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MGnify
Commits
ca720fc3
Commit
ca720fc3
authored
Jun 07, 2021
by
Koehorst, Jasper
Browse files
command execute enabled
parent
db4e58f0
Changes
1
Hide whitespace changes
Inline
Side-by-side
run.py
View file @
ca720fc3
...
...
@@ -47,17 +47,17 @@ def conversion(identifier):
# "-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)
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"
;
print
(
command
)
#
os.system(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"
;
print
(
command
)
#
os.system(command)
os
.
system
(
command
)
if
__name__
==
"__main__"
:
for
line
in
open
(
"identifiers.tsv"
):
...
...
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