From e56be52c1436d999323d364220497b427addc42e Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Tue, 16 Jul 2019 09:46:27 -0500
Subject: [PATCH] create function generate_design. update test
---
workflow/scripts/pool_and_psuedoreplicate.py | 73 ++++++++++++++-----
.../tests/test_pool_and_psuedoreplicate.py | 4 +-
2 files changed, 55 insertions(+), 22 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 4199656..e092864 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -172,26 +172,7 @@ def self_psuedoreplication(tag_file, prefix, paired):
return pseudoreplicate_dict
-def main():
- args = get_args()
- paired = args.paired
- design = args.design
- cutoff_ratio = args.cutoff
-
- # Create a file handler
- handler = logging.FileHandler('experiment_generation.log')
- logger.addHandler(handler)
-
- # Read files as dataframes
- design_df = pd.read_csv(design, sep='\t')
-
- # Get current directory to build paths
- cwd = os.getcwd()
-
- # Check Number of replicates and replicates
- no_reps = check_replicates(design_df)
- no_unique_controls = check_controls(design_df)
-
+def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_controls):
if no_reps == 1:
logger.info("No other replicate specified "
"so processing as an unreplicated experiment.")
@@ -341,6 +322,22 @@ def main():
tmp_metadata['tag_align'] = path_to_file
design_new_df = design_new_df.append(tmp_metadata)
+ # Add in pool experiment
+ tmp_metadata['sample_id'] = experiment_id + '_pooled' else:
+ path_to_pool_control = cwd + '/' + pool_control
+ design_new_df['control_tag_align'] = path_to_pool_control
+
+ # Add in pseudo replicates
+ tmp_metadata = design_new_df.loc[0].copy()
+ tmp_metadata['control_tag_align'] = path_to_pool_control
+ for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
+ tmp_metadata['sample_id'] = experiment_id + '_pr' + str(rep)
+ tmp_metadata['replicate'] = str(rep) + '_pr'
+ tmp_metadata['xcor'] = 'Calculate'
+ path_to_file = cwd + '/' + pseudorep_file
+ tmp_metadata['tag_align'] = path_to_file
+ design_new_df = design_new_df.append(tmp_metadata)
+
# Add in pool experiment
tmp_metadata['sample_id'] = experiment_id + '_pooled'
tmp_metadata['replicate'] = 'pooled'
@@ -353,6 +350,42 @@ def main():
design_new_df.to_csv(experiment_id + '_ppr.tsv',
header=True, sep='\t', index=False)
+ tmp_metadata['replicate'] = 'pooled'
+ tmp_metadata['xcor'] = 'Calculate'
+ path_to_file = cwd + '/' + pool_experiment_se
+ tmp_metadata['tag_align'] = path_to_file
+ design_new_df = design_new_df.append(tmp_metadata)
+
+ return design_new_df
+
+
+def main():
+ args = get_args()
+ paired = args.paired
+ design = args.design
+ cutoff_ratio = args.cutoff
+
+ # Create a file handler
+ handler = logging.FileHandler('experiment_generation.log')
+ logger.addHandler(handler)
+
+ # Read files as dataframes
+ design_df = pd.read_csv(design, sep='\t')
+
+ # Get current directory to build paths
+ cwd = os.getcwd()
+
+ # Check Number of replicates and replicates
+ no_reps = check_replicates(design_df)
+ no_unique_controls = check_controls(design_df)
+
+ # Generate new design file
+ design_new_df = generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_controls)
+
+ # Write out new dataframe
+ design_new_df.to_csv(experiment_id + '_ppr.tsv',
+ header=True, sep='\t', index=False)
+
if __name__ == '__main__':
main()
diff --git a/workflow/tests/test_pool_and_psuedoreplicate.py b/workflow/tests/test_pool_and_psuedoreplicate.py
index eff8fa2..b888605 100644
--- a/workflow/tests/test_pool_and_psuedoreplicate.py
+++ b/workflow/tests/test_pool_and_psuedoreplicate.py
@@ -63,8 +63,8 @@ def test_check_controls_single(design_experiment_3):
@pytest.mark.unit
def test_single_rep(design_experiment_2):
- sys.argv[1](['--design', 'design_experiment_2'])
- single_rep = pool_and_psuedoreplicate.main()
+ cwd = os.getcwd()
+ single_rep = pool_and_psuedoreplicate.generate_design('false', 1.2, design_experiment_2, cwd, 1, 1)
@pytest.mark.singleend
--
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