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  • FixZeroNormScores
  • OrthoFinder.orig.py3
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Created with Raphaël 2.2.022Jan13Dec29Nov28262524221211876422Oct181711420Aug16718Jul210Jun5329May129Apr25821Mar20124Feb6Dec5327Nov21151412109865131Oct302218171112Sep31Aug302930Jul21May161026Apr24181613121110965414Mar1312976128Feb2620191612985231Jan2625161054321Dec930Nov23222120169231Oct30272623201817116129Sep282721201815124Aug421Jul201428Jun201424May23111027Jan16Dec830Nov29252383Oct30Sep2726976230Aug2019181718Jul15118123Jun21158Feb28Jan2715Dec26Nov131229Oct30Sep1514546Aug51Jul29Junupdate to match new version of OrthoFinderrenaming orthofinder/scripts to scripts_of to match new OrthoFinder version (20200122)moving stuff to reorganize the same way as OrthoFindertrying to match the last OrthoFinder version scripts_of/ subdirectorymodifying orthologues.py to fit new orthofinder version, including the issue with self-hits (see commit https://github.com/davidemms/OrthoFinder/commit/17f61266c321edce558e2cb7cc287330294b182c )adding a requirements.txt file for pip (maybe it would be necessary to specify versions of packages)Merge branch 'FixZeroNormScores' into 'master'Merge branch 'master' into 'FixZeroNormScores'FixZeroNormScoresFixZeroNormScoresadding a curve option. Not necessary for normalizing scores (compute faster)debug commented - just in casejSpeciesOpen is not needed as it is the same as iSpeciesOpentry/except in scnorm commented b/c of long duration in computing new normalized scores for self-hitsrenaming NF option to NZ and an info about time consumption. Adding an error margin in the computedebuging retrieving plots from the fitting curveno more error, but still does not workadding a specific option to fix zeros values for self-hits...remove non necessary codewill fix scores in a new loop. Maybe need another option qFixnormalizedzerossys was not importedmoving row compute to the scnorm classmessage error when encountering 0.0 Norm score0.0 ...not the right way to do fix thisupdate code to load a new class from filefitting curve modifiedadding fitting curveadding commentserror in indexerror in indexMerge branch 'master' of https://gitlab.mbb.univ-montp2.fr/remy/orthofindermore explicit error messagecheck ipseciestempfile was not correctly flushed and closedrenaming a functiontempfile was nt created at the right placestill some bugs but nevertheless it gives some resultsbugs fixedNormalize is not compatible with other options. It is a one shot operationadding method to add a new csv file based on normalized scoresmissing parenthesis