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Holly Ruess
celseq2
Commits
cfebaf2f
Commit
cfebaf2f
authored
May 08, 2018
by
yy1533
Browse files
💊
plotly graph on demultiplexing fastqs
parent
f11f7835
Changes
2
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celseq2/celseq2.py
View file @
cfebaf2f
...
...
@@ -43,6 +43,10 @@ Refs:
- https://bitbucket.org/snakemake/snakemake/src/e11a57fe1f62f3f56c815d95d82871811dae81b3/snakemake/__init__.py?at=master&fileviewer=file-view-default#__init__.py-580:1127
'''
task_choices
=
[
'all'
,
'TAG_FASTQ'
,
'ANNOTATION'
,
'ALIGNMENT'
,
'COUNT_MATRIX'
,
'QC_COUNT_MATRIX'
,
'CELSEQ2_TO_ST'
,
'REPORT'
]
def
get_argument_parser
():
desc
=
(
'celseq2: A Python Package for Processing CEL-Seq2 RNA-Seq Data.'
)
...
...
@@ -52,9 +56,9 @@ def get_argument_parser():
"target"
,
nargs
=
"*"
,
default
=
None
,
help
=
"
Targets to build.
May be rules or files."
,
choices
=
[
None
,
'all'
,
'TAG_FASTQ'
,
'ANNOTATION'
,
'ALIGNMENT'
,
'COUNT_MATRIX'
,
'QC_COUNT_MATRIX'
,
'CELSEQ2_TO_ST'
]
)
help
=
(
'
Targets to build.
'
'May be rules or files. '
'Task choices: {}'
).
format
(
', '
.
join
(
task_choices
))
)
parser
.
add_argument
(
"--config-file"
,
metavar
=
"FILE"
,
...
...
celseq2/workflow/celseq2_beta.snakemake
View file @
cfebaf2f
...
...
@@ -679,10 +679,11 @@ rule report_combo_demultiplexing:
output:
html = join_path(DIR_PROJ, SUBDIR_REPORT, 'demultiplexing_fastq.html')
run:
#
Prepare the stats files
#
stats files [/path/item-1/d.csv, /path/item-2/d.csv]
stats_fpaths = glob.glob(join_path(DIR_PROJ, SUBDIR_REPORT,
'item-*', 'demultiplexing.csv'))
stats_fpaths_labels = [base_name(base_name(f)) for f in stats_fpaths]
# labels [item-1, item-2]
stats_fpaths_labels = [base_name(dir_name(f)) for f in stats_fpaths]
work = plotly_demultiplexing_stats(
fpaths=stats_fpaths,
saveto=output.html,
...
...
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