Adding GATK concordance script (connected to #167)

src/toil_scripts/gatk_concordance/gatk_concordance.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python2.7
+
+import argparse
+import multiprocessing
+import os
+import subprocess
+
+from toil.job import Job
+
+from toil_scripts import download_from_s3_url
+from toil_scripts.batch_alignment.bwa_alignment import upload_to_s3, docker_call
+
+def build_parser():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-r', '--reference', required=True, help="Reference Genome URL")
+    parser.add_argument('-i', '--reference_index', required=True, help="Reference Genome index (.fai) URL")
+    parser.add_argument('-e', '--eval_vcf', required=True, help="VCF file URL to evaluate")
+    parser.add_argument('-c', '--comp_vcf', required=True, help="VCF file URL to compare against")
+    parser.add_argument('-o', '--output_dir', required=True, help="Output directory S3 URL")
+    return parser
+
+
+# copied from germline.py
+def download_url_c(job, url, filename):
+    work_dir = job.fileStore.getLocalTempDir()
+    file_path = os.path.join(work_dir, filename)
+    if not os.path.exists(file_path):
+        if url.startswith('s3:'):
+            download_from_s3_url(file_path, url)
+        else:
+            try:
+                subprocess.check_call(['curl', '-fs', '--retry', '5', '--create-dir', url, '-o', file_path])
+            except subprocess.CalledProcessError as cpe:
+                raise RuntimeError(
+                    '\nNecessary file could not be acquired: %s. Got error "%s". Check input URL' % (url, cpe))
+            except OSError:
+                raise RuntimeError('Failed to find "curl". Install via "apt-get install curl"')
+    assert os.path.exists(file_path)
+    return job.fileStore.writeGlobalFile(file_path)
+
+
+# copied from germline.py
+def read_from_filestore_c(job, work_dir, ids, *filenames):
+    for filename in filenames:
+        if not os.path.exists(os.path.join(work_dir, filename)):
+            job.fileStore.readGlobalFile(ids[filename], os.path.join(work_dir, filename))
+
+
+def batch_start(job, input_args):
+    shared_files = ['ref.fa', 'ref.fa.fai', 'eval.vcf', 'comp.vcf']
+    shared_ids = {}
+    for file_name in shared_files:
+        url = input_args[file_name]
+        shared_ids[file_name] = job.addChildJobFn(download_url_c, url, file_name).rv()
+    job.addFollowOnJobFn(concordance, shared_ids, input_args)
+
+
+def concordance(job, shared_ids, input_args):
+    """
+    Evaluate concordance between two VCFs with GATK.
+    """
+    work_dir = job.fileStore.getLocalTempDir()
+    input_files = ['ref.fa', 'ref.fa.fai', 'eval.vcf', 'comp.vcf']
+    read_from_filestore_c(job, work_dir, shared_ids, *input_files)
+
+    eval_name = input_args['eval.vcf'].split('/')[-1]
+    comp_name = input_args['comp.vcf'].split('/')[-1]
+    output = '%s_vs_%s.concordance' % (eval_name, comp_name)
+    command = ['-T', 'GenotypeConcordance',
+               '-R', 'ref.fa',
+               '--eval', 'eval.vcf',
+               '--comp', 'comp.vcf',
+               '-o', output
+    ]
+    try:
+        docker_call(work_dir = work_dir,
+                    tool_parameters = command,
+                    tool = 'quay.io/ucsc_cgl/gatk',
+                    sudo = input_args['sudo'])
+    except:
+        sys.stderr.write("Running concordance with %s in %s failed." % (
+            " ".join(command), work_dir))
+        raise
+
+    upload_to_s3(work_dir, input_args, output)
+
+
+if __name__ == '__main__':
+    args_parser = build_parser()
+    Job.Runner.addToilOptions(args_parser)
+    args = args_parser.parse_args()
+
+    inputs = {'ref.fa': args.reference,
+              'ref.fa.fai': args.reference_index,
+              'eval.vcf', args.eval_vcf,
+              'comp.vcf', args.comp_vcf,
+              's3_dir', args.output_dir,
+              'uuid': None,
+              'cpu_count': str(multiprocessing.cpu_count()),
+              'ssec': None,
+              'sudo': False}
+
+    Job.Runner.startToil(Job.wrapJobFn(batch_start, inputs), args)