '+ '$1' +' --out ' + self.output_directory + " 2> " +' $2',
cmd_format='{EXE} {IN} {OUT}' ,
map=False,
inputs = self.sequencing_summary_file,
......
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