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November 16, 2015 21:14
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from airflow import DAG | |
from airflow.operators import BashOperator, PythonOperator | |
from datetime import datetime, timedelta | |
from sqlalchemy.ext.automap import automap_base | |
from sqlalchemy.orm import Session | |
from sqlalchemy import create_engine | |
from sqlalchemy import or_, and_ | |
from os import system | |
# Commenting out full list of contigs for now leaving only 1-22, X, Y | |
#contig_names = ["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y","MT","GL000207.1","GL000226.1","GL000229.1","GL000231.1","GL000210.1","GL000239.1","GL000235.1","GL000201.1","GL000247.1","GL000245.1","GL000197.1","GL000203.1","GL000246.1","GL000249.1","GL000196.1","GL000248.1","GL000244.1","GL000238.1","GL000202.1","GL000234.1","GL000232.1","GL000206.1","GL000240.1","GL000236.1","GL000241.1","GL000243.1","GL000242.1","GL000230.1","GL000237.1","GL000233.1","GL000204.1","GL000198.1","GL000208.1","GL000191.1","GL000227.1","GL000228.1","GL000214.1","GL000221.1","GL000209.1","GL000218.1","GL000220.1","GL000213.1","GL000211.1","GL000199.1","GL000217.1","GL000216.1","GL000215.1","GL000205.1","GL000219.1","GL000224.1","GL000223.1","GL000195.1","GL000212.1","GL000222.1","GL000200.1","GL000193.1","GL000194.1","GL000225.1","GL000192.1","NC_007605","hs37d5"] | |
contig_names = ["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y"] | |
#donor_index = "23" | |
#sample_id = "f87f8019-db9f-46d0-9e39-d16a37646815" | |
reference_location = "/reference/genome.fa" | |
variants_location = "/shared/data/samples/vcf/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.snv.multibreak.vcf.gz" | |
results_base_path = "/shared/data/results/regenotype" | |
def lookup_sample_location(donor_index): | |
Base = automap_base() | |
engine = create_engine('postgresql://pcawg_admin:pcawg@postgresql.service.consul:5432/germline_genotype_tracking') | |
Base.prepare(engine, reflect=True) | |
SampleLocation = Base.classes.sample_locations | |
session = Session(engine) | |
my_sample_location = session.query(SampleLocation).filter(SampleLocation.donor_index==donor_index).first() | |
if my_sample_location: | |
return my_sample_location.normal_sample_location | |
else: | |
print "Sample location could not be found for donor: " + str(donor_index) | |
exit(1) | |
session.close() | |
engine.dispose() | |
def get_next_sample(): | |
Base = automap_base() | |
engine = create_engine('postgresql://pcawg_admin:pcawg@postgresql.service.consul:5432/germline_genotype_tracking') | |
Base.prepare(engine, reflect=True) | |
PCAWGSample = Base.classes.pcawg_samples | |
SampleLocation = Base.classes.sample_locations | |
GenotypingRun = Base.classes.genotyping_runs | |
session = Session(engine) | |
next_sample = session.query(PCAWGSample).\ | |
join(SampleLocation, PCAWGSample.index == SampleLocation.donor_index).\ | |
outerjoin(GenotypingRun,PCAWGSample.index == GenotypingRun.donor_index).\ | |
filter(\ | |
and_(SampleLocation.normal_sample_location != None, \ | |
or_(GenotypingRun.run_status == None, GenotypingRun.run_status != 1)\ | |
)).\ | |
first() | |
session.close() | |
engine.dispose() | |
if next_sample != None: | |
return (next_sample.index, next_sample.normal_wgs_alignment_gnos_id) | |
else: | |
print "Could not find next sample" | |
exit(1) | |
def set_error(): | |
