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fixed issue too many open files #16

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merged 4 commits into from
Mar 14, 2024
Merged

fixed issue too many open files #16

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017a35b
adding table of graphic data
luissian Mar 12, 2024
5f0c415
trying to fix too many opened files
luissian Mar 13, 2024
a7f53ad
Merge branch 'feature/fixing_issues' into develop
luissian Mar 13, 2024
d3d91de
removed pdb tag
luissian Mar 13, 2024
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4 changes: 4 additions & 0 deletions taranis/distance.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,10 @@ def create_matrix(self) -> pd.DataFrame:
stderr.print(f"{e}")
sys.exit(1)

# Close the file handles
mash_distance_result.stdout.close()
mash_distance_result.stderr.close()

out_data = out.decode("UTF-8").split("\n")
allele_names = [item.split("\t")[0] for item in out_data[1:-1]]
# create file in memory to increase speed
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10 changes: 10 additions & 0 deletions taranis/reference_alleles.py
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Expand Up @@ -282,11 +282,21 @@ def stats_graphics(stats_folder: str, cluster_alleles: dict) -> None:
)
heading = "Locus name,cluster number,average,center allele,number of sequences"
summary_file = os.path.join(out_folder, "evaluate_cluster", "cluster_summary.csv")
locus_clustering_file = os.path.join(
out_folder, "evaluate_cluster", "cluster_per_locus.csv"
)
with open(summary_file, "w") as fo:
fo.write(heading + "\n")
fo.write("\n".join(clusters_list) + "\n")

_ = stats_graphics(out_folder, cluster_data_graph)

with open(locus_clustering_file, "w") as fo:
fo.write("number of clusters, number of locus\n")
sorted_clusters = dict(sorted(cluster_data_graph.items()))
for key, value in sorted_clusters.items():
fo.write(str(key) + "," + str(value) + "\n")

if eval_cluster:
heading = "Locus name,cluster number,result,alleles not match in blast,alleles not found in cluster"
eval_file = os.path.join(
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