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 16:19:44 +0200
Browse Files
Options
Browse Files
Download
Email Patches
Plain Diff
Commit
30b097cb626921b5ae4b7af7dcfd41bcb931b95a
30b097cb
1 parent
0a4f545c
header problems solved
Show whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
2 additions
and
2 deletions
biorseo.py
biorseo.py
View file @
30b097c
...
...
@@ -502,7 +502,7 @@ 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
()
...
...
@@ -742,7 +742,7 @@ 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"
)
...
...
Please
register
or
login
to post a comment