def getWorkdir(self, hide_dir=False, str_=True):
if hide_dir:
return utils.returnPath(
self.workDir / "Scripts" / ("_" + self.name) / "pipeline",
str_)
else:
return utils.returnPath(
self.workDir / "Scripts" / self.name / "pipeline", str_)
def renameLocalDir(self):
work_dir_prefix = utils.returnPath(self.workDir / "Scripts", False)
work_dir_off = work_dir_prefix / ("_" + self.name)
work_dir_on = work_dir_prefix / self.name
if self.run:
work_dir = Path(work_dir_on / "pipeline")
if (os.path.isdir(work_dir_off)):
try:
os.rename(work_dir_off, work_dir_on)
except:
raise OSError(
f"Could not rename {work_dir_off} to {work_dir_on}\n \
try running 'drop update' to reset file structure\n")
else:
logger.info(f"{self.name} has been turned off in the config file")
work_dir = Path(work_dir_off / "pipeline")
if (os.path.isdir(work_dir_on)):
try:
os.rename(work_dir_on, work_dir_off)
except:
raise OSError(
f"Could not rename {work_dir_on} to {work_dir_off}\n \
try running 'drop update' to reset file structure\n")
return work_dir
def getFilePattern(self, str_=True, expandStr=False):
pattern = self.pattern
if expandStr:
pattern = pattern.__str__().replace("{", "{{").replace("}", "}}")
return utils.returnPath(pattern, str_=str_)
def getWorkdir(self, str_=True):
return utils.returnPath(Path("Scripts") / self.name / "pipeline", str_)
def getHtmlFromScript(self, path, str_=True):
path = Path(path).with_suffix(".html")
file_name = wbuild.utils.pathsepsToUnderscore(str(path), dotsToUnderscore=False)
html_output_path = self.getHtmlOutputPath(str_=False)
return utils.returnPath(html_output_path / file_name, str_=str_)
def getHtmlOutputPath(self, str_=True):
return utils.returnPath(self.htmlOutputPath, str_=str_)
def getProcessedResultsDir(self, str_=True):
return utils.returnPath(self.processedResultsDir, str_=str_)
def getRoot(self, str_=True):
return utils.returnPath(self.root, str_=str_)
def getFilePattern(self, str_=True):
return utils.returnPath(self.pattern, str_=str_)
def getFastaDict(self, str_=True):
return utils.returnPath(self.fastaDict, str_)
def getFastaFile(self, str_=True):
return utils.returnPath(self.fastaFile, str_)
