diff --git a/orthofinder/scripts/get_orthologues.py b/orthofinder/scripts/get_orthologues.py index 3cf29a78ff63a003ae61dde3dacc4bac17c06e4a..85786f60aea8ac39df7cbedb45b4bcd08cf76cfc 100755 --- a/orthofinder/scripts/get_orthologues.py +++ b/orthofinder/scripts/get_orthologues.py @@ -104,20 +104,13 @@ class OrthoGroupsSet(object): d = self.speciesIDsEx.GetIDToNameDict() return {k:v.rsplit(".",1)[0] for k,v in d.items()} - def Spec_SeqDict(self, qSplitBar=True): + def Spec_SeqDict(self): if self._Spec_SeqIDs != None: return self._Spec_SeqIDs -# try: seqs = self.SequenceDict() specs = self.SpeciesDict() - self._Spec_SeqIDs = dict() - for seq in seqs: - iSpecies = seq.split("_")[0] - if iSpecies not in specs: continue - if qSplitBar: - self._Spec_SeqIDs[seq] = specs[iSpecies].replace(". ", "_").replace(" ", "_") + "_" + seqs[seq].split("|")[0] - else: - self._Spec_SeqIDs[seq] = specs[iSpecies].replace(". ", "_").replace(" ", "_") + "_" + seqs[seq] + specs_ed = {k:v.replace(".", "_").replace(" ", "_") for k,v in specs.items()} + self._Spec_SeqIDs = {seqID:specs_ed[seqID.split("_")[0]] + "_" + name for seqID, name in seqs.items()} return self._Spec_SeqIDs def OGs(self):