Louis BECQUEY

debugged doublon checking in MSAs

......@@ -557,7 +557,6 @@ class Chain:
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?);""",
many=True, data=list(df.to_records(index=False)), warn_every=10)
def remap(self, columns_to_save, s_seq):
"""Maps the object's sequence to its version in a MSA, to compute nucleotide frequencies at every position.
......@@ -2035,10 +2034,10 @@ def work_realign(rfam_acc):
notify("Aligned new sequences together")
# Detect doublons and remove them
existing_stk = AlignIO.parse(existing_ali_path, "stockholm")
existing_stk = AlignIO.read(existing_ali_path, "stockholm")
existing_ids = [ r.id for r in existing_stk ]
del existing_stk
new_stk = AlignIO.parse(new_ali_path, "stk")
new_stk = AlignIO.read(new_ali_path, "stk")
new_ids = [ r.id for r in new_stk ]
del new_stk
doublons = [ i for i in existing_ids if i in new_ids ]
......