From 45277ef8ea8cf3dfa10ed436f6414a4128c13b05 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 15 Nov 2017 12:34:50 -0600
Subject: [PATCH] Fix syntax.
---
workflow/conf/biohpc.config | 8 ++++----
workflow/scripts/call_peaks_macs.py | 29 ++++++++++++++++++++++++-----
workflow/scripts/utils.py | 13 +++++++------
3 files changed, 35 insertions(+), 15 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index d382fe8..74ee96d 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -40,7 +40,7 @@ process {
executor = 'local'
}
$callPeaksMACS {
- module = ['python/3.6.1-2-anaconda', 'phantompeakqualtools/1.2', 'macs/2.1.0-20151222', 'UCSC_userApps/v317']
+ module = ['python/3.6.1-2-anaconda', 'phantompeakqualtools/1.2', 'macs/2.1.0-20151222', 'UCSC_userApps/v317', 'bedtools/2.26.0']
cpus = 32
}
}
@@ -51,17 +51,17 @@ params {
'GRCh38' {
bwa = '/project/shared/bicf_workflow_ref/GRCh38'
genomesize = 'hs'
- chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/chrom.sizes'
+ chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
}
'GRCh37' {
bwa = '/project/shared/bicf_workflow_ref/GRCh37'
genomesize = 'hs'
- chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/chrom.sizes'
+ chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
}
'GRCm38' {
bwa = '/project/shared/bicf_workflow_ref/GRCm38'
genomesize = 'mm'
- chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/chrom.sizes'
+ chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
}
}
}
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index c89c12e..e670496 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -85,12 +85,19 @@ def check_tools():
raise Exception('Missing MACS2')
bg_bw_path = shutil.which("bedGraphToBigWig")
- if r_path:
+ if bg_bw_path:
logger.info('Found bedGraphToBigWig: %s', bg_bw_path)
else:
logger.error('Missing bedGraphToBigWig')
raise Exception('Missing bedGraphToBigWig')
+ bedtools_path = shutil.which("bedtools")
+ if bedtools_path:
+ logger.info('Found bedtools: %s', bedtools_path)
+ else:
+ logger.error('Missing bedtools')
+ raise Exception('Missing bedtools')
+
def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes):
@@ -119,7 +126,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# Remove coordinates outside chromosome sizes
narrowpeak_fn = '%s_peaks.narrowPeak' % (prefix)
- clipped_narrowpeak_fn = '%s-clipped' % (filename)
+ clipped_narrowpeak_fn = 'clipped-%s' % (narrowpeak_fn)
steps = ['slopBed -i %s -g %s -b 0' % (narrowpeak_fn, chrom_sizes),
@@ -159,15 +166,21 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# Remove coordinates outside chromosome sizes (MACS2 bug)
fc_bedgraph_fn = '%s.fc.signal.bedgraph' % (prefix)
+ fc_bedgraph_sorted_fn = 'sorted-%s' % (fc_bedgraph_fn)
fc_signal_fn = "%s.fc_signal.bw" % (prefix)
steps = ['slopBed -i %s_FE.bdg -g %s -b 0' % (prefix, chrom_sizes),
'bedClip stdin %s %s' % (chrom_sizes, fc_bedgraph_fn)]
out, err = utils.run_pipe(steps)
+ # Sort file
+ out, err = utils.run_pipe([
+ 'sort -k1,1 -k2,2n %s' % (fc_bedgraph_fn)],
+ fc_bedgraph_sorted_fn)
+
# Convert bedgraph to bigwig
command = 'bedGraphToBigWig ' + \
- '%s ' % (fc_bedgraph_fn) + \
+ '%s ' % (fc_bedgraph_sorted_fn) + \
'%s ' % (chrom_sizes) + \
'%s' % (fc_signal_fn)
@@ -182,7 +195,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# min(no. of reads in ChIP, no. of reads in control) / 1,000,000
out, err = utils.run_pipe(['gzip -dc %s' % (experiment), 'wc -l'])
chip_reads = out.strip()
- out, err = common.run_pipe(['gzip -dc %s' % (control), 'wc -l'])
+ out, err = utils.run_pipe(['gzip -dc %s' % (control), 'wc -l'])
control_reads = out.strip()
sval = str(min(float(chip_reads), float(control_reads)) / 1000000)
@@ -201,15 +214,21 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# Remove coordinates outside chromosome sizes (MACS2 bug)
pvalue_bedgraph_fn = '%s.pval.signal.bedgraph' % (prefix)
+ pvalue_bedgraph_sorted_fn = 'sort-%s' % (pvalue_bedgraph_fn)
pvalue_signal_fn = "%s.pvalue_signal.bw" % (prefix)
steps = ['slopBed -i %s_ppois.bdg -g %s -b 0' % (prefix, chrom_sizes),
'bedClip stdin %s %s' % (chrom_sizes, pvalue_bedgraph_fn)]
out, err = utils.run_pipe(steps)
+ # Sort file
+ out, err = utils.run_pipe([
+ 'sort -k1,1 -k2,2n %s' % (fc_bedgraph_fn)],
+ pvalue_bedgraph_sorted_fn)
+
# Convert bedgraph to bigwig
command = 'bedGraphToBigWig ' + \
- '%s ' % (pvalue_bedgraph_fn) + \
+ '%s ' % (pvalue_bedgraph_sorted_fn) + \
'%s ' % (chrom_sizes) + \
'%s' % (fc_signal_fn)
diff --git a/workflow/scripts/utils.py b/workflow/scripts/utils.py
index ffedd7f..5fe8e4f 100644
--- a/workflow/scripts/utils.py
+++ b/workflow/scripts/utils.py
@@ -6,6 +6,7 @@
import shlex
import logging
import subprocess
+import sys
logger = logging.getLogger(__name__)
@@ -48,9 +49,9 @@ def run_pipe(steps, outfile=None):
def block_on(command):
process = subprocess.Popen(shlex.split(command), stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
- for line in iter(process.stdout.readline, ''):
- sys.stdout.buffer.write(line)
- process.wait()
+ for line in iter(process.stdout.readline, b''):
+ sys.stdout.write(line.decode('utf-8'))
+ process.communicate()
return process.returncode
@@ -85,11 +86,11 @@ def count_lines(filename):
def rescale_scores(filename, scores_col, new_min=10, new_max=1000):
n_peaks = count_lines(filename)
- sorted_fn = '%s-sorted' % (filename)
- rescaled_fn = '%s-rescaled' % (filename)
+ sorted_fn = 'sorted-%s' % (filename)
+ rescaled_fn = 'rescaled-%s' % (filename)
out, err = run_pipe([
- 'sort -k %dgr,%dgr %s' % (scores_col, scores_col, fn),
+ 'sort -k %dgr,%dgr %s' % (scores_col, scores_col, filename),
r"""awk 'BEGIN{FS="\t";OFS="\t"}{if (NF != 0) print $0}'"""],
sorted_fn)
--
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