From 23a9f24732bb942c9c50eaf43dfba5f5d8a765cf Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Tue, 16 Jul 2019 09:51:40 -0500
Subject: [PATCH] remove errors from generate_design function
---
workflow/scripts/pool_and_psuedoreplicate.py | 26 -------------------
.../tests/test_pool_and_psuedoreplicate.py | 1 -
2 files changed, 27 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index e092864..c8042f5 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -322,22 +322,6 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
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'
@@ -346,16 +330,6 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
tmp_metadata['tag_align'] = path_to_file
design_new_df = design_new_df.append(tmp_metadata)
- # Write out new dataframe
- 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
diff --git a/workflow/tests/test_pool_and_psuedoreplicate.py b/workflow/tests/test_pool_and_psuedoreplicate.py
index b888605..c32783a 100644
--- a/workflow/tests/test_pool_and_psuedoreplicate.py
+++ b/workflow/tests/test_pool_and_psuedoreplicate.py
@@ -5,7 +5,6 @@ import pandas as pd
from io import StringIO
import os
import pool_and_psuedoreplicate
-import sys
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/design/'
--
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