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ariadne_pipeline.py
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ariadne_pipeline.py
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import luigi
from os import makedirs
from os.path import join as djoin
from os.path import exists
import subprocess
import shutil
from assembly_support import (
barcode_sorter,
complete_reads
)
from evaluate_support import (
fastq_to_table,
generate_summaries
)
# spack load gcc@6.3.0
# PYTHONPATH='.' luigi --module ariadne_pipeline de_Novo_Assembly --local-scheduler
def check_make(curr_dir, sub):
outdir = djoin(curr_dir, sub)
if not exists(outdir):
makedirs(outdir)
return outdir
class Single_Sort_FastQ(luigi.Task):
in_dir = luigi.Parameter()
prefix = luigi.Parameter()
direction = luigi.Parameter()
out_dir = luigi.Parameter()
def output(self):
return luigi.LocalTarget(djoin(self.out_dir, '.'.join([self.prefix + '_bsort', self.direction, 'fastq'])))
def run(self):
barcode_sorter(djoin(self.in_dir, '.'.join([self.prefix, self.direction, 'fastq'])), self.out_dir, False)
class Sort_FastQs_by_Barcode(luigi.Task):
"""Sort raw barcoded reads by barcode."""
def requires(self):
return [Single_Sort_FastQ(in_dir=gp.read_dir, prefix=gp.prefix, direction='R1', out_dir=gp.read_dir),
Single_Sort_FastQ(in_dir=gp.read_dir, prefix=gp.prefix, direction='R2', out_dir=gp.read_dir)]
def output(self):
return self.input()
class cloudSPAdes_init(luigi.Task):
"""Run cloudSPAdes on the sorted read clouds."""
def requires(self):
return Sort_FastQs_by_Barcode()
def output(self):
return luigi.LocalTarget(djoin(gp.cs_init_dir, 'scaffolds.fasta'))
#[luigi.LocalTarget(djoin(gp.cs_init_dir, 'K55', gp.search_dist + '.R1.fastq')), luigi.LocalTarget(djoin(gp.cs_init_dir, 'K55', gp.search_dist + '.R2.fastq'))]
def run(self):
if exists(djoin(gp.cs_init_dir, 'K33', 'assembly_graph.fastg')): # The previous iteration exists, run from the last one.
retcode = subprocess.run(['/home/lam4003/bin/spades/assembler/spades.py', '--restart-from', 'k55', '-o', gp.cs_init_dir])
else: # The initial cloudSPAdes iterations do not exist.
retcode = subprocess.run(['/home/lam4003/bin/spades/assembler/spades.py', '--meta', '--only-assembler', '--gemcode1-1',
self.input()[0].path, '--gemcode1-2', self.input()[1].path, '--search-distance', gp.search_dist,
'--size-cutoff', '6', '-t', gp.num_threads, '-m', gp.memory, '-o', gp.cs_init_dir])
spades_mem = int(gp.memory) + 100
while retcode.returncode:
retcode = subprocess.run(['/home/lam4003/bin/spades/assembler/spades.py', '--restart-from', 'k55', '-m', str(spades_mem), '-o', gp.cs_init_dir])
spades_mem += 100
class Make_Unbarcoded_FastQs(luigi.Task):
pass
class Single_Complete_FastQ(luigi.Task):
"""Complete the Ariadne-deconvolved read dataset i.e.: add missing reads from the original sorted FastQ."""
direction = luigi.Parameter()
def requires(self):
return cloudSPAdes_init() #, Make_Unbarcoded_FastQs()]
def output(self):
return luigi.LocalTarget(
djoin(gp.ariadne_dir, '.'.join([gp.ariadne_prefix, self.direction, 'fastq'])))
def run(self):
# complete_reads(djoin(gp.read_dir, '.'.join([gp.prefix + '_bsort', self.direction, 'fastq'])),
# djoin(gp.cs_init_dir, 'K55', '.'.join([gp.search_dist, self.direction, 'fastq'])),
# djoin(gp.ariadne_dir, '.'.join([gp.search_dist + '_full', self.direction, 'fastq'])))
# yield Single_Sort_FastQ(in_dir = gp.ariadne_dir, prefix = gp.search_dist + '_full', direction = self.direction,
# out_dir = gp.ariadne_dir)
with self.output().open('w') as out_fq:
with open(djoin(gp.cs_init_dir, 'K55', '.'.join([gp.search_dist, self.direction, 'fastq']))) as ari_fq, \
open(djoin(gp.read_dir, '.'.join([gp.prefix + '_nobc', self.direction, 'fastq']))) as nobc_fq:
out_fq.write(ari_fq.read())
out_fq.write(nobc_fq.read())
class Complete_Ariadne_FastQs(luigi.Task):
"""Individually complete the Ariadne-deconvolved FastQs, then sort in order of the first FastQ."""
