Looping in python for multiple samples (h5ad files)

[saeedfc]

Dear Developers/user community,

Thanks for the fantastic tool.
I am new to python. I want to do scvelo for many samples in a loop. I am trying to do the following for a list of h5ad files.

import scvelo as scv
adata = scv.read("/mnt/DATA1/Fibrosis/Full Scale Analysis/scVelo/Fibroblast_scvelo.h5ad")
adata
scv.pp.filter_and_normalize(adata, min_shared_counts=20, n_top_genes=2000)
scv.pp.moments(adata, n_pcs=30, n_neighbors=30)
scv.tl.recover_dynamics(adata)
scv.tl.velocity(adata, mode='dynamical')
scv.tl.velocity_graph(adata)
scv.pl.velocity_embedding_stream(adata, basis='umap')

How would I best do it?

In R, I could make a list of each adata object and make for loop to run over each object in the list as follows.

#file_list is vector of paths to the h5ad files
#name_list is a vector of names for each samples
adata_list <- list()
for(i in 1:length(file_list)) {
adata_list[[i]] <- scv.read(file_list[i])
scv.pp.filter_and_normalize(adata_list[[i]] , min_shared_counts=20, n_top_genes=2000)
scv.pp.moments(adata_list[[i]] , n_pcs=30, n_neighbors=30)
scv.tl.recover_dynamics(adata_list[[i]] )
scv.tl.velocity(adata_list[[i]] , mode='dynamical')
scv.tl.velocity_graph(adata_list[[i]] )
scv.pl.velocity_embedding_stream(adata_list[[i]] , basis='umap', save = paste0(name_list[i], ".png")))
}

Any help is appreciated,
Thanks and Kind regards,

[VolkerBergen]

You could run it along the following lines, after creating a list of filenames.

import scvelo as scv
for fname in filenames:
   adata = scv.read(f"/mnt/DATA1/Fibrosis/Full Scale Analysis/scVelo/{fname}.h5ad")
   scv.pp.filter_and_normalize(adata, min_shared_counts=20, n_top_genes=2000)
   scv.pp.moments(adata, n_pcs=30, n_neighbors=30)
   scv.tl.recover_dynamics(adata)
   scv.tl.velocity(adata, mode='dynamical')
   scv.tl.velocity_graph(adata)
   scv.pl.velocity_embedding_stream(adata, basis='umap')
   adata.write(f"data/{fname}")