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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
jflow
Commits
61fa1721
Commit
61fa1721
authored
Sep 23, 2015
by
Jerome Mariette
Browse files
from python2 to python3 > ok from command line
parent
1dd4412b
Changes
6
Hide whitespace changes
Inline
Side-by-side
workflows/extparsers/mobyle.py
View file @
61fa1721
...
...
@@ -54,7 +54,7 @@ class MobyleParser(ExternalParser):
return
def
fn_define_parameters
(
self
,
**
kwargs
):
for
userarg
in
kwargs
.
keys
():
for
userarg
in
list
(
kwargs
.
keys
()
)
:
if
userarg
not
in
parameters_names
:
raise
Exception
(
"Invalid argument '%s' for %s"
%
(
userarg
,
self
.
get_nameid
()))
...
...
@@ -63,14 +63,14 @@ class MobyleParser(ExternalParser):
pname
=
param
[
'name'
]
param
[
'value'
]
=
param
.
get
(
'vdef'
)
if
kwargs
.
has_key
(
pname
)
:
if
pname
in
kwargs
:
param
[
'value'
]
=
kwargs
[
pname
]
printval
=
param
[
'value'
]
if
param
[
'type'
]
==
'file'
or
type
(
param
[
'value'
])
==
str
:
printval
=
"'"
+
str
(
param
[
'value'
])
+
"'"
exec
"%s = %s"
%
(
pname
,
printval
)
in
globals
(),
locals
()
exec
(
"%s = %s"
%
(
pname
,
printval
)
,
globals
(),
locals
()
)
if
param
[
'isfilename'
]
:
filenames_parameters
.
append
(
param
)
...
...
@@ -93,7 +93,7 @@ class MobyleParser(ExternalParser):
param
[
'value'
]
=
None
elif
param
[
'flist'
]
:
vlist
=
param
[
'flist'
].
keys
()
vlist
=
list
(
param
[
'flist'
].
keys
()
)
# custom string type depending on vlist for keys and convert to flist
class
flist_type
(
jflow
.
extparser
.
_serializable_nested_function
):
...
...
@@ -183,7 +183,7 @@ class MobyleParser(ExternalParser):
continue
# next parameter, no need to add this one
# regexp to match all filenames
regexp
=
"|"
.
join
([
fnmatch
.
translate
(
e
)
for
e
in
param
[
'filenames'
]])
print
">>regex for %s %s"
%
(
pname
,
regexp
)
print
((
">>regex for %s %s"
%
(
pname
,
regexp
)
))
self
.
add_output_file_pattern
(
pname
,
param
[
'help'
],
regexp
,
**
arguments
)
else
:
...
...
@@ -284,7 +284,7 @@ class MobyleParser(ExternalParser):
if
len
(
vdefs
)
==
1
:
param
[
'vdef'
]
=
casting
(
vdefs
[
0
])
if
casting
else
vdefs
[
0
]
else
:
param
[
'vdef'
]
=
map
(
casting
,
vdefs
)
if
casting
else
vdefs
param
[
'vdef'
]
=
list
(
map
(
casting
,
vdefs
)
)
if
casting
else
vdefs
# vlist : choices
if
parameterNode
.
find
(
'./vlist'
)
is
not
None
:
...
...
workflows/mobyle/data/mobyle.cfg
View file @
61fa1721
...
...
@@ -15,9 +15,5 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
--reference-genome
workflows/mobyle/data/reference.fasta
--read-1
workflows/mobyle/data/lib_172.1.fastq.gz
--read-2
workflows/mobyle/data/lib_172.2.fastq.gz
\ No newline at end of file
--fasta-file
workflows/mobyle/data/reference.fasta
\ No newline at end of file
workflows/test/__init__.py
View file @
61fa1721
...
...
@@ -108,14 +108,14 @@ class Test (Workflow):
def
process
(
self
):
sys
.
stdout
=
open
(
os
.
path
.
join
(
self
.
directory
,
"wf_stdout"
),
'w'
)
print
"###################### Workflow ############################"
print
(
"###################### Workflow ############################"
)
for
attr
in
self
.
params_order
:
value
=
getattr
(
self
,
attr
)
print
attr
print
value
print
"class : "
+
value
.
__class__
.
__name__
print
"== None : "
+
str
(
value
==
None
)
print
""
print
(
attr
)
print
(
value
)
print
((
"class : "
+
value
.
__class__
.
__name__
))
print
((
"== None : "
+
str
(
value
==
None
)
))
print
(
""
)
sys
.
stdout
.
close
()
# test_parameters = self.add_component("TestComponentParameters", [
# self.test_B1,
...
...
workflows/test/components/testComponentParameters.py
View file @
61fa1721
...
...
@@ -50,15 +50,15 @@ class TestComponentParameters (Component):
self
.
add_input_file
(
"test_C13"
,
"Multiple InputFile default application.properties."
,
default
=
test_C13
)
def
process
(
self
):
print
"###################### Component ############################"
print
(
"###################### Component ############################"
)
for
attr
in
self
.
params_order
:
value
=
getattr
(
self
,
attr
)
print
attr
print
value
print
"class : "
+
value
.
__class__
.
__name__
print
(
attr
)
print
(
value
)
print
((
"class : "
+
value
.
__class__
.
__name__
))
# print "is None : " + str(value is None)
print
"== None : "
+
str
(
value
==
None
)
print
""
print
((
"== None : "
+
str
(
value
==
None
)
))
print
(
""
)
def
get_version
(
self
):
return
"-"
workflows/variantcalling/__init__.py
View file @
61fa1721
...