def requires(self):
finished_fastqs = []
for i in ['R1', 'R2']:
finished_fastqs.append(Single_Complete_FastQ(direction=i))
return finished_fastqs
def output(self):
return [luigi.LocalTarget(
djoin(gp.ariadne_dir, gp.ariadne_prefix + '.R1.fastq')), luigi.LocalTarget(
djoin(gp.ariadne_dir, gp.ariadne_prefix + '.R2.fastq'))]
class cloudSPAdes_final(luigi.Task):
"""Run cloudSPAdes on the completed Ariadne-deconvolved read clouds."""
def requires(self):
return Complete_Ariadne_FastQs()
def output(self):
return luigi.LocalTarget(djoin(gp.analyses_dir, gp.search_dist + '.scaffolds.fasta'))
def run(self):
fastq_prefix = djoin(gp.cs_init_dir, 'K55', gp.search_dist)
retcode = subprocess.run(['/home/lam4003/bin/spades/assembler/spades.py', '--meta', '--only-assembler', \
'--gemcode1-1', djoin(gp.ariadne_dir, gp.ariadne_prefix + '.R1.fastq'), \
'--gemcode1-2', djoin(gp.ariadne_dir, gp.ariadne_prefix + '.R2.fastq'), \
'--search-distance', '0', '--size-cutoff', '6', '-t', gp.num_threads, '-m', gp.memory, '-o', gp.cs_final_dir])
# '-k', '55', '--assembly-graph', djoin(gp.cs_init_dir, 'assembly_graph.fastg')])
spades_mem = int(gp.memory) + 100
while retcode.returncode:
retcode = subprocess.run(['/home/lam4003/bin/spades/assembler/spades.py', '--restart-from', 'k55', '-m', str(spades_mem), '-o', gp.cs_final_dir])
spades_mem += 100
shutil.copy(djoin(gp.cs_final_dir, 'scaffolds.fasta'), self.output().path)
class Single_FastQ_to_Table(luigi.Task):
direction = luigi.Parameter()
def requires(self):
return cloudSPAdes_init()
def output(self):
return luigi.LocalTarget(djoin(gp.analyses_dir, '.'.join([gp.search_dist, self.direction, 'csv'])))
def run(self):
fastq_to_table(djoin(gp.cs_init_dir, 'K55', '.'.join([gp.search_dist, self.direction, 'fastq'])),
djoin(gp.analyses_dir, '.'.join([gp.gstd_prefix, self.direction, 'csv'])), gp.analyses_dir)
class Summarize_FastQ_Statistics(luigi.Task):
"""Generate size, purity, and entropy summary statistics from enhanced reads."""
def requires(self):
# Match predicted read clouds to actual (reference sequence) read clouds
fastq_tbls = []
for i in ['R1','R2']:
fastq_tbls.append(Single_FastQ_to_Table(direction = i))
return fastq_tbls
def output(self):
return luigi.LocalTarget(djoin(gp.analyses_dir, gp.search_dist + '.statistics.csv'))
def run(self):
# Generate read cloud quality statistics tables
generate_summaries(self.input()[0].path, self.input()[1].path, gp.analyses_dir, None)
class de_Novo_Assembly(luigi.WrapperTask):
"""Top-level function calling cloudSPAdes and enhancement summaries."""
read_dir = luigi.Parameter()
prefix = luigi.Parameter()
search_dist = luigi.Parameter()
gold_standard = luigi.Parameter()
master_dir = luigi.Parameter()
num_threads = luigi.Parameter()
memory = luigi.Parameter()
def requires(self):
gp.set_params(self.read_dir, self.prefix, self.search_dist, self.gold_standard, self.master_dir, self.num_threads, self.memory)
yield cloudSPAdes_final()
yield Summarize_FastQ_Statistics()
class Global_Parameters:
"""Store parameters, prefixes, and target paths. Adapted from https://stackoverflow.com/questions/51152485/luigi-global-variables."""
def __init__(self):
self.read_dir = None
self.work_dir = None
self.prefix = None
self.search_dist = None
self.gstd_prefix = None
self.num_threads = None
self.memory = None
self.cs_init_dir = None
self.ariadne_dir = None
self.cs_final_dir = None
self.analyses_dir = None
def set_params(self, read_dir, prefix, search_dist, gold_standard, master_dir, num_threads, memory):
self.read_dir = read_dir
self.work_dir = check_make(master_dir, prefix + '_' + search_dist)
self.prefix = prefix
self.search_dist = search_dist
self.ariadne_prefix = search_dist + '_full_bsort'
self.gstd_prefix = gold_standard
self.num_threads = num_threads
self.memory = memory
self.cs_init_dir = check_make(self.work_dir, 'cloudSPAdes_init')
self.ariadne_dir = check_make(self.work_dir, 'ariadne_intermediate')
self.cs_final_dir = check_make(self.work_dir, 'cloudSPAdes_final')
self.analyses_dir = check_make(master_dir, prefix + '_' + 'analyses')
gp = Global_Parameters()
if __name__ == '__main__':
luigi.run(main_cls_task=de_Novo_Assembly)