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Louis BECQUEY
/
biorseo
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Authored by
Louis BECQUEY
2019-06-07 11:41:08 +0200
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Commit
247acbf32a7eee4169adeb927ab294b3f7ea4587
247acbf3
2 parents
3349ebbc
a86eaa30
Merge branch 'master' of
https://github.com/persalteas/biominserter
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2 deletions
test_on_RNAstrand.py
test_on_RNAstrand.py
View file @
247acbf
...
...
@@ -1003,7 +1003,7 @@ for nt, number in ignored_nt_dict.items():
tot
=
len
(
RNAcontainer
)
print
(
"Loaded
%
d RNAs of length between 10 and 100.
%
d of them contain pseudoknots."
%
(
tot
,
pk_counter
))
#
#
================= PREDICTION OF STRUCTURES ===============================
#================= PREDICTION OF STRUCTURES ===============================
#define job list
joblist
=
[]
...
...
@@ -1050,7 +1050,7 @@ for instance in RNAcontainer:
joblist
.
append
(
Job
(
command
=
[
biorseoDir
+
"/bin/biorseo"
,
"-s"
,
outputDir
+
basename
+
".fa"
,
"-d"
,
descfolder
,
"-o"
,
outputDir
+
"PK/"
+
basename
+
".rawA"
,
"--type"
,
"A"
],
priority
=
4
,
timeout
=
3600
,
how_many_in_parallel
=
3
,
checkFunc
=
check_biorseoRawA
,
checkArgs
=
[
basename
,
True
]))
joblist
.
append
(
Job
(
command
=
[
biorseoDir
+
"/bin/biorseo"
,
"-s"
,
outputDir
+
basename
+
".fa"
,
"-d"
,
descfolder
,
"-o"
,
outputDir
+
"PK/"
+
basename
+
".rawB"
,
"--type"
,
"B"
],
priority
=
4
,
timeout
=
3600
,
how_many_in_parallel
=
3
,
checkFunc
=
check_biorseoRawB
,
checkArgs
=
[
basename
,
True
]))
# RNA-MoIP
joblist
.
append
(
Job
(
function
=
launch_RNAMoIP
,
args
=
[
instance
.
seq_
,
instance
.
header_
,
basename
],
priority
=
3
,
timeout
=
3600
,
checkFunc
=
check_RNAMoIP
,
checkArgs
=
[
basename
]))
#
joblist.append(Job(function=launch_RNAMoIP, args=[instance.seq_, instance.header_, basename], priority=3, timeout=3600, checkFunc=check_RNAMoIP, checkArgs=[basename]))
# Biokop
joblist
.
append
(
Job
(
command
=
[
biorseoDir
+
"/../biokop/biokop"
,
"-n1"
,
"-i"
,
outputDir
+
basename
+
".fa"
,
"-o"
,
outputDir
+
basename
+
".biok"
],
priority
=
5
,
timeout
=
15000
,
how_many_in_parallel
=
3
,
checkFunc
=
check_biokop
,
checkArgs
=
[
basename
]))
...
...
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