type error in add_anno

[schmucr1]

Hi
I believe there should be a conversion to str in the if-statement for the error message: instead of len(notmatched) , it should be str(len(notmatched)). Otherwise, concatenation for the print statement does not work.

Original code:

def add_anno(adata, cnames, mycol, clusters='leiden'):
    """ Adds annotation generated with make_anno to a AnnData object
    Takes as input the AnnData object to which annotation will be appended and the annotation pd
    Generates a pd.Series that can be added as a adata.obs column with annotation at a level
    Parameters
    ----------
    adata: AnnData
      AnnData object that is to be annotated
    cnames: panda.DataFrame
      a list of cluster names generated with make_anno
    mycol: string
      column to be added
    clusters: string
      initial cluster used for annotation (column in adata.obs)
    returns
    -------
    pd.Series
        the annotated cells
    """

    newlab = adata.obs[clusters]
    # mycol='celltype0'

    notmatched = list(set(list(cnames.index))-set(newlab))
    if len(notmatched) > 0:
        errm = 'Please check that you have indexed the correct clustering. ' + \
            len(notmatched) + 'clusterIDs not found in ' + clusters
        return(errm)
    else:
        for i in list(set(newlab)):
            newlab = newlab.replace(i, cnames.loc[i, mycol]).copy()
        return(newlab)

[alberto-valdeolivas]

Hello @schmucr1.

I think this have been fixed in the new pull request

Thanks