From 477530aaf4c4df46d2b4c3bef526db14e6685176 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 27 Oct 2017 17:16:29 -0500
Subject: [PATCH] Fix syntax issues and libaries.
---
workflow/main.nf | 4 ++--
workflow/scripts/pool_and_psuedoreplicate.py | 14 +++++++-------
workflow/scripts/utils.py | 12 ++++++------
3 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 98ebe10..6c560aa 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -297,12 +297,12 @@ process poolAndPsuedoReads {
if (pairedEnd) {
"""
- python3 $baseDir/scripts/pool_and_psuedoreplicate.py -t $experimentObjs -p -c cutoffRatio
+ python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -p -c cutoffRatio
"""
}
else {
"""
- python3 $baseDir/scripts/pool_and_psuedoreplicate.py -t $experimentObjs -c cutoffRatio
+ python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -c cutoffRatio
"""
}
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 7167797..06fb8e8 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -82,9 +82,9 @@ def pool(tag_files, outfile, paired):
'''Pool files together.'''
if paired:
- file_extension = 'bedpe.gz'
+ file_extension = '.bedpe.gz'
else:
- file_extension = 'bedse.gz'
+ file_extension = '.bedse.gz'
pooled_filename = outfile + file_extension
@@ -98,7 +98,7 @@ def pool(tag_files, outfile, paired):
def self_psuedoreplication(tag_file, prefix, paired):
- '''Make n number of self-psuedoreplicates equivlent to reps.'''
+ '''Make 2 self-psuedoreplicates.'''
# Get total number of reads
no_lines = utils.count_lines(tag_file)
@@ -124,7 +124,7 @@ def self_psuedoreplication(tag_file, prefix, paired):
# Convert read pairs to reads into standard tagAlign file
- for i, index in enumerate(list(range(0, reps))):
+ for i, index in enumerate([0, 1]):
steps = ['cat %s' % (splits_prefix + index)]
if paired:
steps.extend([r"""awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}'"""])
@@ -139,7 +139,7 @@ def main():
args = get_args()
paired = args.paired
design = args.design
- cutoff_ratio = args.cutoff_ratio
+ cutoff_ratio = args.cutoff
# Create a file handler
handler = logging.FileHandler('experiment_generation.log')
@@ -149,7 +149,7 @@ def main():
design_df = pd.read_csv(design, sep='\t')
# Get current directory to build paths
- cwd = os.getwd()
+ cwd = os.getcwd()
# Check Number of replicates and replicates
no_reps = check_replicates(design_df)
@@ -217,7 +217,7 @@ def main():
# Make self psuedoreplicates equivalent to number of replicates
pseudoreplicates_dict = {}
for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
- replicate_prefix = experiment_id + '_' + rep
+ replicate_prefix = experiment_id + '_' + str(rep)
pr_dict = self_psuedoreplication(tag_file, replicate_prefix, paired)
pseudoreplicates_dict[rep] = pr_dict
diff --git a/workflow/scripts/utils.py b/workflow/scripts/utils.py
index 11c4170..2643c6e 100644
--- a/workflow/scripts/utils.py
+++ b/workflow/scripts/utils.py
@@ -56,19 +56,19 @@ def strip_extensions(filename, extensions):
def count_lines(filename):
- from magic import from_file
+ import mimetypes
compressed_mimetypes = [
- "application/x-compress",
- "application/x-bzip2",
- "application/x-gzip"
+ "compress",
+ "bzip2",
+ "gzip"
]
- mime_type = from_file(fname, mime=True)
+ mime_type = mimetypes.guess_type(filename)[1]
if mime_type in compressed_mimetypes:
catcommand = 'gzip -dc'
else:
catcommand = 'cat'
out, err = run_pipe([
- '%s %s' % (catcommand, fname),
+ '%s %s' % (catcommand, filename),
'wc -l'
])
return int(out)
--
GitLab