def _make_permutations(recipe, output_dir, overwrite):
"""
Runs Cactus, then outputs preprocessesed results into output_dir
"""
work_dir = os.path.join(output_dir, CACTUS_WORKDIR)
files = {}
if overwrite and os.path.isdir(work_dir):
shutil.rmtree(work_dir)
if os.path.isdir(work_dir):
#using existing results
logger.warning("Using existing Cactus results from previous run")
logger.warning("Use --overwrite to force alignment")
for block_size in recipe["blocks"]:
block_dir = os.path.join(work_dir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
if not os.path.isfile(coords_file):
raise BackendException("Exitsing results are incompatible "
"with input recipe")
files[block_size] = os.path.abspath(coords_file)
else:
#running cactus
for genome, params in recipe["genomes"].items():
if "fasta" not in params:
raise BackendException("FASTA file for {0} is not "
"specified".format(genome))
os.mkdir(work_dir)
config_path = _make_cactus_config(recipe, work_dir)
ref_genome = recipe["target"]
maf_file = _run_cactus(config_path, ref_genome, work_dir)
logger.info("Converting maf to synteny")
if not m2s.make_synteny(maf_file, work_dir, recipe["blocks"]):
raise BackendException("Something went wrong with maf2synteny")
for block_size in recipe["blocks"]:
block_dir = os.path.join(work_dir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
files[block_size] = os.path.abspath(coords_file)
if not os.path.exists(coords_file):
raise BackendException("Something bad happened!")
return files
def _make_permutations(recipe, output_dir, overwrite):
work_dir = os.path.join(output_dir, CACTUS_WORKDIR)
files = {}
if overwrite and os.path.isdir(work_dir):
shutil.rmtree(work_dir)
if os.path.isdir(work_dir):
#using existing results
logger.warning("Using existing Cactus results from previous run")
logger.warning("Use --overwrite to force alignment")
for block_size in recipe["blocks"]:
block_dir = os.path.join(work_dir, str(block_size))
perm_file = os.path.join(block_dir, "genomes_permutations.txt")
if not os.path.isfile(perm_file):
raise BackendException("Exitsing results are incompatible "
"with input recipe")
files[block_size] = os.path.abspath(perm_file)
else:
#running cactus
for genome, params in recipe["genomes"].items():
if "fasta" not in params:
raise BackendException("FASTA file for {0} is not "
"specified".format(genome))
os.mkdir(work_dir)
config_path = _make_cactus_config(recipe, work_dir)
ref_genome = recipe["target"]
maf_file = _run_cactus(config_path, ref_genome, work_dir)
logger.info("Converting maf to synteny")
if not m2s.make_synteny(maf_file, work_dir, recipe["blocks"]):
raise BackendException("Something went wrong with maf2synteny")
for block_size in recipe["blocks"]:
block_dir = os.path.join(work_dir, str(block_size))
perm_file = os.path.join(block_dir, "genomes_permutations.txt")
files[block_size] = os.path.abspath(perm_file)
if not os.path.exists(perm_file):
raise BackendException("Something bad happened!")
return files
def run_backend(self, recipe, output_dir, overwrite):
logger.warning("Maf support is deprecated and will be removed "
"in future releases. Use hal istead.")
workdir = os.path.join(output_dir, MAF_WORKDIR)
if overwrite and os.path.isdir(workdir):
shutil.rmtree(workdir)
if "maf" not in recipe or not os.path.exists(recipe["maf"]):
raise BackendException("Could not open MAF file "
"or it is not specified")
files = {}
if os.path.isdir(workdir):
#using existing results
logger.warning("Using synteny blocks from previous run")
logger.warning("Use --overwrite to force alignment")
for block_size in self.blocks:
block_dir = os.path.join(workdir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
if not os.path.isfile(coords_file):
raise BackendException("Exitsing results are incompatible "
"with input recipe")
files[block_size] = os.path.abspath(coords_file)
else:
os.mkdir(workdir)
logger.info("Converting MAF to synteny")
if not m2s.make_synteny(recipe["maf"], workdir, self.blocks):
raise BackendException("Something went wrong with maf2synteny")
for block_size in self.blocks:
block_dir = os.path.join(workdir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
files[block_size] = os.path.abspath(coords_file)
if not os.path.exists(coords_file):
raise BackendException("Something bad happened!")
