From 4e68354ecc306d3aa431324d68dd19a7410a80af Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 17 Oct 2017 16:00:32 -0500
Subject: [PATCH] Add in deeptools code to generate QC from deeptools.
---
astrocyte_pkg.yml | 1 +
test_data/design_ENCSR238SGC_SE.txt | 8 +-
test_data/design_ENCSR729LGA_PE.txt | 8 +-
workflow/conf/biohpc.config | 4 +
workflow/main.nf | 25 +++
workflow/scripts/experiment_qc.py | 244 +++++++++++++++++++--------
workflow/tests/test_experiment_qc.py | 42 +++++
workflow/tests/test_utils.py | 2 +-
8 files changed, 251 insertions(+), 83 deletions(-)
create mode 100644 workflow/tests/test_experiment_qc.py
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 0239682..62c6297 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -47,6 +47,7 @@ workflow_modules:
- 'samtools/1.4.1'
- 'sambamba/0.6.6'
- 'bedtools/2.26.0'
+ - 'deeptools/2.5.0.1'
# A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter:
diff --git a/test_data/design_ENCSR238SGC_SE.txt b/test_data/design_ENCSR238SGC_SE.txt
index d024a4c..45cf863 100644
--- a/test_data/design_ENCSR238SGC_SE.txt
+++ b/test_data/design_ENCSR238SGC_SE.txt
@@ -1,5 +1,5 @@
sample_id experiment_id biosample factor treatment replicate control_id fastq_read1
-ENCBS844FSC ENCSR238SGC limb H3K4me1 None 1 ENCBS844FSC ENCFF833BLU.fastq.gz
-ENCBS892NXC ENCSR238SGC limb H3K4me1 None 2 ENCBS892NXC ENCFF646LXU.fastq.gz
-ENCBS844FSC ENCSR687ALB limb Control None 1 ENCBS844FSC ENCFF524CAC.fastq.gz
-ENCBS892NXC ENCSR687ALB limb Control None 2 ENCBS892NXC ENCFF163AJI.fastq.gz
+ENCLB144FDT ENCSR238SGC limb H3K4me1 None 1 ENCLB304SBJ ENCFF833BLU.fastq.gz
+ENCLB831RUI ENCSR238SGC limb H3K4me1 None 2 ENCLB410VVO ENCFF646LXU.fastq.gz
+ENCLB304SBJ ENCSR687ALB limb Control None 1 ENCLB304SBJ ENCFF524CAC.fastq.gz
+ENCLB410VVO ENCSR687ALB limb Control None 2 ENCLB410VVO ENCFF163AJI.fastq.gz
diff --git a/test_data/design_ENCSR729LGA_PE.txt b/test_data/design_ENCSR729LGA_PE.txt
index 0e33564..1d74d03 100644
--- a/test_data/design_ENCSR729LGA_PE.txt
+++ b/test_data/design_ENCSR729LGA_PE.txt
@@ -1,5 +1,5 @@
sample_id experiment_id biosample factor treatment replicate control_id fastq_read1 fastq_read2
-ENCBS609QTY ENCSR729LGA MCF-7 SP1 None 1 ENCBS216AOQ ENCFF957SQS.fastq.gz ENCFF582IOZ.fastq.gz
-ENCBS200IWR ENCSR729LGA MCF-7 SP1 None 2 ENCBS034XKZ ENCFF330MCZ.fastq.gz ENCFF293YFE.fastq.gz
-ENCBS216AOQ ENCSR217LRF MCF-7 Control None 1 ENCBS216AOQ ENCFF002DTU.fastq.gz ENCFF002EFI.fastq.gz
-ENCBS034XKZ ENCSR217LRF MCF-7 Control None 2 ENCBS034XKZ ENCFF002EFG.fastq.gz ENCFF002DTS.fastq.gz
+ENCLB637LZP ENCSR729LGA MCF-7 SP1 None 1 ENCLB678IDC ENCFF957SQS.fastq.gz ENCFF582IOZ.fastq.gz
+ENCLB568IYX ENCSR729LGA MCF-7 SP1 None 2 ENCLB336TVW ENCFF330MCZ.fastq.gz ENCFF293YFE.fastq.gz
+ENCLB678IDC ENCSR217LRF MCF-7 Control None 1 ENCLB678IDC ENCFF002DTU.fastq.gz ENCFF002EFI.fastq.gz
+ENCLB336TVW ENCSR217LRF MCF-7 Control None 2 ENCLB336TVW ENCFF002EFG.fastq.gz ENCFF002DTS.fastq.gz
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 3268a6e..f9d95c2 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -19,6 +19,10 @@ process {
module = ['python/3.6.1-2-anaconda', 'samtools/1.4.1', 'sambamba/0.6.6', 'bedtools/2.26.0']
cpus = 32
}
+ $experimentQC {
+ module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1']
+ executor = 'local'
+ }
}
params {
diff --git a/workflow/main.nf b/workflow/main.nf
index fd0c59d..384596c 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -162,3 +162,28 @@ process filterReads {
}
}
+
+// Define channel collecting new design file
+dedupDesign = dedupReads.
