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prepare.cre.py
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prepare.cre.py
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import os
import sys
import glob
import argparse
import pprint
import subprocess
from collections import OrderedDict
ALLOWED_INPUT_EXTENSIONS = OrderedDict({"*.fq": "fastq","*.fastq": "fastq","*.fq.gz":"fastq","*.fastq.gz":"fastq","*.cram":"cram","*.bam":"bam"})
parser = argparse.ArgumentParser()
parser.add_argument("-u", "--upload-dir", help="Directory containing uploaded files for samples", required=True)
parser.add_argument("-d", "--processing-dir", help="Directory to create pipeline folders in", required=True)
parser.add_argument("-s", "--sample-list", help="File with SampleIDs. One per line. SampleIDs must be in the format famID_sampleName", required=True)
args = parser.parse_args()
if args.upload_dir is not None:
if os.path.exists(args.upload_dir) and os.path.isdir(args.upload_dir):
UPLOAD_DIRECTORY = args.upload_dir
else:
print(args.upload_dir+" is not a valid directory")
sys.exit(0)
if args.processing_dir is not None:
if os.path.exists(args.processing_dir) and os.path.isdir(args.processing_dir):
PROCESSING_DIRECTORY = args.processing_dir
os.chdir(PROCESSING_DIRECTORY)
SUBMIT_SCRIPTS_DIRECTORY = os.path.join(PROCESSING_DIRECTORY,"submit_scripts")
SUBMIT_LOG_DIRECTORY = os.path.join(PROCESSING_DIRECTORY,"submit_logs")
for directory in (SUBMIT_SCRIPTS_DIRECTORY, SUBMIT_LOG_DIRECTORY):
if not os.path.exists(directory):
subprocess.run(['mkdir',directory])
else:
print(args.processing_dir+" is not a valid directory")
sys.exit(0)
if args.sample_list is not None:
if os.path.exists(args.sample_list) and os.path.isfile(args.sample_list):
SAMPLE_FILE = args.sample_list
else:
print(args.sample_list + " is not a valid file")
sys.exit(0)
def check_and_return_input_files(family_id, sample_name):
input_files = []
input_file_type = None
sample_id = '_'.join([family_id, sample_name])
for extension,filetype in ALLOWED_INPUT_EXTENSIONS.items():
for dirpath,dirnames,filename in os.walk(UPLOAD_DIRECTORY):
for subdirectory in dirnames:
if subdirectory == sample_id: ## upload folders must be named in sample_id format
input_files = glob.glob(os.path.join(dirpath,subdirectory,extension))
if filetype == "fastq" and len(input_files) >0:
input_files = list(filter(lambda elem: '_R1_' in elem or '_R2_' in elem, input_files))
if len(input_files) == 0:
print("Fastq files for this sample do not have _R1_ or _R2_ in them")
if len(input_files) >0:
input_file_type = filetype
break
if len(input_files) >0:
break
if len(input_files) >0:
break
return (input_files,input_file_type)
def prepare_input_files(inputs):
family_id, sample_name = inputs['sample_id'].split("_")
job_name = inputs['sample_id'] + "_" + inputs['command']
job_file = os.path.join(SUBMIT_SCRIPTS_DIRECTORY,job_name+".sh")
input_files_directory = os.path.join(PROCESSING_DIRECTORY,family_id,"input")
cram_files_directory = os.path.join(PROCESSING_DIRECTORY,family_id,"cram")
with open(job_file,"w") as submit_fh:
#print_headers here
#submit_fh.write("#PBS -l walltime=20:00:00,nodes=1:ppn=1\n#PBS -joe \n#PBS -o {1}\n#PBS -d {0}\n#PBS -l vmem=30g,mem=30g\n\n".format(PROCESSING_DIRECTORY,SUBMIT_LOG_DIRECTORY))
submit_fh.write("#PBS -l walltime=20:00:00,nodes=1:ppn=1\n#PBS -o {1}\n#PBS -d {0}\n#PBS -l vmem=30g,mem=30g\n\n".format(PROCESSING_DIRECTORY,SUBMIT_LOG_DIRECTORY))
submit_fh.write("mkdir -p {0}\n".format(input_files_directory))
if inputs['input_files'][0].endswith('.cram'):
submit_fh.write("mkdir -p {0}\n".format(cram_files_directory))
if inputs['input_file_type'] == 'fastq':
inp_link = None
for input_file in inputs['input_files']:
if '_R1_' in input_file:
inp_link = family_id + "_" + sample_name + "_1.fq"
if '_R2_' in input_file:
inp_link = family_id + "_" + sample_name + "_2.fq"
if input_file.endswith(".gz"):
