from preprocess.reference_genome import load_and_pickle_reference_genome, load_pickled_reference_genome
try:
PULSE_PATH = os.environ['PULSE_PATH']
except KeyError:
print('Environment variable PULSE_PATH not setup')
print('Using working directory')
PULSE_PATH = os.getcwd()
if __name__ == "__main__":
all_cell_lines = os.listdir(PULSE_PATH + "/input/cell_lines")
print(all_cell_lines)
PREPROCESS_SETTINGS = PULSE_PATH + '/preprocess/preprocess_settings.json'
# Uncomment below to load and pickle reference genome.
print("LOADING AND PICKLING REFERENCE GENOME.")
load_and_pickle_reference_genome(PULSE_PATH, PREPROCESS_SETTINGS)
print("SUCCESSFULLY PICKLED REFERENCE GENOME!")
print("LOADING PICKLED REFERENCE GENOME (happens only once for all cell lines)...")
ref_genome = load_pickled_reference_genome(PULSE_PATH)
print("PICKLED REFERENCE GENOME LOADED!")
for cell_line in all_cell_lines:
submit_new_job('for_preprocess/cufflinks.py', ['-p', PULSE_PATH, '-c', cell_line])
PREPROCESS_OUTPUT_PATH = PULSE_PATH + '/output/preprocess/' + cell_line
submit_new_job('preprocess/main.py', ['-c', cell_line, '-r', ref_genome, '-p', PULSE_PATH,
'-o', PREPROCESS_OUTPUT_PATH])
# The most time-expensive tasks are for_preprocessing
# (cufflinks and samtools) and preprocessing (blast)
# For every cell line, this script submits a cufflinks task.
# For dependencies, check for_preprocess/cufflinks
import os
from submit_job import submit_new_job
from for_preprocess import for_preprocess, cufflinks, samtools
try:
PULSE_PATH = os.environ['PULSE_PATH']
except KeyError:
print('Environment variable PULSE_PATH not setup')
print('Using working directory')
PULSE_PATH = os.getcwd()
if __name__ == "__main__":
all_cell_lines = os.listdir(PULSE_PATH + "/input/cell_lines")
print(all_cell_lines)
for cell_line in all_cell_lines:
for_preprocess.create_paths_for_cell_line(cell_line)
submit_new_job('for_preprocess/cufflinks.py', ['-p', PULSE_PATH, '-c', cell_line])
# The most time-expensive tasks are for_preprocessing
# (cufflinks and samtools) and preprocessing (blast)
# For every cell line, this script submits a samtools task.
import os
from submit_job import submit_new_job
from for_preprocess import for_preprocess, cufflinks, samtools
try:
PULSE_PATH = os.environ['PULSE_PATH']
except KeyError:
print('Environment variable PULSE_PATH not setup')
print('Using working directory')
PULSE_PATH = os.getcwd()
if __name__ == "__main__":
all_cell_lines = os.listdir(PULSE_PATH + "/input/cell_lines")
print(all_cell_lines)
for cell_line in all_cell_lines:
for_preprocess.create_paths_for_cell_line(cell_line)
submit_new_job('for_preprocess/samtools.py', ['-p', PULSE_PATH, '-c', cell_line])
