From c0e0b003d2ed4aa66b6903a2303cf58135b20292 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 30 Oct 2017 15:20:10 -0500
Subject: [PATCH] Fix string and comparing of values.
---
workflow/scripts/pool_and_psuedoreplicate.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 26db98c..c0d0d76 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -162,16 +162,16 @@ def main():
replicated = False
else:
- logger.info("Multiple replicates specified"
+ logger.info("Multiple replicates specified "
"so processing as a replicated experiment.")
replicated = True
if no_unique_controls == 1 and replicated:
- logger.info("Only a single control was specified"
+ logger.info("Only a single control was specified "
"so using same control for replicates, pool and psuedoreplicates.")
single_control = True
else:
- logger.info("Will merge only unique controls for pooled")
+ logger.info("Will merge only unique controls for pooled.")
single_control = False
# Pool the controls for checking
@@ -235,7 +235,7 @@ def main():
# Check controls against cutoff_ratio
# if so replace with pool_control
path_to_pool_control = cwd + '/' + pool_control
- if control_df[control_df > cutoff_ratio].values.any():
+ if if control_df.values.max() > 1.2:
logger.info("Number of reads in controls differ by " +
" > factor of %f. Using pooled controls." % (cutoff_ratio))
design_new_df['control_tag_align'] = path_to_pool_control
@@ -254,8 +254,8 @@ def main():
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' + rep
- tmp_metadata['replicate'] = rep + '_pr'
+ 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
--
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