def run_bh(configs_dir, execution_home, cfg, ext_python_modules_home, log):
addsitedir(ext_python_modules_home)
import pyyaml
dst_configs = os.path.join(cfg.output_dir, "configs")
if os.path.exists(dst_configs):
shutil.rmtree(dst_configs)
shutil.copytree(os.path.join(configs_dir, "hammer"), dst_configs)
cfg_file_name = os.path.join(dst_configs, "config.info")
# removing template configs
for root, dirs, files in os.walk(dst_configs):
for cfg_file in files:
cfg_file = os.path.join(root, cfg_file)
if cfg_file.endswith('.info.template'):
if os.path.isfile(cfg_file.split('.template')[0]):
os.remove(cfg_file)
else:
os.rename(cfg_file, cfg_file.split('.template')[0])
prepare_config_bh(cfg_file_name, cfg, log)
command = os.path.join(execution_home, "hammer") + " " +\
os.path.abspath(cfg_file_name)
log.info("\n== Running read error correction tool: " + command + "\n")
support.sys_call(command, log)
corrected_dataset_yaml_filename = os.path.join(cfg.tmp_dir, "corrected.yaml")
corrected_dataset_data = pyyaml.load(file(corrected_dataset_yaml_filename, 'r'))
if cfg.gzip_output:
log.info("\n== Compressing corrected reads (with gzip)")
support.move_dataset_files(corrected_dataset_data, cfg.output_dir, log, cfg.gzip_output)
corrected_dataset_yaml_filename = os.path.join(cfg.output_dir, "corrected.yaml")
pyyaml.dump(corrected_dataset_data, file(corrected_dataset_yaml_filename, 'w'))
log.info("\n== Dataset description file created: " + corrected_dataset_yaml_filename + "\n")
shutil.rmtree(cfg.tmp_dir)
return corrected_dataset_yaml_filename
if not options_storage.output_dir:
support.error("the output_dir is not set! It is a mandatory parameter (-o output_dir).", log)
if not os.path.isdir(options_storage.output_dir):
os.makedirs(options_storage.output_dir)
if options_storage.dataset_yaml_filename:
try:
dataset_data = pyyaml.load(file(options_storage.dataset_yaml_filename, "r"))
except pyyaml.YAMLError, exc:
support.error(
"exception caught while parsing YAML file (" + options_storage.dataset_yaml_filename + "):\n" + str(exc)
)
else:
dataset_data = support.correct_dataset(dataset_data)
options_storage.dataset_yaml_filename = os.path.join(options_storage.output_dir, "input_dataset.yaml")
pyyaml.dump(dataset_data, file(options_storage.dataset_yaml_filename, "w"))
support.check_dataset_reads(dataset_data, log)
if support.dataset_has_only_mate_pairs_libraries(dataset_data):
support.error(
"you should specify at least one paired-end or unpaired library (only mate-pairs libraries were found)!"
)
if options_storage.rectangles and (len(dataset_data) > 1):
support.error("rectangle graph algorithm for repeat resolution cannot work with multiple libraries!")
### FILLING cfg
cfg["common"] = empty_config()
cfg["dataset"] = empty_config()
if not options_storage.only_assembler:
cfg["error_correction"] = empty_config()
if not options_storage.only_error_correction:
def create_text_and_key(self, selected_text):
# The source file's pathreload
source = self.view.file_name()
key_link = selected_text.replace(" ", "_")[0:30].strip("_").lower()
# Get the file path
source_path = os.path.dirname(source)
fileName = os.path.basename(source).replace(".html", "").replace(".erb", "").replace(".haml", "").strip("_")
rails_view_path = os.path.dirname(source_path)
rails_view_path2 = os.path.dirname(rails_view_path)
rails_view_path3 = os.path.dirname(rails_view_path2)
rails_view_path4 = os.path.dirname(rails_view_path3)
if is_rails_view(source_path):
# If we're a rails view file, change the target path to the rails root and add path to locales
target_file = os.path.abspath(source_path + "/../../") + "/config/locales/en.yml"
yaml_dict = pyyaml.load(file(target_file, 'r'))
if not yaml_dict["en"].has_key(str(fileName)):
yaml_dict["en"][str(fileName)] = {}
yaml_dict["en"][str(fileName)][str(key_link)] = str(selected_text)
rails_view_path = source_path
if is_rails_view(rails_view_path):
# If we're a rails view file, change the target path to the rails root and add path to locales
target_file = os.path.abspath(source_path + "/../../../") + "/config/locales/en.yml"
key = source_path.replace(rails_view_path, "").strip("/")
yaml_dict = pyyaml.load(file(target_file, 'r'))
if not yaml_dict["en"].has_key(str(key)):
yaml_dict["en"][str(key)] = {}
if not yaml_dict["en"][str(key)].has_key(str(fileName)):
yaml_dict["en"][str(key)][str(fileName)] = {}
yaml_dict["en"][str(key)][str(fileName)][str(key_link)] = str(selected_text)
rails_view_path = rails_view_path
if is_rails_view(rails_view_path2):
# If we're a rails view file, change the target path to the rails root and add path to locales
target_file = os.path.abspath(source_path + "/../../../../") + "/config/locales/en.yml"
key = rails_view_path.replace(rails_view_path2, "").strip("/")
key2 = source_path.replace(rails_view_path, "").strip("/")
yaml_dict = pyyaml.load(file(target_file, 'r'))
if not yaml_dict["en"].has_key(str(key)):
yaml_dict["en"][str(key)] = {}
if not yaml_dict["en"][str(key)].has_key(str(key2)):
yaml_dict["en"][str(key)][str(key2)] = {}
if not yaml_dict["en"][str(key)][str(key2)].has_key(str(fileName)):
yaml_dict["en"][str(key)][str(key2)][str(fileName)] = {}
yaml_dict["en"][str(key)][str(key2)][str(fileName)][str(key_link)] = str(selected_text)
rails_view_path = rails_view_path2
if is_rails_view(rails_view_path3):
# If we're a rails view file, change the target path to the rails root and add path to locales
target_file = os.path.abspath(source_path + "/../../../../../") + "/config/locales/en.yml"
key = rails_view_path.replace(rails_view_path3, "").strip("/")
key2 = rails_view_path.replace(rails_view_path2, "").strip("/")
key = key.replace("/"+key2, "")
key3 = source_path.replace(rails_view_path, "").strip("/")
yaml_dict = pyyaml.load(file(target_file, 'r'))
if not yaml_dict["en"].has_key(str(key)):
yaml_dict["en"][str(key)] = {}
if not yaml_dict["en"][str(key)].has_key(str(key2)):
yaml_dict["en"][str(key)][str(key2)] = {}
if not yaml_dict["en"][str(key)][str(key2)].has_key(str(key3)):
yaml_dict["en"][str(key)][str(key2)][str(key3)] = {}
if not yaml_dict["en"][str(key)][str(key2)][str(key3)].has_key(str(fileName)):
yaml_dict["en"][str(key)][str(key2)][str(key3)][str(fileName)] = {}
yaml_dict["en"][str(key)][str(key2)][str(key3)][str(fileName)][str(key_link)] = str(selected_text)
rails_view_path = rails_view_path3
if os.path.isfile(target_file):
#insert key to view file
stream = file(target_file, 'w')
pyyaml.dump(yaml_dict, stream, default_flow_style=False)
stream.close()
self.insert_key_link(key_link, source)
else:
self.display_message(target_file + " not exist")