+ collectFile(name:'design_dedup.tsv', seed:"sample_id\tbam_reads\tbam_index\tbiosample\tfactor\ttreatment\treplicate\controlId\n", storeDir:""$baseDir/output/design")
+
+// Quality Metrics using deeptools
+process experimentQC {
+
+ publishDir "$baseDir/output/${task.process}", mode: 'copy'
+
+ input:
+
+ file dedupDesign
+
+ output:
+
+ file '*.{png,npz}' into deepToolsStats
+
+ script:
+
+ """
+ python3 $baseDir/scripts/experiment_qc.py -d $dedupDesign
+ """
+
+}
diff --git a/workflow/scripts/experiment_qc.py b/workflow/scripts/experiment_qc.py
index 7565517..47a3983 100644
--- a/workflow/scripts/experiment_qc.py
+++ b/workflow/scripts/experiment_qc.py
@@ -1,81 +1,177 @@
-#!/usr/bin/python
-# programmer : bbc
-# usage:
+#!/usr/bin/env python3
-import sys
-import argparse as ap
+'''Experiment correlation and enrichment of reads over genome-wide bins.'''
+
+
+import argparse
import logging
import subprocess
+import shutil
import pandas as pd
-from multiprocessing import Pool
-logging.basicConfig(level=10)
-
-
-def prepare_argparser():
- description = "Make wig file for given bed using bam"
- epilog = "For command line options of each command, type %(prog)% COMMAND -h"
- argparser = ap.ArgumentParser(description=description, epilog = epilog)
- argparser.add_argument("-i","--input",dest = "infile",type=str,required=True, help="input BAM file")
- argparser.add_argument("-g","--genome",dest = "genome",type=str,required=True, help="genome", default="hg19")
- #argparser.add_argument("-b","--bed",dest="bedfile",type=str,required=True, help = "Gene locus in bed format")
- #argparser.add_argument("-s","--strandtype",dest="stranded",type=str,default="none", choices=["none","reverse","yes"])
- #argparser.add_argument("-n","--name",dest="trackName",type=str,default="UserTrack",help = "track name for bedgraph header")
- return(argparser)
-
-def run_qc(files, controls, labels):
- mbs_command = "multiBamSummary bins --bamfiles "+' '.join(files)+" -out sample_mbs.npz"
- p = subprocess.Popen(mbs_command, shell=True)
- #logging.debug(mbs_command)
- p.communicate()
- pcor_command = "plotCorrelation -in sample_mbs.npz --corMethod spearman --skipZeros --plotTitle \"Spearman Correlation of Read Counts\" --whatToPlot heatmap --colorMap RdYlBu --plotNumbers -o experiment.deeptools.heatmap_spearmanCorr_readCounts_v2.png --labels "+" ".join(labels)
- #logging.debug(pcor_command)
- p = subprocess.Popen(pcor_command, shell=True)
- p.communicate()
- #plotCoverage
- pcov_command = "plotCoverage -b "+" ".join(files)+" --plotFile experiment.deeptools_coverage.png -n 1000000 --plotTitle \"sample coverage\" --ignoreDuplicates --minMappingQuality 10"
- p = subprocess.Popen(pcov_command, shell=True)
- p.communicate()
- #draw fingerprints plots
- for treat,ctrl,name in zip(files,controls,labels):
- fp_command = "plotFingerprint -b "+treat+" "+ctrl+" --labels "+name+" control --plotFile "+name+".deeptools_fingerprints.png"
- p = subprocess.Popen(fp_command, shell=True)
- p.communicate()
-
-def bam2bw_wrapper(command):
- p = subprocess.Popen(command, shell=True)
- p.communicate()
-
-def run_signal(files, labels, genome):
- #compute matrix and draw profile and heatmap
- gene_bed = genome+"/gene.bed"#"/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/genome/"+genome+"/gene.bed"
- bw_commands = []
- for f in files:
- bw_commands.append("bamCoverage -bs 10 -b "+f+" -o "+f.replace("bam","bw"))
- work_pool = Pool(min(len(files), 12))
- work_pool.map(bam2bw_wrapper, bw_commands)
- work_pool.close()
- work_pool.join()
