basilkhuder/Seurat-to-RNA-Velocity

raise ValueError"cannot reindex from a duplicate axis"

wenyl1919 opened this issue · 3 comments

wenyl1919 commented

HI, when i run the following command, i encounter the following error:

import anndata
import scvelo as scv
import pandas as pd
import numpy as np
import matplotlib as plt

C183 = anndata.read_loom("C183.loom",validate=False)
C184 = anndata.read_loom("C184.loom",validate=False)
C185 = anndata.read_loom("C185.loom",validate=False)

sample_obs = pd.read_csv("hspc.three.cellID_obs.csv")
umap_cord = pd.read_csv("hspc.three.cell_embeddings.csv")
cell_clusters = pd.read_csv("hspc.three.clusters.csv")

C183.obs=C183.obs.rename(index = lambda x: x.replace('C183:', ''))
C183.obs=C183.obs.rename(index = lambda x: x.replace('x', ''))
C183.obs.head()

C184.obs=C184.obs.rename(index = lambda x: x.replace('C184:', ''))
C184.obs=C184.obs.rename(index = lambda x: x.replace('x', ''))
C184.obs.head()

C185.obs=C185.obs.rename(index = lambda x: x.replace('C185:', ''))
C185.obs=C185.obs.rename(index = lambda x: x.replace('x', ''))
C185.obs.head()

sample_obs.x=sample_obs.x.replace({"C183_":""},regex=True)
sample_obs.x=sample_obs.x.replace({"C184_":""},regex=True)
sample_obs.x=sample_obs.x.replace({"C185_":""},regex=True)

C183 = C183[np.isin(C183.obs.index,sample_obs["x"])]

C184 = C184[np.isin(C184.obs.index,sample_obs["x"])]

C185 = C185[np.isin(C185.obs.index,sample_obs["x"])]

###merge file

sample_one = C183.concatenate(C183,C184,C185)

the error as following:
Traceback (most recent call last):
File "", line 1, in
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/anndata/_core/anndata.py", line 1757, in concatenate
out = concat(
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/anndata/_core/merge.py", line 81 8, in concat
alt_annot = merge_dataframes(
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/anndata/_core/merge.py", line 53 1, in merge_dataframes
dfs = [df.reindex(index=new_index) for df in dfs]
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/anndata/_core/merge.py", line 53 1, in
dfs = [df.reindex(index=new_index) for df in dfs]
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/pandas/util/_decorators.py", lin e 324, in wrapper
return func(*args, **kwargs)
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/pandas/core/frame.py", line 4767 , in reindex
return super().reindex(**kwargs)
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/pandas/core/generic.py", line 48 09, in reindex
return self._reindex_axes(
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/pandas/core/frame.py", line 4592 , in _reindex_axes
frame = frame._reindex_index(
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/pandas/core/frame.py", line 4611 , in _reindex_index
return self._reindex_with_indexers(
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/pandas/core/generic.py", line 48 74, in _reindex_with_indexers
new_data = new_data.reindex_indexer(
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/pandas/core/internals/managers.p y", line 663, in reindex_indexer
self.axes[axis]._validate_can_reindex(indexer)
File "/home/wenyl/miniconda3/lib/python3.8/site-packages/pandas/core/indexes/base.py", li ne 3785, in _validate_can_reindex
raise ValueError("cannot reindex from a duplicate axis")

I checked the cellid of three samples and found no same. I didin't know how to fix.

JoshuaCumming commented

Hi,

I am having the same issue. Did you find a solution?

wenyl1919 commented
JoshuaCumming commented

This fixed it, thanks :)

Best,

JC