From f6de14de697b15a9e0898df7a70106ee7b275cb9 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 13 Jan 2019 16:01:43 -0600
Subject: [PATCH] Make file names consistent.
---
workflow/scripts/pool_and_psuedoreplicate.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 91f89b7..7d27b97 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -25,7 +25,7 @@ logger.setLevel(logging.INFO)
# strip_extensions strips from the right inward, so
# the expected right-most extensions should appear first (like .gz)
# Modified from J. Seth Strattan
-STRIP_EXTENSIONS = ['.gz', '.tagAlign', '.bedse', 'bedpe']
+STRIP_EXTENSIONS = ['.gz', '.tagAlign', '.bedse', '.bedpe']
def get_args():
@@ -93,7 +93,10 @@ def pool(tag_files, outfile, paired):
else:
file_extension = '.bedse.gz'
- pooled_filename = outfile + file_extension
+ pool_basename = os.path.basename(
+ utils.strip_extensions(outfile, STRIP_EXTENSIONS))
+
+ pooled_filename = pool_basename + file_extension
# Merge files
out, err = utils.run_pipe([
@@ -106,7 +109,7 @@ def pool(tag_files, outfile, paired):
def bedpe_to_tagalign(tag_file, outfile):
'''Convert read pairs to reads into standard tagAlign file.'''
- se_tag_filename = outfile + "tagAlign.gz"
+ se_tag_filename = outfile + ".tagAlign.gz"
# Convert read pairs to reads into standard tagAlign file
tag_steps = ["zcat -f %s" % (tag_file)]
--
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