-
- cm_command = "computeMatrix scale-regions -R "+gene_bed+" -a 3000 -b 3000 --regionBodyLength 5000 --skipZeros -S *.bw -o samples.deeptools_generegionscalematrix.gz"
- p = subprocess.Popen(cm_command, shell=True)
- p.communicate()
- hm_command = "plotHeatmap -m samples.deeptools_generegionscalematrix.gz -out samples.deeptools_readsHeatmap.png"
- p = subprocess.Popen(hm_command, shell=True)
- p.communicate()
-
-def run(dfile,genome):
- #parse dfile, suppose data files are the same folder as design file
- dfile = pd.read_csv(dfile)
- #QC: multiBamSummary and plotCorrelation
- run_qc(dfile['bamReads'], dfile['bamControl'], dfile['SampleID'])
- #signal plots
- run_signal(dfile['bamReads'],dfile['SampleID'],genome)
+from multiprocessing import cpu_count
+
+EPILOG = '''
+For more details:
+ %(prog)s --help
+'''
+
+# SETTINGS
+
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+logger.propagate = False
+logger.setLevel(logging.INFO)
+
+
+def get_args():
+ '''Define arguments.'''
+ parser = argparse.ArgumentParser(
+ description=__doc__, epilog=EPILOG,
+ formatter_class=argparse.RawDescriptionHelpFormatter)
+
+ parser.add_argument('-d', '--design',
+ help="The design file to run QC (tsv format).",
+ required=True)
+
+ args = parser.parse_args()
+ return args
+
+
+def check_tools():
+ '''Checks for required componenets on user system.'''
+
+ logger.info('Checking for required libraries and components on this system')
+
+ deeptools_path = shutil.which("deeptools")
+ if deeptools_path:
+ logger.info('Found deeptools: %s', deeptools_path)
+ else:
+ logger.error('Missing deeptools')
+ raise Exception('Missing deeptools')
+
+
+def generate_read_summary(design):
+ '''Generate summary of data based on read counts.'''
+
+ bam_files = ' '.join(design['bam_reads'])
+ labels = ' '.join(design['sample_id'])
+ mbs_filename = 'sample_mbs.npz'
+
+ mbs_command = (
+ "multiBamSummary bins -p %d --bamfiles %s --labels %s -out %s"
+ % (cpu_count(), bam_files, labels, mbs_filename)
+ )
+
+ logger.info("Running deeptools with %s", mbs_command)
+
+ read_summary = subprocess.Popen(mbs_command, shell=True)
+ out, err = read_summary.communicate()
+
+ return mbs_filename
+
+
+def check_correlation(mbs):
+ '''Check Spearman pairwise correlation of samples based on read counts.'''
+
+ spearman_filename = 'heatmap_SpearmanCorr.png'
+ spearman_params = "--corMethod spearman --skipZero" + \
+ " --plotTitle \"Spearman Correlation of Read Counts\"" + \
+ " --whatToPlot heatmap --colorMap RdYlBu --plotNumbers"
+
+ spearman_command = (
+ "plotCorrelation -in %s %s -o %s"
+ % (mbs, spearman_params, spearman_filename)
+ )
+
+ logger.info("Running deeptools with %s", spearman_command)
+
+ spearman_correlation = subprocess.Popen(spearman_command, shell=True)
+ out, err = spearman_correlation.communicate()
+
+
+def check_coverage(design):
+ '''Asses the sequencing depth of samples.'''
+
+ bam_files = ' '.join(design['bam_reads'])
+ labels = ' '.join(design['sample_id'])
+ coverage_filename = 'coverage.png'
+ coverage_params = "-n 1000000 --plotTitle \"Sample Coverage\"" + \
+ " --ignoreDuplicates --minMappingQuality 10"
+
+ coverage_command = (
+ "plotCoverage -b %s --labels %s %s --plotFile %s"
+ % (bam_files, labels, coverage_params, coverage_filename)
+ )
+
+ logger.info("Running deeptools with %s", coverage_command)
+
+ coverage_summary = subprocess.Popen(coverage_command, shell=True)
+ out, err = coverage_summary.communicate()
+
+
+def update_controls(design):
+ '''Update design file to append controls list.'''
