From 2948ddca1a09a1a135129cd8e787a24b1fa4681a Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 10 Oct 2017 11:29:12 -0500
Subject: [PATCH] Update samtools version and synxtax to fix bugs in last push.
---
astrocyte_pkg.yml | 2 +-
workflow/conf/biohpc.config | 2 +-
workflow/scripts/map_qc.py | 47 ++++++++++++++++++-------------------
3 files changed, 25 insertions(+), 26 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 51b4b74..0239682 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -44,7 +44,7 @@ workflow_modules:
- 'cutadapt/1.9.1'
- 'fastqc/0.11.2'
- 'bwa/intel/0.7.12'
- - 'samtools/intel/1.3'
+ - 'samtools/1.4.1'
- 'sambamba/0.6.6'
- 'bedtools/2.26.0'
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index ab28999..3268a6e 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -16,7 +16,7 @@ process {
cpus = 32
}
$filterReads{
- module = ['python/3.6.1-2-anaconda', 'samtools/intel/1.3', 'sambamba/0.6.6', 'bedtools/2.26.0']
+ module = ['python/3.6.1-2-anaconda', 'samtools/1.4.1', 'sambamba/0.6.6', 'bedtools/2.26.0']
cpus = 32
}
}
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index d4fbaaa..e386ecf 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -9,7 +9,6 @@ import shutil
import shlex
import logging
from multiprocessing import cpu_count
-import json
import utils
EPILOG = '''
@@ -66,18 +65,18 @@ def check_tools():
raise Exception('Missing samtools')
sambamba_path = shutil.which("sambamba")
- if bwa_path:
- logger.info('Found sambamba: %s', bwa_path)
+ if sambamba_path:
+ logger.info('Found sambamba: %s', sambamba_path)
else:
logger.error('Missing sambamba')
raise Exception('Missing sambamba')
bedtools_path = shutil.which("bedtools")
- if bwa_path:
- logger.info('Found sambamba: %s', bwa_path)
+ if bedtools_path:
+ logger.info('Found bedtools: %s', bedtools_path)
else:
- logger.error('Missing sambamba')
- raise Exception('Missing sambamba')
+ logger.error('Missing bedtools')
+ raise Exception('Missing bedtools')
def filter_mapped_pe(bam, bam_basename):
@@ -93,7 +92,7 @@ def filter_mapped_pe(bam, bam_basename):
# Remove low MAPQ reads
# Only keep properly paired reads
# Obtain name sorted BAM file
- out, err = common.run_pipe([
+ out, err = utils.run_pipe([
# filter: -F 1804 FlAG bits to exclude; -f 2 FLAG bits to reqire;
# -q 30 exclude MAPQ < 30; -u uncompressed output
# exclude FLAG 1804: unmapped, next segment unmapped, secondary
@@ -103,14 +102,14 @@ def filter_mapped_pe(bam, bam_basename):
# sort: -n sort by name; - take input from stdin;
# out to specified filename
# Will produce name sorted BAM
- "samtools sort -n -@%d -o %s" % (cpu_count(), tmp_filt_bam_filename)])
+ "samtools sort -n -@ %d -o %s" % (cpu_count(), tmp_filt_bam_filename)])
if err:
logger.error("samtools filter error: %s" % (err))
# Remove orphan reads (pair was removed)
# and read pairs mapping to different chromosomes
# Obtain position sorted BAM
- out, err = common.run_pipe([
+ out, err = utils.run_pipe([
# fill in mate coordinates, ISIZE and mate-related flags
# fixmate requires name-sorted alignment; -r removes secondary and
# unmapped (redundant here because already done above?)
@@ -119,7 +118,7 @@ def filter_mapped_pe(bam, bam_basename):
# repeat filtering after mate repair
"samtools view -F 1804 -f 2 -u -",
# produce the coordinate-sorted BAM
- "samtools sort -@%d -o %s" % (cpu_count(), filt_bam_filename)])
+ "samtools sort -@ %d -o %s" % (cpu_count(), filt_bam_filename)])
os.remove(tmp_filt_bam_filename)
return filt_bam_filename
@@ -138,7 +137,7 @@ def filter_mapped_se(bam, bam_basename):
with open(filt_bam_filename, 'w') as fh:
samtools_filter_command = (
"samtools view -F 1804 -q 30 -b %s"
- % (samtools_params, input_bam)
+ % (bam)
)
logger.info(samtools_filter_command)
subprocess.check_call(
@@ -154,17 +153,17 @@ def dedup_mapped(bam, bam_basename, paired):
# Markduplicates
dup_file_qc_filename = bam_basename + ".dup.qc"
tmp_dup_mark_filename = bam_basename + ".dupmark.bam"
- sambamba_parms = "--hash-table-size=17592186044416 \
- --overflow-list-size=20000000 --io-buffer-size=256"
+ sambamba_parms = "--hash-table-size=17592186044416" + \
+ " --overflow-list-size=20000000 --io-buffer-size=256"
with open(dup_file_qc_filename, 'w') as fh:
sambamba_markdup_command = (
"sambamba markdup -t %d %s %s %s"
- % (cpu_count, sambamba_parms, bam, tmp_dup_mark_filename)
+ % (cpu_count(), sambamba_parms, bam, tmp_dup_mark_filename)
)
logger.info(sambamba_markdup_command)
subprocess.check_call(
- shlex.split(sambamba_markdup),
- stdout=fh)
+ shlex.split(sambamba_markdup_command),
+ stderr=fh)
os.remove(tmp_dup_mark_filename + '.bai')
@@ -174,10 +173,10 @@ def dedup_mapped(bam, bam_basename, paired):
if paired: # paired-end data
samtools_dedupe_command = \
- "samtools view -F 1804 -f 2 -b %s" % (filt_bam_filename)
+ "samtools view -F 1804 -f 2 -b %s" % (bam)
else:
samtools_dedupe_command = \
- "samtools view -F 1804 -b %s" % (filt_bam_filename)
+ "samtools view -F 1804 -b %s" % (bam)
with open(final_bam_filename, 'w') as fh:
logger.info(samtools_dedupe_command)
@@ -187,7 +186,7 @@ def dedup_mapped(bam, bam_basename, paired):
# Index final bam file
sambamba_index_command = \
- "samtools index -t %d %s" % (cpu_count(), final_bam_filename)
+ "samtools index -@ %d %s" % (cpu_count(), final_bam_filename)
logger.info(sambamba_index_command)
subprocess.check_output(shlex.split(sambamba_index_command))
@@ -199,9 +198,10 @@ def dedup_mapped(bam, bam_basename, paired):
logger.info(flagstat_command)
subprocess.check_call(shlex.split(flagstat_command), stdout=fh)
- os.remove(filt_bam_filename)
+ os.remove(bam)
return final_bam_filename
+
def compute_complexity(bam, paired, bam_basename):
'''Calculate library complexity .'''
@@ -236,7 +236,7 @@ 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 = common.run_pipe(steps, pbc_file_qc_filename)
+ out, err = utils.run_pipe(steps, pbc_file_qc_filename)
if err:
logger.error("PBC file error: %s" % (err))
@@ -247,13 +247,12 @@ def main():
bam = args.bam
# Create a file handler
- handler = logging.FileHandler('filter_qc.log')
+ handler = logging.FileHandler('map_qc.log')
logger.addHandler(handler)
# Check if tools are present
check_tools()
-
# Run filtering for either PE or SE
bam_basename = os.path.basename(
utils.strip_extensions(bam, STRIP_EXTENSIONS))
--
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