From f574ee50b5938a0d33f0d7022cbd9b91e36405d3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 May 2019 14:37:10 +0200
Subject: [PATCH] rmi_splitter.py: fix ntuple handling in parameters
---
src/rmi_splitter/rmi_splitter.py | 28 ++++++++-------------
src/rmi_splitter/tests/rmi_splitter_test.py | 2 +-
2 files changed, 12 insertions(+), 18 deletions(-)
diff --git a/src/rmi_splitter/rmi_splitter.py b/src/rmi_splitter/rmi_splitter.py
index 095931c..cd5ab50 100644
--- a/src/rmi_splitter/rmi_splitter.py
+++ b/src/rmi_splitter/rmi_splitter.py
@@ -305,7 +305,7 @@ def list_reads_number(config):
if not adaptator == 'conditions':
if int(config[adaptator]['coords']['reads']) > read_number:
read_number = int(config[adaptator]['coords']['reads'])
- return list(range(0, read_number + 1))
+ return read_number + 1
def create_barcode_dictionaries(config, mismatch=None):
@@ -962,23 +962,17 @@ def main(argv=None):
main function
"""
- try:
- parameters['mismatch']
- except Exception as e:
- parse_ntuples_fastqs(fastqs=parameters['inputfiles'],
- config=config,
- results_path=parameters['outputfolder'],
- verbose=parameters['verbose'],
- ntuple_param=parameters['ntuple'],
- gzed=parameters['gzed'])
+ if 'mismatch' not in parameters:
+ parameters['mismatch'] = None
else:
- parse_ntuples_fastqs(fastqs=parameters['inputfiles'],
- config=config,
- results_path=parameters['outputfolder'],
- verbose=parameters['verbose'],
- mismatch=int(parameters['mismatch']),
- ntuple_param=parameters['ntuple'],
- gzed=parameters['gzed'])
+ parameters['mismatch'] = int(parameters['mismatch'])
+ parse_ntuples_fastqs(fastqs=parameters['inputfiles'],
+ config=config,
+ results_path=parameters['outputfolder'],
+ verbose=parameters['verbose'],
+ mismatch=parameters['mismatch'],
+ ntuple_param=parameters['ntuple'],
+ gzed=parameters['gzed'])
if __name__ == "__main__":
diff --git a/src/rmi_splitter/tests/rmi_splitter_test.py b/src/rmi_splitter/tests/rmi_splitter_test.py
index ac2d0be..520e7a3 100644
--- a/src/rmi_splitter/tests/rmi_splitter_test.py
+++ b/src/rmi_splitter/tests/rmi_splitter_test.py
@@ -611,7 +611,7 @@ class HandleFastqTest(unittest.TestCase):
rmi_splitter.list_reads_number(
config=data_test.CONFIG_TOY_PAIRED
),
- [0, 1, 2]
+ 3
)
def test_assign_reads_single(self):
--
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