From c3689d16bce03c36e12e1107fb73f882e64b9dc1 Mon Sep 17 00:00:00 2001
From: David Emms <david_emms@hotmail.com>
Date: Wed, 7 Sep 2016 10:28:54 +0100
Subject: [PATCH] Don't split accessions at '|' for gene trees
---
orthofinder/scripts/get_orthologues.py | 13 +++----------
1 file changed, 3 insertions(+), 10 deletions(-)
diff --git a/orthofinder/scripts/get_orthologues.py b/orthofinder/scripts/get_orthologues.py
index 3cf29a7..85786f6 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):
--
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