os.system("/tmp/germline-regenotyper/scripts/update-sample-status.py {{ task_instance.xcom_pull(task_ids='get_sample_assignment')[0] }} {{ task_instance.xcom_pull(task_ids='get_sample_assignment')[1] }} 3") | |
def run_freebayes(**kwargs): | |
contig_name = kwargs["contig_name"] | |
ti = kwargs["ti"] | |
donor_index = ti.xcom_pull(task_ids='get_sample_assignment')[0] | |
sample_id = ti.xcom_pull(task_ids='get_sample_assignment')[1] | |
sample_location = lookup_sample_location(donor_index) | |
result_filename = "/tmp/" + sample_id + "_regenotype_" + contig_name + ".vcf" | |
freebayes_command = "freebayes -r " + contig_name +\ | |
" -f " + reference_location +\ | |
" -@ " + variants_location +\ | |
" -l " + sample_location +\ | |
" > " + result_filename | |
os.system(freebayes_command) | |
return result_filename | |
default_args = { | |
'owner': 'airflow', | |
'depends_on_past': False, | |
'start_date': datetime(2015, 11, 9), | |
'email': ['airflow@airflow.com'], | |
'email_on_failure': False, | |
'email_on_retry': False, | |
'retries': 1, | |
'retry_delay': timedelta(minutes=5), | |
# 'queue': 'bash_queue', | |
# 'pool': 'backfill', | |
# 'priority_weight': 10, | |
# 'end_date': datetime(2016, 1, 1), | |
} | |
dag = DAG("freebayes-regenotype", default_args=default_args) | |
get_sample_assignment_task = PythonOperator( | |
task_id = "get_sample_assignment", | |
python_callable = get_next_sample, | |
dag = dag) | |
reserve_sample_task = BashOperator( | |
task_id = "reserve_sample", | |
bash_command = "python /tmp/germline-regenotyper/scripts/update-sample-status.py {{ task_instance.xcom_pull(task_ids='get_sample_assignment')[0] }} {{ task_instance.xcom_pull(task_ids='get_sample_assignment')[1] }} 1", | |
dag = dag) | |
reserve_sample_task.set_upstream(get_sample_assignment_task) | |
release_sample_task = BashOperator( | |
task_id = "release_sample", | |
bash_command = "python /tmp/germline-regenotyper/scripts/update-sample-status.py {{ task_instance.xcom_pull(task_ids='get_sample_assignment')[0] }} {{ task_instance.xcom_pull(task_ids='get_sample_assignment')[1] }} 2", | |
dag = dag) | |
for contig_name in contig_names: | |
genotyping_task = PythonOperator( | |
task_id = "regenotype_" + contig_name, | |
python_callable = run_freebayes, | |
op_kwargs={"contig_name": contig_name}, | |
dag = dag) | |
genotyping_task.set_upstream(reserve_sample_task) | |
data_compress_task = BashOperator( | |
task_id = "compress_result_" + contig_name, | |
bash_command = "/usr/local/bin/bgzip -c {{ task_instance.xcom_pull(task_ids='regenotype_" + contig_name + "') }} > {{ task_instance.xcom_pull(task_ids='regenotype_" + contig_name + "') }}.gz", | |
dag = dag) | |
data_compress_task.set_upstream(genotyping_task) | |
generate_tabix_task = BashOperator( | |
task_id = "generate_tabix_" + contig_name, | |
bash_command = "/usr/local/bin/tabix -f -p vcf {{ task_instance.xcom_pull(task_ids='regenotype_" + contig_name + "') }}.gz", | |
dag = dag) | |
generate_tabix_task.set_upstream(data_compress_task) | |
data_copy_task = BashOperator( | |
task_id = "copy_result_" + contig_name, | |
bash_command = 'mkdir -p ' + results_base_path + '/{{ task_instance.xcom_pull(task_ids="get_sample_assignment")[1] }}/ && cp /tmp/{{ task_instance.xcom_pull(task_ids="get_sample_assignment")[0] }}_regenotype_' + contig_name + '.vcf.gz* "$_"', | |
dag = dag) | |
data_copy_task.set_upstream(generate_tabix_task) | |
release_sample_task.set_upstream(data_copy_task) | |
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