inp_link +=".gz"
submit_fh.write("ln -s {} {}\n".format(input_file,os.path.join(input_files_directory,inp_link)))
if inputs['input_file_type'] == 'bam':
inp_link = inputs['sample_id'] + ".bam"
submit_fh.write("ln -s {} {}\n".format(inputs['input_files'][0],os.path.join(input_files_directory,inp_link)))
if inputs['input_file_type'] == 'cram':
inp_link = inputs['sample_id'] + ".cram"
submit_fh.write("ln -s {} {}\n\n".format(inputs['input_files'][0],os.path.join(cram_files_directory,inp_link)))
submit_fh.write("module load java\n\n")
submit_fh.write("cramtools fastq -Xmx10g -F {} --skip-md5-check -z -I {} -R /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa\n\n".format(inputs['sample_id'],os.path.join(cram_files_directory,inp_link)))
submit_fh.write("mv {} {}\n".format(os.path.join(PROCESSING_DIRECTORY,inputs['sample_id']+"_1.fastq.gz"),os.path.join(input_files_directory,inputs['sample_id']+"_1.fq.gz")))
submit_fh.write("mv {} {}\n".format(os.path.join(PROCESSING_DIRECTORY,inputs['sample_id']+"_2.fastq.gz"),os.path.join(input_files_directory,inputs['sample_id']+"_2.fq.gz")))
submit_fh.close()
return job_file
def prepare_config_files(inputs):
family_id, sample_name = inputs['sample_id'].split("_")
job_name = family_id + "_" + inputs['command']
job_file = os.path.join(SUBMIT_SCRIPTS_DIRECTORY,job_name+".sh")
with open(job_file,"w") as submit_fh:
#print_headers here
submit_fh.write("#PBS -l walltime=1:00:00,nodes=1:ppn=1\n#PBS -joe\n#PBS -o {1}\n#PBS -d {0}\n#PBS -l vmem=20g,mem=20g\n\n".format(PROCESSING_DIRECTORY,SUBMIT_LOG_DIRECTORY))
submit_fh.write("~/cre/cre.prepare_bcbio_run.sh "+ str(family_id))
submit_fh.close()
return job_file
def submit_job(**params):
family_id, sample_name = params['sample_id'].split("_")
job_to_submit = None
if params['command'] == 'prepare':
job_to_submit = prepare_input_files(params)
elif params['command'] == 'config':
job_to_submit = prepare_config_files(params)
elif params['command'] == 'bcbio':
job_to_submit = ' ~/cre/bcbio.pbs -v project='+ str(family_id)
elif params['command'] == 'cre':
job_to_submit = ' ~/cre/cre.sh -v family='+ str(family_id)+',cleanup=1'
if job_to_submit is not None:
if len(params['previous_job_ids']) == 0:
output = subprocess.run(["qsub",job_to_submit], stdout=subprocess.PIPE)
else:
previous_job_id_str = ":".join(params['previous_job_ids'])
output = subprocess.run(["qsub -W depend=afterok:"+previous_job_id_str+" "+job_to_submit],shell=True, stdout=subprocess.PIPE)
job_id = output.stdout.decode('utf-8').rstrip()
return str(job_id)
steps = ["prepare","config","bcbio","cre"]
families = {}
with open(SAMPLE_FILE,"r") as inp_fh:
for line in inp_fh:
line = line.rstrip()
if '_' not in line:
print(line + " not in correct format. sample_id must be in the format famid_samplename")
sys.exit(0)
family_id, sample_name = line.split("_")
if family_id not in families:
families[family_id] =[]
families[family_id].append(sample_name)
inp_fh.close()
for family_id in families:
print("Processing family "+ str(family_id))
job_ids = []
run_bcbio = 1
for sample_name in families[family_id]:
sample_id = family_id+"_"+sample_name
input_files, input_file_type = check_and_return_input_files(family_id, sample_name)
if len(input_files) == 0:
print("No recognized input files for sample "+sample_id+ ". Not setting up this family")
run_bcbio = 0
continue
if (input_file_type == 'bam' or input_file_type == 'cram') and len(input_files)>1:
print("Multiple bam/cram files exist for sample "+sample_id+". Not setting up this family")
run_bcbio = 0
continue
job_ids.append(submit_job(sample_id=sample_id,previous_job_ids=[],command="prepare",input_files=input_files, input_file_type=input_file_type))
if run_bcbio:
for step in steps[1:]:
job_id = submit_job(sample_id=sample_id, previous_job_ids=job_ids, command=step, input_files=input_files, input_file_type=input_file_type)
job_ids = [job_id]