Commit 1075a48e authored by Koehorst, Jasper's avatar Koehorst, Jasper
Browse files

run commands added

parent 17706d86
......@@ -48,10 +48,20 @@ def conversion(identifier):
command = "java -jar ./MGnifyParser.jar -tool conversion -f ./genome/" + identifier + "/" + identifier + ".fna -gff2rdf -i ./genome/" + identifier + "/" + identifier + ".gff -id " + identifier + " -codon 11 -topology linear -o ./genome/" + identifier + "/" + identifier + ".conversion.ttl"
print(command)
def interproscan(identifier):
command = "java -jar ./MGnifyParser.jar -tool interpro -i ./genome/" + identifier + "/" + identifier + ".conversion.ttl -o ./genome/" + identifier + "/" + identifier + ".interproscan.ttl -tsv ./genome/" +identifier +"/" + identifier + "_InterProScan.tsv -version InterProScan-v5_35-74_0";
print(command)
def eggnog(identifier):
command = "java -jar ./MGnifyParser.jar -tool eggnog -i ./genome/" + identifier + "/" + identifier + ".interproscan.ttl -o ./genome/" + identifier + "/" + identifier + ".interproscan.eggnog.ttl -tsv ./genome/" +identifier +"/" + identifier + "_eggNOG.tsv";
print(command)
if __name__ == "__main__":
for line in open("identifiers.tsv"):
identifier = line.strip().split("\t")[1]
accession = line.strip().split("\t")[2]
if (identifier.startswith("MGYG")):
retrieval(identifier, accession)
conversion(identifier)
\ No newline at end of file
conversion(identifier)
interproscan(identifier)
eggnog(identifier)
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