bug fix blast DB computation (#23)

.gitignore

@@ -128,6 +128,13 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# DS_store
+**/.DS_Store
+/fdog/.DS_Store
+/fdog/data/.DS_Store
+/fdog/bin/.DS_Store
+/fdog/setup/.DS_Store
+
 #Hannah
 /fdog/data/core_orthologs/
 /fdog/data/assembly_dir/

fdog/.gitignore

@@ -0,0 +1,143 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# DS_store
+**/.DS_Store
+/fdog/.DS_Store
+/fdog/data/.DS_Store
+/fdog/bin/.DS_Store
+/fdog/setup/.DS_Store
+
+#Hannah
+/fdog/data/core_orthologs/
+/fdog/data/assembly_dir/
+/fdog/fdog_goes_assembly/tmp/ 
+taxdump*
+/fdog/fDOGassembly.py

fdog/fDOGassembly.py

@@ -721,6 +721,9 @@ def ortholog_search_tblastn(args):
  assembly_path = assemblyDir + "/" + asName + "/" + asName + ".fa"
  db_path = assemblyDir + "/" + asName + "/blast_dir/" + asName + ".fa"
  blast_dir_path = assemblyDir + "/" + asName + "/blast_dir/"
+ if not os.path.exists(blast_dir_path):
+ cmd = 'mkdir ' + blast_dir_path
+ starting_subprocess(cmd, 'silent')
  db_check = searching_for_db(blast_dir_path)
 
  if db_check == 0:

fdog/runMulti.py

@@ -75,7 +75,7 @@ def prepare(args, step):
  return(basicArgs, ioArgs, pathArgs, coreArgs, orthoArgs, fasArgs, otherArgs, mute)
 
 def getSeedName(seedFile):
- seqName = seedFile.split('.')[0]
+ seqName = seedFile.rsplit('.', 1)[0]
  seqName = re.sub('[\|\.]', '_', seqName)
  return(seqName)
 
@@ -217,14 +217,11 @@ def createConfigPP(outpath, jobName, refspec):
  settings['rank'] = 'species'
  settings['refspec'] = refspec
  settings['clusterProfile'] = 'TRUE'
- print("HERER")
- print(settings)
- print('%s/%s.config.yml' % (outpath, jobName))
  with open('%s/%s.config.yml' % (outpath, jobName), 'w') as configfile:
  yaml.dump(settings, configfile, default_flow_style = False)
 
 def main():
- version = '0.0.51'
+ version = '0.0.52'
  parser = argparse.ArgumentParser(description='You are running fdogs.run version ' + str(version) + '.')
  parser.add_argument('--version', action='version', version=str(version))
  required = parser.add_argument_group('Required arguments')
@@ -535,7 +532,10 @@ def main():
  ### join output
  finalFa = joinOutputs(outpath, jobName, seeds, keep, silent)
  else:
- print("%s.extended.fa found in %s! If you want to re-run the ortholog search, please use --force option." % (jobName, outpath))
+ if append == True:
+ sys.exit("Currently the append option is not available. Please use fdog.run if you need this option!")
+ else:
+ sys.exit("%s.extended.fa found in %s! If you want to re-run the ortholog search, please use --force or --append option." % (jobName, outpath))
  ### calculate FAS scores
  if fasoff == False:
  if os.path.exists('%s/%s.phyloprofile' % (outpath, jobName)):

fdog/runSingle.py

@@ -199,7 +199,7 @@ def getTaxName(taxId):
  return(name)
 
 def main():
- version = '0.0.51'
+ version = '0.0.52'
  parser = argparse.ArgumentParser(description='You are running fdog.run version ' + str(version) + '.')
  parser.add_argument('--version', action='version', version=str(version))
  required = parser.add_argument_group('Required arguments')

setup.py

@@ -26,7 +26,7 @@
 
 setup(
  name="fdog",
- version="0.0.51",
+ version="0.0.52",
 
  python_requires='>=3.7.0',
  description="Feature-aware Directed OrtholoG search tool",