Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
O
openstructure
Manage
Activity
Members
Code
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Deploy
Releases
Container registry
Model registry
Analyze
Contributor analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
schwede
openstructure
Commits
3bd0466f
Commit
3bd0466f
authored
5 years ago
by
Studer Gabriel
Browse files
Options
Downloads
Patches
Plain Diff
undo temporary depug output for CI investigation
parent
1d7038b8
Branches
Branches containing commit
Tags
Tags containing commit
No related merge requests found
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
modules/bindings/pymod/hhblits.py
+0
-5
0 additions, 5 deletions
modules/bindings/pymod/hhblits.py
modules/bindings/tests/test_hhblits.py
+0
-7
0 additions, 7 deletions
modules/bindings/tests/test_hhblits.py
with
0 additions
and
12 deletions
modules/bindings/pymod/hhblits.py
+
0
−
5
View file @
3bd0466f
...
@@ -611,23 +611,18 @@ class HHblits:
...
@@ -611,23 +611,18 @@ class HHblits:
sout
,
serr
=
job
.
communicate
()
sout
,
serr
=
job
.
communicate
()
lines
=
sout
.
decode
().
splitlines
()
lines
=
sout
.
decode
().
splitlines
()
ost
.
LogError
(
"
SecStruct stdout :
"
)
for
line
in
lines
:
for
line
in
lines
:
ost
.
LogError
(
line
.
strip
())
ost
.
LogVerbose
(
line
.
strip
())
ost
.
LogVerbose
(
line
.
strip
())
if
'
error
'
in
line
.
lower
():
if
'
error
'
in
line
.
lower
():
raise
RuntimeError
(
'
Predicting secondary structure for MSA
'
+
raise
RuntimeError
(
'
Predicting secondary structure for MSA
'
+
'
(%s) failed, on command: %s
'
%
(
a3m_file
,
line
))
'
(%s) failed, on command: %s
'
%
(
a3m_file
,
line
))
ost
.
LogError
(
"
SecStruct stderr:
"
)
lines
=
serr
.
decode
().
splitlines
()
lines
=
serr
.
decode
().
splitlines
()
for
line
in
lines
:
for
line
in
lines
:
ost
.
LogError
(
line
.
strip
())
ost
.
LogError
(
line
.
strip
())
ost
.
LogError
(
line
.
strip
())
if
'
error
'
in
line
.
lower
():
if
'
error
'
in
line
.
lower
():
raise
RuntimeError
(
'
Predicting secondary structure for MSA
'
+
raise
RuntimeError
(
'
Predicting secondary structure for MSA
'
+
'
(%s) failed, on command: %s
'
%
(
a3m_file
,
line
))
'
(%s) failed, on command: %s
'
%
(
a3m_file
,
line
))
ost
.
LogError
(
"
SecStruct done
"
)
return
a3m_file
return
a3m_file
...
...
This diff is collapsed.
Click to expand it.
modules/bindings/tests/test_hhblits.py
+
0
−
7
View file @
3bd0466f
...
@@ -133,13 +133,6 @@ class TestHHblitsBindings(unittest.TestCase):
...
@@ -133,13 +133,6 @@ class TestHHblitsBindings(unittest.TestCase):
'
TSKYR
'
)
'
TSKYR
'
)
self
.
hh
=
hhblits
.
HHblits
(
query_seq
,
self
.
hhroot
)
self
.
hh
=
hhblits
.
HHblits
(
query_seq
,
self
.
hhroot
)
a3m
=
self
.
hh
.
BuildQueryMSA
(
'
testfiles/hhblitsdb/unittestdb
'
)
a3m
=
self
.
hh
.
BuildQueryMSA
(
'
testfiles/hhblitsdb/unittestdb
'
)
ost
.
LogError
(
"
Im the bad guy
"
)
with
open
(
a3m
)
as
fh
:
for
line
in
fh
.
readlines
():
ost
.
LogError
(
line
)
ost
.
LogError
(
"
Bad guy over n out
"
)
self
.
assertTrue
(
filecmp
.
cmp
(
a3m
,
"
testfiles/testali_two.a3m
"
))
self
.
assertTrue
(
filecmp
.
cmp
(
a3m
,
"
testfiles/testali_two.a3m
"
))
def
testA3mToProfileFileName
(
self
):
def
testA3mToProfileFileName
(
self
):
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment