From 977b3a31add6619772e9d935887834dc0f584110 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 17 Nov 2017 22:15:26 -0600
Subject: [PATCH] Fix the python erros.
---
workflow/scripts/call_peaks_macs.py | 1 -
workflow/scripts/pool_and_psuedoreplicate.py | 6 +++---
workflow/scripts/utils.py | 1 -
3 files changed, 3 insertions(+), 5 deletions(-)
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index b82516c..23174e0 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -250,7 +250,6 @@ def main():
chrom_size = args.size
paired = args.paired
-
# Create a file handler
handler = logging.FileHandler('call_peaks.log')
logger.addHandler(handler)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 318c037..1ee66a7 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -192,13 +192,13 @@ def main():
design_new_df['replicate'] = design_new_df['replicate'].astype(str)
design_new_df.at[1, 'sample_id'] = experiment_id + '_pr1'
design_new_df.at[1, 'replicate'] = '1_pr'
- design_new_df.at[1,'xcor'] = 'Calculate'
+ design_new_df.at[1, 'xcor'] = 'Calculate'
design_new_df.at[2, 'sample_id'] = experiment_id + '_pr2'
design_new_df.at[2, 'replicate'] = '2_pr'
- design_new_df.at[2,'xcor'] = 'Calculate'
+ design_new_df.at[2, 'xcor'] = 'Calculate'
design_new_df.at[3, 'sample_id'] = experiment_id + 'pooled'
design_new_df.at[3, 'replicate'] = 'pooled'
- design_new_df.at[3,'xcor'] = 'Calculate'
+ design_new_df.at[3, 'xcor'] = 'Calculate'
# Make 2 self psuedoreplicates
self_pseudoreplicates_dict = {}
diff --git a/workflow/scripts/utils.py b/workflow/scripts/utils.py
index 5fe8e4f..e9f4a77 100644
--- a/workflow/scripts/utils.py
+++ b/workflow/scripts/utils.py
@@ -85,7 +85,6 @@ def count_lines(filename):
def rescale_scores(filename, scores_col, new_min=10, new_max=1000):
- n_peaks = count_lines(filename)
sorted_fn = 'sorted-%s' % (filename)
rescaled_fn = 'rescaled-%s' % (filename)
--
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