Commit c65f84e5 authored by Mikaël Salson's avatar Mikaël Salson

repseq_vdj.py: Field renaming for MiXCR

parent 50c032e4
...@@ -155,16 +155,16 @@ class MiXCR_Result(Result): ...@@ -155,16 +155,16 @@ class MiXCR_Result(Result):
return None return None
def populate(self): def populate(self):
self.vdj[V] = [self['Best V hit']] self.vdj[V] = [self['bestVHit']]
if self['Best D hit']: if self['bestDHit']:
self.vdj[D] = [self['Best D hit']] self.vdj[D] = [self['bestDHit']]
self.vdj[J] = [self['Best J hit']] self.vdj[J] = [self['bestJHit']]
self.vdj[N1] = self['N. Seq. VDJunction'] self.vdj[N1] = self['nSeqVDJunction']
self.vdj[N2] = self['N. Seq. DJJunction'] self.vdj[N2] = self['nSeqDJJunction']
self.vdj[N] = self['N. Seq. VJJunction'] self.vdj[N] = self['nSeqVJJunction']
self.vdj[JUNCTION] = self['AA. Seq. CDR3'] self.vdj[JUNCTION] = self['aaSeqCDR3']
def header_mixcr_results(ff_mixcr): def header_mixcr_results(ff_mixcr):
...@@ -177,7 +177,7 @@ def header_mixcr_results(ff_mixcr): ...@@ -177,7 +177,7 @@ def header_mixcr_results(ff_mixcr):
while True: while True:
l = f.next() l = f.next()
result = MiXCR_Result(l) result = MiXCR_Result(l)
yield result['Description R1'], result.to_vdj() yield result['descrsR1'], result.to_vdj()
......
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