Commit d362d5b3 authored by Koehorst, Jasper's avatar Koehorst, Jasper
Browse files

output check for existence

parent ca720fc3
......@@ -44,18 +44,21 @@ def run_command(command):
return result.stdout.decode('ascii')
def conversion(identifier):
if os.path.isfile("./genome/" + identifier + "/" + identifier + ".conversion.ttl"): return
# "-tool", "conversion", "-f", fasta.getAbsolutePath(), "-gff2rdf", "-i", gff.getAbsolutePath(), "-o", output.getAbsolutePath(), "-id", "MGYG-HGUT-00001", "-codon", "11", "-topology", "linear"
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)
os.system(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";
if os.path.isfile("./genome/" + identifier + "/" + identifier + ".interproscan.ttl"): return
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)
os.system(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 -v v2-db5.0";
if os.path.isfile("./genome/" + identifier + "/" + identifier + ".interproscan.eggnog.ttl"): return
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 -v v2-db5.0"
print(command)
os.system(command)
......
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