+
+ logger.info("Running control file update.")
+
+ file_dict = design[['sample_id', 'bam_reads']] \
+ .set_index('sample_id').T.to_dict()
+
+ design['control_reads'] = design['control_id'] \
+ .apply(lambda x: file_dict[x]['bam_reads'])
+
+ logger.info("Removing rows that are there own control.")
+
+ design = design[design['control_id'] != design['sample_id']]
+
+ return design
+
+
+def check_enrichment(sample_id, control_id, sample_reads, control_reads):
+ '''Asses the enrichment per sample.'''
+
+ fingerprint_filename = sample_id + '_fingerprint.png'
+
+ fingerprint_command = (
+ "plotFingerprint -b %s %s --labels %s %s --plotFile %s"
+ % (sample_reads, control_reads, sample_id, control_id, fingerprint_filename)
+ )
+
+ logger.info("Running deeptools with %s", fingerprint_command)
+
+ fingerprint_summary = subprocess.Popen(fingerprint_command, shell=True)
+ out, err = fingerprint_summary.communicate()
+
def main():
- argparser = prepare_argparser()
- args = argparser.parse_args()
- run(args.infile, args.genome)
-
+ args = get_args()
+
+ # Create a file handler
+ handler = logging.FileHandler('experiment_qc.log')
+ logger.addHandler(handler)
+
+ # Check if tools are present
+ check_tools()
+
+ # Read files
+ design_file = pd.read_csv(args.design, sep='\t')
+
+ # Run correlation
+ mbs_filename = generate_read_summary(design_file)
+ check_correlation(mbs_filename)
+
+ # Run coverage
+ check_coverage(design_file)
+
+ # Run enrichment
+ new_design = update_controls(design_file)
+ for index, row in new_design.iterrows():
+ check_enrichment(
+ row['sample_id'],
+ row['control_id'],
+ row['bam_reads'],
+ row['control_reads'])
+
-if __name__=="__main__":
- main()
+if __name__ == '__main__':
+ main()
diff --git a/workflow/tests/test_experiment_qc.py b/workflow/tests/test_experiment_qc.py
new file mode 100644
index 0000000..ad5a867
--- /dev/null
+++ b/workflow/tests/test_experiment_qc.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python3
+
+import pytest
+import os
+import pandas as pd
+from io import StringIO
+import experiment_qc
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+ '/../output/filterReads/'
+
+DESIGN_STRING = """sample_id\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\tbam_reads
+A_1\tA\tLiver\tH3K27ac\tNone\t1\tB_1\tA_1.bam
+A_2\tA\tLiver\tH3K27ac\tNone\t2\tB_2\tA_2.bam
+B_1\tB\tLiver\tInput\tNone\t1\tB_1\tB_1.bam
+B_2\tB\tLiver\tInput\tNone\t2\tB_2\tB_2.bam
+"""
+
+
+@pytest.fixture
+def design_bam():
+ design_file = StringIO(DESIGN_STRING)
+ design_df = pd.read_csv(design_file, sep="\t")
+ return design_df
+
+
+def test_check_update_controls(design_bam):
+ new_design = experiment_qc.update_controls(design_bam)
+ assert new_design.loc[0, 'control_reads'] == "B_1.bam"
+
+
+def test_experiment_qc_singleend():
+ assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
+ assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'coverage.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_fingerprint.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI_fingerprint.png'))
+
+
+def test_experiment_qc_pairedend():
+ # Do the same thing for paired end data
+ pass
diff --git a/workflow/tests/test_utils.py b/workflow/tests/test_utils.py
index b5a18a6..0abba1b 100644
--- a/workflow/tests/test_utils.py
+++ b/workflow/tests/test_utils.py
@@ -30,7 +30,7 @@ def steps_2(steps_1):
def test_run_one_step(steps_1, capsys):
- check_output = 'ENCBS844FSC\tENCSR238SGC\tlimb\tH3K4me1\tNone\t1\tENCBS844FSC\tENCFF833BLU.fastq.gz'.encode('UTF-8')
+ check_output = 'ENCLB144FDT\tENCSR238SGC\tlimb\tH3K4me1\tNone\t1\tENCLB304SBJ\tENCFF833BLU.fastq.gz'.encode('UTF-8')
out, err = utils.run_pipe(steps_1)
output, errors = capsys.readouterr()
assert "first step shlex to stdout" in output
--
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