class GenomeIndexPipeline(object):
def __init__(self, config):
self.config = config
# assert self.config.genome.version == 'hg19'
self.genome = Genome(self.config)
assert self.genome.aligner is not None
def copy_chromes_files(self):
self.config.check_nonempty_workdir(self.config.genome.genome_dir)
for chrom in self.genome.version.CHROMS_ALL:
if chrom == 'chrY':
continue
src = os.path.join(
self.config.genome.genome_pristine_dir,
"{}.fa".format(chrom)
)
dst = os.path.join(
self.config.genome.genome_dir,
"{}.fa".format(chrom)
)
print(colored(
"copying chromosome {} from {} into "
"working directory {}".format(
chrom, src, dst),
"green"))
if not self.config.dry_run:
shutil.copy(src, dst)
def mask_pars(self):
dst = self.genome.chrom_filename('chrY')
print(colored(
"masking pseudoautosomal regions in chrY",
"green")
)
if os.path.exists(dst) and not self.config.force:
print(colored(
"destination file for masked chrY already exists",
"red"
))
raise ValueError("dst file already exists")
if not self.config.dry_run:
masked = self.genome.mask_chrY_pars()
self.genome.save_chrom(masked, 'chrY')
def concatenate_all_chroms(self):
dirname = self.config.genome.genome_dir
dst = os.path.join(
dirname,
'genome.fa'
)
if os.path.exists(dst) and not self.config.force:
print(colored(
"destination genome file already exists"
"use --force to overwrite", "red"))
raise ValueError("destination file exists... use --force")
if not self.config.dry_run:
with open(dst, 'wb') as output:
for chrom in self.genome.version.CHROMS_ALL:
src = self.genome.chrom_filename(chrom, pristine=False)
print(colored(
"appending {} to {}".format(src, dst),
"green"))
with open(src, 'rb') as src:
if not self.config.dry_run:
shutil.copyfileobj(src, output, 1024 * 1024 * 10)
def build_aligner_index(self):
print(colored(
f"building genome index of {self.genome.sequence_filename} "
f"into {self.genome.index_prefix}",
"green"))
command = " ".join(self.genome.aligner.build_index_command(
self.genome.sequence_filename,
self.genome.index_prefix
))
print(colored(
f"going to execute aligner genome index build: {command}",
"green"))
test_filename = self.genome.aligner.genome_index_filenames[0]
print(colored(f"checking for index file: {test_filename}", "green"))
if os.path.exists(test_filename) and not self.config.force:
print(colored(
"output genome index {} already exists".format(test_filename),
"red"))
raise ValueError("destination file already exists")
if not self.config.dry_run:
subprocess.check_call(command, shell=True)
def run(self, **kwargs):
self.copy_chromes_files()
self.mask_pars()
self.concatenate_all_chroms()
self.build_aligner_index()
class GenomeIndexPipeline(object):
def __init__(self, config):
self.config = config
# assert self.config.genome.version == 'hg19'
self.hg = Genome(self.config)
def copy_chromes_files(self):
self.config.check_nonempty_workdir(
self.config.abspath(self.config.genome.work_dir))
for chrom in self.hg.version.CHROMS_ALL:
if chrom == 'chrY':
continue
src = os.path.join(
self.config.genome.data_dir,
"{}.fa".format(chrom)
)
dst = os.path.join(
self.config.genome.work_dir,
"{}.fa".format(chrom)
)
print(colored(
"copying chromosome {} from {} into "
"working directory {}".format(
chrom, src, dst),
"green"))
if not self.config.dry_run:
shutil.copy(src, dst)
def mask_pars(self):
dst = self.config.chrom_filename('chrY')
print(colored(
"masking pseudoautosomal regions in chrY",
"green")
)
if os.path.exists(dst) and not self.config.force:
print(colored(
"destination file for masked chrY already exists",
"red"
))
raise ValueError("dst file already exists")
if not self.config.dry_run:
masked = self.hg.mask_chrY_pars()
self.hg.save_chrom(masked, 'chrY')
def concatenate_all_chroms(self):
dirname = self.config.genome.work_dir
dst = os.path.join(
dirname,
'genome.fa'
)
if os.path.exists(dst) and not self.config.force:
print(colored(
"destination genome file already exists"
"use --force to overwrite", "red"))
raise ValueError("destination file exists... use --force")
if not self.config.dry_run:
with open(dst, 'wb') as output:
for chrom in self.hg.version.CHROMS_ALL:
src = self.config.chrom_filename(chrom, pristine=False)
print(colored(
"appending {} to {}".format(src, dst),
"green"))
with open(src, 'rb') as src:
if not self.config.dry_run:
shutil.copyfileobj(src, output, 1024 * 1024 * 10)
def build_bowtie_index(self):
src = os.path.join(
self.config.genome.work_dir,
'genome.fa'
)
dst = os.path.join(
self.config.genome.work_dir,
self.config.genome.index
)
print(colored(
"building bowtie index of {} into {}".format(src, dst),
"green"))
command = "bowtie-build -f {} {}".format(src, dst)
print(colored(
"executing bowtie-build: {}".format(command),
"green"))
test_filename = "{}.1.bt2".format(dst)
if os.path.exists(test_filename) and not self.config.force:
print(colored(
"output bowtie index {} already exists".format(test_filename),
"red"))
raise ValueError("destination file already exists")
if not self.config.dry_run:
subprocess.check_call(command, shell=True)
def run(self):
self.copy_chromes_files()
self.mask_pars()
self.concatenate_all_chroms()
self.build_bowtie_index()