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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
ng6
Commits
affb6437
Commit
affb6437
authored
Jul 15, 2014
by
Claire Kuchly
Browse files
concatenate fastq for casava directory analyse
parent
ed6713e6
Changes
1
Hide whitespace changes
Inline
Side-by-side
workflows/illumina_matepair/__init__.py
View file @
affb6437
...
...
@@ -34,15 +34,23 @@ class IlluminaMatePair (NG6Workflow):
# manage the sequences files
group_prefix
=
None
print
self
.
args
[
'files_read'
]
print
self
.
args
[
'sample_description'
][
'lane_number'
]
print
self
.
project
.
get_name
()
print
self
.
args
[
'sample_description'
][
'casava_directory'
]
print
"---------------------"
if
self
.
args
[
'sample_description'
][
'casava_directory'
]
is
not
None
:
if
self
.
args
[
'sample_description'
][
'lane_number'
]
is
None
:
raise
ValueError
,
"lane-number must be specified with casava-directory."
mids_desc_array
,
self
.
read1_files
,
self
.
read2_files
=
Utils
.
filesFromCasava
(
self
.
args
[
'sample_description'
][
'casava_directory'
],
self
.
project
.
get_name
(),
self
.
args
[
'sample_description'
][
'lane_number'
]
)
mids_desc_array
,
self
.
read1_files
,
self
.
read2_files
,
undetermined_read1_files
,
undetermined_read2_files
=
Utils
.
filesFromCasava
(
self
.
args
[
'sample_description'
][
'casava_directory'
],
self
.
project
.
get_name
(),
self
.
args
[
'sample_description'
][
'lane_number'
]
)
#print mids_desc_array, self.read1_files, self.read2_files, undetermined_read1_files, undetermined_read2_files
group_prefix
=
(
Utils
.
get_group_basenames
(
self
.
read1_files
+
self
.
read2_files
,
"read"
)).
keys
()
self
.
runobj
.
add_mids_description
(
mids_desc_array
)
# statistics about demultiplexing
if
len
(
undetermined_read1_files
)
>
0
:
demultiplex_stats
=
self
.
add_component
(
"DemultiplexStats"
,
[
self
.
read1_files
,
undetermined_read1_files
])
elif
(
self
.
args
[
'files_read'
][
0
][
'read_1'
]
is
not
None
)
and
(
len
(
self
.
args
[
'files_read'
][
0
][
'read_1'
])
>
0
)
:
print
self
.
args
[
'files_read'
][
0
]
self
.
read1_files
=
[]
...
...
@@ -101,7 +109,10 @@ class IlluminaMatePair (NG6Workflow):
contamination_search
=
self
.
add_component
(
"ContaminationSearch"
,
[
filtered_read1_files
+
filtered_read2_files
,
self
.
args
[
"databank"
],
reads_prefixes
],
parent
=
fastqilluminafilter
)
# mate_pair analyse
cutadapt
=
self
.
add_component
(
"CutAdapt"
,[
filtered_read1_files
,
filtered_read2_files
,{
"g"
:[
"CTGTCTCTT"
,
"ATACACATCT"
,
"AGATCTAT"
,
"AAGAGACAG"
]},{
"g"
:[
"CTGTCTCTT"
,
"ATACACATCT"
,
"AGATCTAT"
,
"AAGAGACAG"
]},
is_paired_end
,
0.1
,
4
,
20
],
parent
=
fastqilluminafilter
)
concatenate1
=
self
.
add_component
(
"ConcatenateFilesGroups"
,
[
filtered_read1_files
,
(
Utils
.
get_group_basenames
(
self
.
read1_files
,
"read"
)).
keys
()],
component_prefix
=
"read1"
)
concatenate2
=
self
.
add_component
(
"ConcatenateFilesGroups"
,
[
filtered_read2_files
,
(
Utils
.
get_group_basenames
(
self
.
read2_files
,
"read"
)).
keys
()],
component_prefix
=
"read2"
)
cutadapt
=
self
.
add_component
(
"CutAdapt"
,[
concatenate1
.
concat_files
,
concatenate2
.
concat_files
,{
"g"
:[
"CTGTCTCTT"
,
"ATACACATCT"
,
"AGATCTAT"
,
"AAGAGACAG"
]},{
"g"
:[
"CTGTCTCTT"
,
"ATACACATCT"
,
"AGATCTAT"
,
"AAGAGACAG"
]},
is_paired_end
,
0.1
,
4
,
20
],
parent
=
fastqilluminafilter
)
#reverse_complement
...
...
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