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Beatrice Tan
CNAprioritization
Commits
80b3c845
Commit
80b3c845
authored
Feb 07, 2018
by
Beatrice Tan
Browse files
Updated wrappers.
parent
6869823f
Changes
2
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Inline
Side-by-side
wrappers/GISTIC2/wrapper.py
View file @
80b3c845
...
...
@@ -10,7 +10,7 @@ from snakemake.shell import shell
segments
=
os
.
path
.
abspath
(
snakemake
.
input
.
seg
)
gistic_dir
=
os
.
path
.
abspath
(
snakemake
.
input
.
gistic_directory
).
split
(
"/gistic2"
)[
0
]
outfolder
=
os
.
path
.
abspath
(
snakemake
.
output
[
0
]).
split
(
"all_lesions"
)[
0
]
print
(
outfolder
)
#Select reference file
ref
=
snakemake
.
params
.
get
(
"ref"
,
""
)
ref_file
=
snakemake
.
params
.
get
(
"ref_file"
,
""
)
...
...
@@ -27,10 +27,11 @@ if cnv_file != "":
cnv_arg
=
" --cnv "
+
cnv_file
if
os
.
stat
(
cnv_file
).
st_size
!=
0
else
" "
else
:
cnv_arg
=
" "
print
(
cnv_arg
)
#Additional arguments
extra
=
snakemake
.
params
.
get
(
"extra"
,
""
)
if
snakemake
.
params
.
confidence
!=
""
:
extra
+=
"-conf 0."
+
snakemake
.
params
.
confidence
#Make output directory, go to gistic2 directory and run gistic2
command
=
"./gistic2 -b "
+
outfolder
+
" -seg "
+
segments
+
" -refgene "
+
reference
+
cnv_arg
+
extra
...
...
wrappers/topgo/wrapper.R
View file @
80b3c845
...
...
@@ -43,7 +43,7 @@ resultWeight <- getSigGroups(GOdata, test.stat)
allRes
<-
GenTable
(
GOdata
,
classic
=
resultFisher
,
#KS = resultKS,
weight
=
resultWeight
,
orderBy
=
"weight"
,
ranksOf
=
"classic"
,
topNodes
=
50
)
orderBy
=
"weight"
,
ranksOf
=
"classic"
)
#
, topNodes = 50)
print
(
allRes
)
write.table
(
allRes
,
file
=
snakemake
@
output
[[
1
]],
quote
=
FALSE
,
sep
=
"\t"
,
eol
=
"\n"
)
...
...
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