config = appconfig.read("config.yaml")
nest = Nest()
wrap = SConsWrap(nest, config["hic_folder"])
env = Environment(ENV=os.environ)
# Constants
wrap.add("seed", [config["seed"]], create_dir=False)
wrap.add("refseq", [config["community"]["seq"]], create_dir=False)
wrap.add("hic_base", [config["hic_base"]], create_dir=False)
wrap.add("hic_inter_prob", [config["hic_inter_prob"]], create_dir=False)
wrap.add("hic_read_length", [config["hic_read_length"]], create_dir=False)
# Variation
genomes = appconfig.find_files(config["community"]["folder"], config["community"]["seq"])
commPaths = [os.path.dirname(pn) for pn in genomes]
wrap.add("community", commPaths)
tableFolder = os.path.join(config["reference"]["folder"], config["reference"]["table_folder"])
tablePaths = appconfig.get_files(tableFolder, "table")
wrap.add("comm_table", tablePaths, label_func=os.path.basename)
wrap.add("hic_n_frag", config["hic_n_frag"])
@wrap.add_target("generate_hic")
def generate_hic(outdir, c):
source = "{1[community][folder]}/{0[community]}/{0[refseq]}".format(c, config)
target = "{od}/{0[hic_base]}.fasta".format(c, od=outdir)
action = (
wrap = SConsWrap(nest, config['quast_folder'])
env = Environment(ENV=os.environ)
# Used for resolving what type of execution environment will be used.
exec_env = appconfig.ExecutionEnvironment(ARGUMENTS, supported_env=['pbs', 'sge'])
# Constants
wrap.add('seed', [config['seed']], create_dir=False)
wrap.add('refseq', [config['community']['seq']], create_dir=False)
wrap.add('wgs_read_length', [config['wgs_read_length']], create_dir=False)
wrap.add('wgs_insert_length', [config['wgs_insert_length']], create_dir=False)
wrap.add('wgs_insert_sd', [config['wgs_insert_sd']], create_dir=False)
wrap.add('wgs_base', [config['wgs_base']], create_dir=False)
# Variation
genomes = appconfig.find_files(config['community']['folder'], config['community']['seq'])
commPaths = [os.path.dirname(pn) for pn in genomes]
wrap.add('community', commPaths)
tableFolder = os.path.join(config['reference']['folder'], config['reference']['table_folder'])
tablePaths = appconfig.get_files(tableFolder, 'table')
wrap.add('comm_table', tablePaths, label_func=os.path.basename)
wrap.add('wgs_xfold', config['wgs_xfold'])
@wrap.add_target('run_quast')
@name_targets
def generate_wgs(outdir, c):
asm_path = os.path.join(config['wgs_folder'], '/'.join(outdir.split('/')[1:]), config['wgs_asmdir'])
ctg_file = '{0}/{1}.contigs.fasta'.format(asm_path, config['wgs_base'])
env = Environment(ENV=os.environ)
# Used for resolving what type of execution environment will be used.
exec_env = appconfig.ExecutionEnvironment(ARGUMENTS,
supported_env=['pbs', 'sge'])
# Constants
wrap.add('seed', [config['seed']], create_dir=False)
wrap.add('refseq', [config['community']['seq']], create_dir=False)
wrap.add('wgs_read_length', [config['wgs_read_length']], create_dir=False)
wrap.add('wgs_insert_length', [config['wgs_insert_length']], create_dir=False)
wrap.add('wgs_insert_sd', [config['wgs_insert_sd']], create_dir=False)
wrap.add('wgs_base', [config['wgs_base']], create_dir=False)
# Variation
genomes = appconfig.find_files(config['community']['folder'],
config['community']['seq'])
commPaths = [os.path.dirname(pn) for pn in genomes]
wrap.add('community', commPaths)
tableFolder = os.path.join(config['reference']['folder'],
config['reference']['table_folder'])
tablePaths = appconfig.get_files(tableFolder, 'table')
wrap.add('comm_table', tablePaths, label_func=os.path.basename)
wrap.add('wgs_xfold', config['wgs_xfold'])
@wrap.add_target('run_quast')
@name_targets
def generate_wgs(outdir, c):