Toggle navigation
Toggle navigation
This project
Loading...
Sign in
Louis BECQUEY
/
biorseo
Go to a project
Toggle navigation
Toggle navigation pinning
Projects
Groups
Snippets
Help
Project
Activity
Repository
Pipelines
Graphs
Issues
0
Merge Requests
0
Network
Create a new issue
Builds
Commits
Authored by
Louis BECQUEY
2019-06-17 16:24:30 +0200
Browse Files
Options
Browse Files
Download
Plain Diff
Commit
720602576982d5fa19ed03e99769ef4a153edb05
72060257
2 parents
2e2ec263
73734e9d
Merge branch 'master' of
https://github.com/persalteas/biominserter
Expand all
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
3 additions
and
3 deletions
biorseo.py
test_on_RNAstrand.py
biorseo.py
View file @
7206025
...
...
@@ -549,7 +549,7 @@ class BiorseoInstance:
cmd
=
[
"java"
,
"-jar"
,
jar3dexec
,
filename
,
ILmotifDir
+
"/all.txt"
,
loop
.
header
[
1
:]
+
".ILloop.csv"
,
loop
.
header
[
1
:]
+
".ILseq.csv"
]
nowhere
=
open
(
devnull
,
'w'
)
logfile
=
open
(
"
log_of_the_run.sh"
,
'a'
)
logfile
=
open
(
biorseoDir
+
"/
log_of_the_run.sh"
,
'a'
)
logfile
.
write
(
' '
.
join
(
cmd
))
logfile
.
write
(
"
\n
"
)
logfile
.
close
()
...
...
@@ -789,7 +789,7 @@ class BiorseoInstance:
if
c
==
0
:
seq
=
l
[:
-
1
]
.
upper
()
if
is_canonical_nts
(
seq
):
header
=
header
.
replace
(
'/'
,
'_'
)
.
replace
(
'
\'
'
,
''
)
.
replace
(
'('
,
''
)
.
replace
(
')'
,
''
)
header
=
header
.
replace
(
'/'
,
'_'
)
.
replace
(
'
\'
'
,
''
)
.
replace
(
'('
,
''
)
.
replace
(
')'
,
''
)
.
replace
(
' '
,
'_'
)
RNAcontainer
.
append
(
RNA
(
header
,
seq
))
if
not
path
.
isfile
(
self
.
outputf
+
header
+
".fa"
):
rna
=
open
(
self
.
outputf
+
header
+
".fa"
,
"w"
)
...
...
@@ -845,4 +845,4 @@ class BiorseoInstance:
self
.
joblist
.
append
(
Job
(
command
=
command
,
priority
=
priority
,
timeout
=
3600
,
how_many_in_parallel
=
3
))
BiorseoInstance
(
opts
)
BiorseoInstance
(
opts
)
\ No newline at end of file
...
...
test_on_RNAstrand.py
View file @
7206025
This diff is collapsed. Click to expand it.
Please
register
or
login
to post a comment