return files
def run_backend(self, recipe, output_dir, overwrite):
logger.warning("Maf support is deprecated and will be removed "
"in future releases. Use hal istead.")
workdir = os.path.join(output_dir, MAF_WORKDIR)
if overwrite and os.path.isdir(workdir):
shutil.rmtree(workdir)
if "maf" not in recipe or not os.path.exists(recipe["maf"]):
raise BackendException("Could not open MAF file "
"or it is not specified")
files = {}
if os.path.isdir(workdir):
#using existing results
logger.warning("Using synteny blocks from previous run")
logger.warning("Use --overwrite to force alignment")
for block_size in self.blocks:
block_dir = os.path.join(workdir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
if not os.path.isfile(coords_file):
raise BackendException("Exitsing results are incompatible "
"with input recipe")
files[block_size] = os.path.abspath(coords_file)
else:
os.mkdir(workdir)
logger.info("Converting MAF to synteny")
if not m2s.make_synteny(recipe["maf"], workdir, self.blocks):
raise BackendException("Something went wrong with maf2synteny")
for block_size in self.blocks:
block_dir = os.path.join(workdir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
files[block_size] = os.path.abspath(coords_file)
if not os.path.exists(coords_file):
raise BackendException("Something bad happened!")
return files
def run_backend(self, recipe, output_dir, overwrite):
workdir = os.path.join(output_dir, MAF_WORKDIR)
if overwrite and os.path.isdir(workdir):
shutil.rmtree(workdir)
if "maf" not in recipe or not os.path.exists(recipe["maf"]):
raise BackendException("Could not open MAF file "
"or it is not specified")
files = {}
if os.path.isdir(workdir):
#using existing results
logger.warning("Using synteny blocks from previous run")
logger.warning("Use --overwrite to force alignment")
for block_size in recipe["blocks"]:
block_dir = os.path.join(workdir, str(block_size))
perm_file = os.path.join(block_dir, "genomes_permutations.txt")
if not os.path.isfile(perm_file):
raise BackendException("Exitsing results are incompatible "
"with input recipe")
files[block_size] = os.path.abspath(perm_file)
else:
os.mkdir(workdir)
logger.info("Converting MAF to synteny")
if not m2s.make_synteny(recipe["maf"], workdir, recipe["blocks"]):
raise BackendException("Something went wrong with maf2synteny")
for block_size in recipe["blocks"]:
block_dir = os.path.join(workdir, str(block_size))
perm_file = os.path.join(block_dir, "genomes_permutations.txt")
files[block_size] = os.path.abspath(perm_file)
if not os.path.exists(perm_file):
raise BackendException("Something bad happened!")
return files
def run_backend(self, recipe, output_dir, overwrite):
workdir = os.path.join(output_dir, MAF_WORKDIR)
if overwrite and os.path.isdir(workdir):
shutil.rmtree(workdir)
if "maf" not in recipe or not os.path.exists(recipe["maf"]):
raise BackendException("Could not open MAF file "
"or it is not specified")
files = {}
if os.path.isdir(workdir):
#using existing results
logger.warning("Using synteny blocks from previous run")
logger.warning("Use --overwrite to force alignment")
for block_size in recipe["blocks"]:
block_dir = os.path.join(workdir, str(block_size))
perm_file = os.path.join(block_dir, "genomes_permutations.txt")
if not os.path.isfile(perm_file):
raise BackendException("Exitsing results are incompatible "
"with input recipe")
files[block_size] = os.path.abspath(perm_file)
else:
os.mkdir(workdir)
logger.info("Converting MAF to synteny")
if not m2s.make_synteny(recipe["maf"], workdir, recipe["blocks"]):
raise BackendException("Something went wrong with maf2synteny")
for block_size in recipe["blocks"]:
block_dir = os.path.join(workdir, str(block_size))
perm_file = os.path.join(block_dir, "genomes_permutations.txt")
files[block_size] = os.path.abspath(perm_file)
if not os.path.exists(perm_file):
raise BackendException("Something bad happened!")
