From 9b65c0bd7c2ad355a8a4297ea9dfac736e9bd071 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 10 Oct 2017 12:46:16 -0500
Subject: [PATCH] Add header to pbc file.
---
workflow/scripts/map_qc.py | 19 +++++++++++++++++--
1 file changed, 17 insertions(+), 2 deletions(-)
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index e386ecf..fe47bc3 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -10,6 +10,7 @@ import shlex
import logging
from multiprocessing import cpu_count
import utils
+import pandas as pd
EPILOG = '''
For more details:
@@ -205,7 +206,8 @@ def dedup_mapped(bam, bam_basename, paired):
def compute_complexity(bam, paired, bam_basename):
'''Calculate library complexity .'''
- pbc_file_qc_filename = bam_basename + "filt.nodup.pbc.qc"
+ pbc_file_qc_filename = bam_basename + ".filt.nodup.pbc.qc"
+ tmp_pbc_file_qc_filename = "tmp.%s" % (pbc_file_qc_filename)
# Sort by name
# convert to bedPE and obtain fragment coordinates
@@ -220,6 +222,13 @@ def compute_complexity(bam, paired, bam_basename):
# NRF=Distinct/Total [tab]
# PBC1=OnePair/Distinct [tab]
# PBC2=OnePair/TwoPair
+ pbc_headers = ['TotalReadPairs',
+ 'DistinctReadPairs',
+ 'OneReadPair',
+ 'TwoReadPairs',
+ 'NRF',
+ 'PBC1',
+ 'PBC2']
if paired:
steps = [
@@ -236,10 +245,16 @@ def compute_complexity(bam, paired, bam_basename):
"uniq -c",
r"""awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}'"""
])
- out, err = utils.run_pipe(steps, pbc_file_qc_filename)
+ out, err = utils.run_pipe(steps, tmp_pbc_file_qc_filename)
if err:
logger.error("PBC file error: %s" % (err))
+ # Add headers
+ pbc_file = pd.read_csv(tmp_pbc_file_qc_filename, sep='\t', header=None,
+ names=pbc_headers)
+ pbc_file.to_csv(pbc_file_qc_filename, header=True, sep='\t', index=False)
+ os.remove(tmp_pbc_file_qc_filename)
+
def main():
args = get_args()
--
GitLab