From cd9551eb8bf5320432c71c68f6a3f32280008fb3 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 19 Jun 2018 14:28:45 -0500
Subject: [PATCH] Fix utils reference.
---
workflow/conf/biohpc.config | 2 +-
workflow/scripts/call_peaks_macs.py | 2 +-
workflow/scripts/convert_reads.py | 2 +-
workflow/scripts/frip.py | 84 ++++++++++++++++++++
workflow/scripts/map_reads.py | 2 +-
workflow/scripts/pool_and_psuedoreplicate.py | 2 +-
workflow/scripts/xcor.py | 2 +-
7 files changed, 90 insertions(+), 6 deletions(-)
create mode 100644 workflow/scripts/frip.py
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index df20dd9..21a5343 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -70,7 +70,7 @@ params {
tssfile = '/project/shared/bicf_workflow_ref/GRCh38/gencode.tss'
}
'GRCm38' {
- bwa = '/project/shared/bicf_workflow_ref/GRCm38'
+ git'
genomesize = 'mm'
chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
tssfile = '/project/shared/bicf_workflow_ref/GRCh38/gencode.tss'
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index d853f17..62e8e34 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -7,7 +7,7 @@ import argparse
import shutil
import logging
from multiprocessing import cpu_count
-from python_utils import utils
+import utils
from quality_metrics.xcor import xcor as calculate_xcor
EPILOG = '''
diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py
index 72e5d98..d099794 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -9,7 +9,7 @@ import subprocess
import shlex
import logging
from multiprocessing import cpu_count
-from python_utils import utils
+import utils
EPILOG = '''
For more details:
diff --git a/workflow/scripts/frip.py b/workflow/scripts/frip.py
new file mode 100644
index 0000000..18e2782
--- /dev/null
+++ b/workflow/scripts/frip.py
@@ -0,0 +1,84 @@
+#!/usr/bin/env python3
+
+'''Generate FRiP from data.'''
+
+import sys
+import os
+import argparse
+import utils
+import logging
+import subprocess
+
+
+# SETTINGS
+
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+logger.propagate = False
+logger.setLevel(logging.INFO)
+
+
+EPILOG = '''
+For more details:
+ %(prog)s --help
+'''
+
+
+def parse_arguments():
+
+ parser = argparse.ArgumentParser(
+ description=__doc__, epilog=EPILOG,
+ formatter_class=argparse.RawDescriptionHelpFormatter)
+
+ parser.add_argument('-p', '--peak',
+ help='The peak file to perform qc on.',
+ required=True)
+
+ parser.add_argument('-t', '--tag',
+ help="The tagAlign file to perform qc on.",
+ required=True)
+
+ args = parser.parse_args()
+
+ args = parser.parse_args()
+ return args
+
+# Functions
+
+def frip(tag, peak):
+ '''Calculate FRiP'''
+
+ prefix = os.path.basename(utils.strip_extensions(peak, ['.narrowPeak']))
+
+ frip_qc = '{}.frip.qc'.format(prefix)
+
+
+ cmd = 'bedtools intersect -a {} -b {} -wa -u'
+ cmd = cmd.format(
+ tag, # ta
+ peak) # peak
+ out, err = utils.run_pipe([
+ '%s' % (cmd),
+ 'wc -l'
+ ])
+ val2 = utils.count_lines(tag)
+ qc_val = str(float(out)/float(val2))
+ f = open(frip_qc, 'w+')
+ f.write(qc_val)
+ return frip_qc
+
+
+def main():
+ # read params
+ args = parse_arguments()
+ tag = args.tag
+ peak = args.peak
+
+ handler = logging.FileHandler('frip.log')
+ logger.addHandler(handler)
+
+ frip_qc = frip(tag, peak)
+
+
+if __name__=='__main__':
+ main()
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index 877c7c7..dee86d5 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -9,7 +9,7 @@ import shutil
import shlex
import logging
from multiprocessing import cpu_count
-from python_utils import utils
+import utils
EPILOG = '''
For more details:
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 20369ff..a39a79a 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -8,7 +8,7 @@ import pandas as pd
import numpy as np
import os
import sys
-from python_utils import utils
+import utils
EPILOG = '''
For more details:
diff --git a/workflow/scripts/xcor.py b/workflow/scripts/xcor.py
index 5047469..09e2cb6 100644
--- a/workflow/scripts/xcor.py
+++ b/workflow/scripts/xcor.py
@@ -7,7 +7,7 @@ import argparse
import shutil
import logging
from multiprocessing import cpu_count
-from python_utils import utils
+import utils
EPILOG = '''
For more details:
--
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