Commit 887d7415 authored by Jasper Koehorst's avatar Jasper Koehorst
Browse files
parents 457db65e e2ce5013
genome
xml
*.gff
MGnifyParser/build
MGnifyParser/gradle
GPs/pygenprop/__pycache__
MGnifyParser/src/test/resources/output
MGnifyParser/.gradle
MGnifyParser/.idea
.DS_Store
GPs/__pycache__
GPs/pygenprop/__pycache__
GPs/pygenprop/dump/__pycache__
GPs/pygenprop/dump
>>>>>>> e29354cfbd7fdfb2bf03a64260bf3422344b5e80
......@@ -38,4 +38,5 @@ for f in onlyfiles:
assignment = parse_interproscan_file(inputFile)
results = GenomePropertiesResults(assignment, properties_tree=tree)
outFileName = "results/" + f.replace(".tsv", ".csv")
results.property_results.to_csv(outFileName)
\ No newline at end of file
results.property_results.to_csv(outFileName)
# Parse output file and add description?
\ No newline at end of file
......@@ -102,13 +102,15 @@ if __name__ == "__main__":
identifiers = set()
for line in open("identifiers.tsv"):
if "MGYG" not in line: continue
identifier = line.strip().split("\t")[1]
accession = line.strip().split("\t")[2]
if (identifier.startswith("MGYG")):
retrieval(identifier, accession)
identifiers.add(identifier)
conversion_stage(identifier)
# break
# Number of cores
# num_cores = 3 # multiprocessing.cpu_count()
# results = Parallel(n_jobs=num_cores)(delayed(conversion_stage)(identifier) for identifier in identifiers)
if "MGYG-HGUT-03178" in line or "MGYG-HGUT-00360" in line:
print(line)
identifier = line.strip().split("\t")[1]
accession = line.strip().split("\t")[2]
if (identifier.startswith("MGYG")):
retrieval(identifier, accession)
identifiers.add(identifier)
conversion_stage(identifier)
# break
# Number of cores
# num_cores = 3 # multiprocessing.cpu_count()
# results = Parallel(n_jobs=num_cores)(delayed(conversion_stage)(identifier) for identifier in identifiers)
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