From bc24ca3473eef3a9467a748a7c5a1e6da4539889 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Dernat=20R=C3=A9my?= <remy.dernat@umontpellier.fr> Date: Fri, 8 Nov 2019 16:12:30 +0100 Subject: [PATCH] adding necessary addtionnal conditions for Normalize option --- orthofinder/scripts/files.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/orthofinder/scripts/files.py b/orthofinder/scripts/files.py index e527af0..06ef1d7 100644 --- a/orthofinder/scripts/files.py +++ b/orthofinder/scripts/files.py @@ -166,7 +166,13 @@ class __Files_new_dont_manually_create__(object): wd1 = previous_files_locator.GetStartFromBlast() self.StartFromOrthogroupsOrSequenceSearch(wd1, base_dir, - user_name=options.name) + user_name=options.name) + + elif options.qNormalize: + wd1 = previous_files_locator.GetStartFromBlast() + self.StartFromOrthogroupsOrSequenceSearch(wd1, + base_dir, + user_name=options.name) elif options.qStartFromGroups: wd1, clustersFilename_pairs = previous_files_locator.GetStartFromOGs() @@ -575,7 +581,7 @@ class PreviousFilesLocator_new(PreviousFilesLocator): PreviousFilesLocator.__init__(self) if not continuationDir.endswith("/"): continuationDir += "/" self.home_for_results = continuationDir + "../" - if (options.qStartFromFasta and not options.qStartFromBlast): + if (options.qStartFromFasta and not ( options.qStartFromBlast or options.qNormalize ): # there are no files to find return if not self._IsNewDirStructure(continuationDir): raise Unprocessable("Input directory structure is not processable as new structure") @@ -659,7 +665,7 @@ class PreviousFilesLocator_old(PreviousFilesLocator): self.wd_base_prev, self.orthofinderResultsDir, self.clustersFilename_pairs = self._GetOGsFile(ogs_dir) if options.qStartFromTrees: self._FindFromTrees(continuationDir, options.speciesTreeFN) - elif options.qStartFromBlast: + elif options.qStartFromBlast or options.qNormalize: if self._IsWorkingDirectory(continuationDir): self.wd_base_prev = continuationDir elif self._IsWorkingDirectory(continuationDir + "WorkingDirectory/"): @@ -803,7 +809,7 @@ def InitialiseFileHandler(options, fastaDir=None, continuationDir=None, resultsD """ # 1 & 2 # If starting from scratch, no need for a PreviousFileLocator - if options.qStartFromFasta and not options.qStartFromBlast: + if options.qStartFromFasta and not ( options.qStartFromBlast or options.qNormalize ): pfl = None base_dir = resultsDir_nonDefault if resultsDir_nonDefault != None else fastaDir + "OrthoFinder/" else: -- GitLab