def _run_sibelia(fasta_files, block_size, out_dir):
logger.info("Running Sibelia with block size " + str(block_size))
if not utils.which(SIBELIA_EXEC):
raise BackendException("Sibelia is not installed")
devnull = open(os.devnull, "w")
cmdline = [SIBELIA_EXEC, "-s", "fine", "-m", str(block_size), "-o", out_dir]
cmdline.extend(fasta_files)
subprocess.check_call(cmdline, stdout=devnull)
os.remove(os.path.join(out_dir, "d3_blocks_diagram.html"))
shutil.rmtree(os.path.join(out_dir, "circos"))
return os.path.join(out_dir, "genomes_permutations.txt")
def check_binary():
"""
Checks if the native binary is available and runnable
"""
binary = which(OVERLAP_EXEC)
if not binary:
logger.error("\"%s\" native module not found", OVERLAP_EXEC)
return False
try:
devnull = open(os.devnull, "w")
subprocess.check_call([OVERLAP_EXEC, "--help"], stderr=devnull)
except subprocess.CalledProcessError as e:
logger.error("Some error inside native module: %s", str(e))
return False
return True
def _run_sibelia(fasta_files, block_size, out_dir):
logger.info("Running Sibelia with block size %d", block_size)
if not utils.which(SIBELIA_EXEC):
raise BackendException("Sibelia is not installed")
stagefile = os.path.join(out_dir, "stagefile.txt")
_make_stagefile(config.vals["sibelia"], stagefile)
devnull = open(os.devnull, "w")
cmdline = [SIBELIA_EXEC, "--nopostprocess", "--stagefile", stagefile,
"--minblocksize", str(block_size), "--outdir", out_dir]
cmdline.extend(fasta_files)
subprocess.check_call(cmdline, stdout=devnull)
os.remove(stagefile)
os.remove(os.path.join(out_dir, "d3_blocks_diagram.html"))
shutil.rmtree(os.path.join(out_dir, "circos"))
def _run_sibelia(fasta_files, block_size, out_dir):
logger.info("Running Sibelia with block size " + str(block_size))
if not utils.which(SIBELIA_EXEC):
raise BackendException("Sibelia is not installed")
stagefile = os.path.join(out_dir, "stagefile.txt")
_make_stagefile(config.vals["sibelia"], stagefile)
devnull = open(os.devnull, "w")
cmdline = [SIBELIA_EXEC, "--nopostprocess", "--stagefile", stagefile,
"--minblocksize", str(block_size), "--outdir", out_dir]
cmdline.extend(fasta_files)
subprocess.check_call(cmdline, stdout=devnull)
os.remove(stagefile)
os.remove(os.path.join(out_dir, "d3_blocks_diagram.html"))
shutil.rmtree(os.path.join(out_dir, "circos"))
def check_binary():
"""
Checks if the native binary is available and runnable
"""
binary = which(OVERLAP_EXEC)
if not binary:
logger.error("\"{0}\" native module not found".format(OVERLAP_EXEC))
return False
try:
devnull = open(os.devnull, "w")
subprocess.check_call([OVERLAP_EXEC, "--help"], stderr=devnull)
except subprocess.CalledProcessError as e:
logger.error("Some error inside native {0} module: {1}"
.format(OVERLAP_EXEC, e))
return False
return True
def _run_sibelia(fasta_files, block_size, out_dir):
logger.info("Running Sibelia with block size " + str(block_size))
if not utils.which(SIBELIA_EXEC):
raise BackendException("Sibelia is not installed")
devnull = open(os.devnull, "w")
cmdline = [
SIBELIA_EXEC, "-s", "fine", "-m",
str(block_size), "-o", out_dir
]
cmdline.extend(fasta_files)
subprocess.check_call(cmdline, stdout=devnull)
os.remove(os.path.join(out_dir, "d3_blocks_diagram.html"))
shutil.rmtree(os.path.join(out_dir, "circos"))
return os.path.join(out_dir, "genomes_permutations.txt")
def check_binary():
"""
Checks if native binary is available and runnable
"""
binary = which(M2S_EXEC)
if not binary:
logger.error("\"{0}\" native module not found".format(M2S_EXEC))
return False
try:
devnull = open(os.devnull, "w")
subprocess.check_call([M2S_EXEC, "-h"], stderr=devnull)
except subprocess.CalledProcessError as e:
logger.error("Some error inside native {0} module: {1}".format(
M2S_EXEC, e))
return False
return True
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
if utils.which(HAL2MAF) and utils.which(HAL2FASTA) and utils.which(HAL_STATS):
SyntenyBackend.register_backend("hal", HalBackend())
def _check_installation():
return bool(utils.which(SIBELIA_EXEC))
def _check_installation():
return bool(utils.which(SIBELIA_EXEC))
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
if utils.which(HAL2MAF) and utils.which(HAL2FASTA) and utils.which(HAL_STATS):
SyntenyBackend.register_backend("hal", HalBackend())