...
@@ -19,8 +19,8 @@ from jflow.workflow import Workflow
import
os
import
sys
import
StringIO
from
C
onfig
P
arser
import
ConfigParser
from
io
import
StringIO
from
c
onfig
p
arser
import
ConfigParser
from
jflow
import
seqio
...
...
@@ -67,7 +67,7 @@ class VariantCalling (Workflow):
single_fastq
,
pair1_fastq
,
pair2_fastq
=
[],
[],
[]
single_librairies_sequencers
,
pair_librairies_sequencers
=
[],
[]
for
lib_arg
in
self
.
library
:
if
lib_arg
[
"sample"
]
!=
None
and
not
samples
.
has_key
(
lib_arg
[
"sample"
]
)
:
if
lib_arg
[
"sample"
]
!=
None
and
not
lib_arg
[
"sample"
]
in
samples
:
samples
[
lib_arg
[
"sample"
]]
=
{
"paired"
:
list
(),
"single"
:
list
()
}
if
lib_arg
[
"R2"
]
!=
None
and
lib_arg
[
"R2"
]
!=
""
:
if
lib_arg
[
"sample"
]
!=
None
:
...
...
@@ -154,7 +154,7 @@ class VariantCalling (Workflow):
gatk_preprocess_bams
=
list
()
processed_idx_paired
=
dict
()
processed_idx_single
=
dict
()
for
sample_name
in
samples
.
keys
():
for
sample_name
in
list
(
samples
.
keys
()
)
:
current_sample
=
samples
[
sample_name
]
bams
=
list
()
for
idx_bam
in
current_sample
[
'paired'
]:
...
...
@@ -167,11 +167,11 @@ class VariantCalling (Workflow):
gatk_preprocess_bams
.
append
(
merged_bam
.
merged_bam
)
if
len
(
pair2_fastq
)
>
0
:
for
idx
,
bam_path
in
enumerate
(
gatk_preprocess_paired
.
output_files
):
if
not
processed_idx_paired
.
has_key
(
idx
)
:
if
not
idx
in
processed_idx_paired
:
gatk_preprocess_bams
.
append
(
bam_path
)
if
len
(
single_fastq
)
>
0
:
for
idx
,
bam_path
in
enumerate
(
gatk_preprocess_single
.
output_files
):
if
not
processed_idx_single
.
has_key
(
idx
)
:
if
not
idx
in
processed_idx_single
:
gatk_preprocess_bams
.
append
(
bam_path
)
# Variant calling
...
...
@@ -199,7 +199,7 @@ class VariantCalling (Workflow):
@
staticmethod
def
config_parser
(
arg_lines
):
config
=
ConfigParser
()
config
.
readfp
(
StringIO
.
StringIO
(
'
\n
'
.
join
(
arg_lines
)))
config
.
readfp
(
StringIO
(
'
\n
'
.
join
(
arg_lines
)))
arguments
=
[]
section
=
'General'
...
...
@@ -223,7 +223,7 @@ class VariantCalling (Workflow):
items
=
config
.
items
(
section
)
for
tag
,
value
in
items
:
lib_id
,
param
=
tag
.
split
(
'.'
)
if
not
lib
raries
.
has_key
(
lib_id
)
:
if
not
lib
_id
in
libraries
:
libraries
[
lib_id
]
=
list
()
if
param
==
'r1'
:
libraries
[
lib_id
].
append
(
'R1='
+
value
)
...
...
@@ -247,4 +247,5 @@ class VariantCalling (Workflow):
if
config
.
has_option
(
section
,
'two_steps_calling'
)
and
config
.
getboolean
(
section
,
'two_steps_calling'
):
arguments
.
extend
(
[
'--two-steps-calling'
]
)
return
arguments
\ No newline at end of file
return
arguments
\ No newline at end of file
workflows/variantcalling/components/index_fai_dict.py
View file @
61fa1721
...
...
@@ -42,7 +42,7 @@ def create_dictionary(exec_path, dict, input_fasta, databank, stdout_path, stder
stdeh
=
open
(
stderr_path
)
error_msg
=
""
.
join
(
map
(
str
,
stdeh
.
readlines
())
)
stdeh
.
close
()
raise
StandardError
(
"Error in subprocess create_dictionary.
\n\t
Cmd : "
+
" "
.
join
(
cmd
)
+
"
\n\t
Error : "
+
error_msg
)
raise
Exception
(
"Error in subprocess create_dictionary.
\n\t
Cmd : "
+
" "
.
join
(
cmd
)
+
"
\n\t
Error : "
+
error_msg
)
def
samtools_faidx
(
exec_path
,
databank
,
fai
,
stdout_path
,
stderr_path
):
from
subprocess
import
Popen
,
PIPE
...
...
@@ -63,7 +63,7 @@ def samtools_faidx(exec_path, databank, fai, stdout_path, stderr_path):
stdeh
=
open
(
stderr_path
)
error_msg
=
""
.
join
(
map
(
str
,
stdeh
.
readlines
())
)
stdeh
.
close
()
raise
StandardError
(
"Error in subprocess samtools_faidx.
\n\t
Cmd : "
+
" "
.
join
(
cmd
)
+
"
\n\t
Error : "
+
error_msg
)
raise
Exception
(
"Error in subprocess samtools_faidx.
\n\t
Cmd : "
+
" "
.
join
(
cmd
)
+
"
\n\t
Error : "
+
error_msg
)
class
IndexFaiDict
(
Component
):
...
...
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