Python read Examples

Example #1

File: SConstruct_hic.py Project: koadman/proxigenomics

from nestly import Nest, stripext
from nestly.scons import SConsWrap, name_targets
import os
import os.path
import appconfig

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"])

Example #2

File: SConstruct_quast.py Project: koadman/proxigenomics

from nestly import Nest, stripext
from nestly.scons import SConsWrap, name_targets
import os
import os.path
import appconfig

config = appconfig.read('config.yaml')

nest = Nest()
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)

Example #3

File: SConstruct_srmcl.py Project: thebevrishot/proxigenomics

from nestly import Nest
from nestly.scons import SConsWrap, name_targets
import os
import os.path
import numpy
import appconfig

config = appconfig.read('config.yaml')

# Base folder
nest = Nest()
wrap = SConsWrap(
    nest,
    os.path.join(config['cluster']['folder'],
                 config['cluster']['algorithms']['srmcl']['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', 'local'])

# Variation

# don't include root as we don't want it embedded in this nest hierarchy
hic_paths = appconfig.get_precedents(config['map_folder'],
                                     config['hic2ctg'],
                                     prepend_root=False,
                                     tips_only=True)
wrap.add('hic_path', hic_paths)