From 648dc44d7b512db3d63f31c0b17399f6f643124e Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 25 Oct 2017 16:17:02 -0500
Subject: [PATCH] Fix syntax of get_args across all scripts.
---
workflow/scripts/check_design.py | 3 ++-
workflow/scripts/convert_reads.py | 1 +
workflow/scripts/experiment_design.py | 1 +
workflow/scripts/experiment_qc.py | 1 +
workflow/scripts/map_qc.py | 1 +
workflow/scripts/map_reads.py | 1 +
workflow/scripts/trim_reads.py | 1 +
workflow/scripts/xcor.py | 1 +
8 files changed, 9 insertions(+), 1 deletion(-)
diff --git a/workflow/scripts/check_design.py b/workflow/scripts/check_design.py
index 161660e..6bd822f 100644
--- a/workflow/scripts/check_design.py
+++ b/workflow/scripts/check_design.py
@@ -21,6 +21,7 @@ logger.setLevel(logging.INFO)
def get_args():
'''Define arguments.'''
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -98,7 +99,7 @@ def check_replicates(design):
unique_replicates = set(replicates)
if len(replicates) != len(unique_replicates):
duplicated_replicates.append(experiment)
-
+
if len(duplicated_replicates) > 0:
logger.error('Duplicate replicates in experiments: %s', list(duplicated_replicates))
raise Exception("Duplicate replicates in experiments: %s" %
diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py
index d745047..62faf72 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -25,6 +25,7 @@ logger.setLevel(logging.INFO)
def get_args():
'''Define arguments.'''
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
diff --git a/workflow/scripts/experiment_design.py b/workflow/scripts/experiment_design.py
index ca135e8..3d6697a 100644
--- a/workflow/scripts/experiment_design.py
+++ b/workflow/scripts/experiment_design.py
@@ -21,6 +21,7 @@ logger.setLevel(logging.INFO)
def get_args():
'''Define arguments.'''
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
diff --git a/workflow/scripts/experiment_qc.py b/workflow/scripts/experiment_qc.py
index 47a3983..711da18 100644
--- a/workflow/scripts/experiment_qc.py
+++ b/workflow/scripts/experiment_qc.py
@@ -25,6 +25,7 @@ logger.setLevel(logging.INFO)
def get_args():
'''Define arguments.'''
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index 4451d91..3f07068 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -34,6 +34,7 @@ STRIP_EXTENSIONS = ['.bam', '.srt']
def get_args():
'''Define arguments.'''
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index ba6bbd0..b7d3144 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -33,6 +33,7 @@ STRIP_EXTENSIONS = ['.gz', '.fq', '.fastq', '_trimmed']
def get_args():
'''Define arguments.'''
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
diff --git a/workflow/scripts/trim_reads.py b/workflow/scripts/trim_reads.py
index f9f2524..2f7f3e5 100644
--- a/workflow/scripts/trim_reads.py
+++ b/workflow/scripts/trim_reads.py
@@ -22,6 +22,7 @@ logger.setLevel(logging.INFO)
def get_args():
'''Define arguments.'''
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
diff --git a/workflow/scripts/xcor.py b/workflow/scripts/xcor.py
index 88750b6..0bf51e6 100644
--- a/workflow/scripts/xcor.py
+++ b/workflow/scripts/xcor.py
@@ -24,6 +24,7 @@ logger.setLevel(logging.INFO)
def get_args():
'''Define arguments.'''
+
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
--
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