return files
def run_backend(self, recipe, output_dir, overwrite):
workdir = os.path.join(output_dir, HAL_WORKDIR)
if overwrite and os.path.isdir(workdir):
shutil.rmtree(workdir)
if "hal" not in recipe or not os.path.exists(recipe["hal"]):
raise BackendException("Could not open HAL file "
"or it is not specified")
files = {}
#using existing results
if os.path.isdir(workdir):
logger.warning("Using synteny blocks from previous run")
logger.warning("Use --overwrite to force alignment")
all_good = True
for block_size in self.blocks:
block_dir = os.path.join(workdir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
if not os.path.isfile(coords_file):
all_good = False
break
files[block_size] = os.path.abspath(coords_file)
target_fasta = os.path.join(workdir, TARGET_FASTA)
if not os.path.isfile(target_fasta):
all_good = False
else:
self.target_fasta = target_fasta
if not all_good:
raise BackendException("Exitsing results are incompatible "
"with current run")
else:
os.mkdir(workdir)
logger.info("Extracting FASTA from HAL")
target_fasta = os.path.join(workdir, TARGET_FASTA)
cmdline = [HAL2FASTA, recipe["hal"], recipe["target"],
"--inMemory"]
subprocess.check_call(cmdline, stdout=open(target_fasta, "w"))
self.target_fasta = target_fasta
logger.info("Converting HAL to MAF")
out_maf = os.path.join(workdir, "alignment.maf")
ref_genome = recipe["target"] #Tricky notation, huh?
export_genomes = ",".join(recipe["genomes"])
cmdline = [HAL2MAF, recipe["hal"], out_maf, "--noAncestors",
"--numProc", str(self.threads), "--refGenome",
ref_genome, "--targetGenomes", export_genomes]
logger.debug(" ".join(cmdline))
subprocess.check_call(cmdline, stdout=open(os.devnull, "w"))
logger.info("Extracting synteny blocks from MAF")
if not m2s.make_synteny(out_maf, workdir, self.blocks):
raise BackendException("Something went wrong with maf2synteny")
for block_size in self.blocks:
block_dir = os.path.join(workdir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
files[block_size] = os.path.abspath(coords_file)
if not os.path.exists(coords_file):
raise BackendException("Something bad happened!")
return files
def run_backend(self, recipe, output_dir, overwrite):
workdir = os.path.join(output_dir, HAL_WORKDIR)
if overwrite and os.path.isdir(workdir):
shutil.rmtree(workdir)
if "hal" not in recipe or not os.path.exists(recipe["hal"]):
raise BackendException("Could not open HAL file "
"or it is not specified")
files = {}
#using existing results
if os.path.isdir(workdir):
logger.warning("Using synteny blocks from previous run")
logger.warning("Use --overwrite to force alignment")
all_good = True
for block_size in self.blocks:
block_dir = os.path.join(workdir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
if not os.path.isfile(coords_file):
all_good = False
break
files[block_size] = os.path.abspath(coords_file)
target_fasta = os.path.join(workdir, TARGET_FASTA)
if not os.path.isfile(target_fasta):
all_good = False
else:
self.target_fasta = target_fasta
if not all_good:
raise BackendException("Exitsing results are incompatible "
"with current run")
else:
os.mkdir(workdir)
logger.info("Extracting FASTA from HAL")
target_fasta = os.path.join(workdir, TARGET_FASTA)
cmdline = [HAL2FASTA, recipe["hal"], recipe["target"],
"--inMemory"]
subprocess.check_call(cmdline, stdout=open(target_fasta, "w"))
self.target_fasta = target_fasta
logger.info("Converting HAL to MAF")
out_maf = os.path.join(workdir, "alignment.maf")
ref_genome = recipe["target"] #Tricky notation, huh?
export_genomes = ",".join(recipe["genomes"])
cmdline = [HAL2MAF, recipe["hal"], out_maf, "--noAncestors",
"--numProc", str(self.threads), "--refGenome",
ref_genome, "--targetGenomes", export_genomes]
logger.debug(" ".join(cmdline))
subprocess.check_call(cmdline, stdout=open(os.devnull, "w"))
logger.info("Extracting synteny blocks from MAF")
if not m2s.make_synteny(out_maf, workdir, self.blocks):
raise BackendException("Something went wrong with maf2synteny")
for block_size in self.blocks:
block_dir = os.path.join(workdir, str(block_size))
coords_file = os.path.join(block_dir, "blocks_coords.txt")
files[block_size] = os.path.abspath(coords_file)
if not os.path.exists(coords_file):
raise BackendException("Something bad happened!")
return files