AllonKleinLab/SPRING_dev

The python2.7 was so older that i can not install the module that your workflow need

Opened this issue · 14 comments

honghh2018 commented

Hi, developer
I want to return the spring_dev, but i get the module miss error, like below:

9835bca8486868ce080bfc6c3010d9b
3924301455e34a35dacb1976014c3c9
64b0c942406e2c11c78c3f137c71a43

this module can not be install by pip.i already had solve the the preprocessing_python and the helper_functions module.
but the tables can not be solved by myself. it was complicated than i though.
Hope you help to fix this issue.
Best
Hanhuihong

honghh2018 commented

Hi @calebweinreb @AllonMKlein everybody,
Had anyone hear this?

Best
Hanhuihong

honghh2018 commented

Hi @AllonMKlein,
how can i do for this issue?

calebweinreb commented
honghh2018 commented

Hi @calebweinreb ,
Excellent, it work on my virtual environmnt. you are bloody genius, and tremendously give me a mega help for this urgent project.
Thanks, God bless you
Best

honghh2018 commented

Hi @calebweinreb ,
There is another issue showing up.
the code lying below:

#Save merged samples
merge_setup = {'/Dataset_v1':sample_list}
for s, smerge in merge_setup.items():
print smerge
t0 = time.time()
print t0
print '________________', s

cell_ix = np.in1d(samp_id_flat, smerge)

run_all_spring_1_6(E[cell_ix,:],
                 list(merged_list), s, main_spring_dir, normalize=False, tot_counts_final = total_counts[cell_ix],
                 min_counts = 3, min_cells = 3, min_vscore_pctl = 90, 
                 show_vscore_plot = True, num_pc = 50, pca_method = '', k_neigh=4, use_approxnn = False,
                 output_spring = True, num_force_iter = 2000,
                 cell_groupings = {'Sample': list(samp_id_flat[cell_ix])})

print time.time() - t0

np.save(main_spring_dir + s + '/cell_filter.npy', np.nonzero(cell_ix)[0])
np.savetxt(main_spring_dir + s + '/cell_filter.txt', np.nonzero(cell_ix)[0], fmt='%i')

print time.time() - t0

the error showing below:

['CTRL2', 'FI_3M', 'SRR8872326', 'SRR8872330', 'WT5M1', 'WT6W', 'F20_3M', 'PRT17', 'SRR8872327', 'SRR8872331', 'WT15M', 'WT5M2', 'WT9M']
1643102870.03
________________ /Dataset_v1
Filtering genes
Using 1835 genes
Running PCA
Building kNN graph
kNN built in 192.32610 sec
Saving SPRING files to /share/nas1/Data/Users/honghh/temp/spring-dev/test_data/Dataset_v1
{'Total Counts': array([1149, 2069, 2547, ..., 1361, 1552, 727])}

TypeError Traceback (most recent call last)
in ()
14 show_vscore_plot = True, num_pc = 50, pca_method = '', k_neigh=4, use_approxnn = False,
15 output_spring = True, num_force_iter = 2000,
---> 16 cell_groupings = {'Sample': list(samp_id_flat[cell_ix])})
17
18 print time.time() - t0

in run_all_spring_1_6(E, gene_list, sample_name, save_dir, base_ix, normalize, exclude_dominant_frac, min_counts, min_cells, min_vscore_pctl, show_vscore_plot, exclude_gene_names, num_pc, pca_method, pca_norm, k_neigh, cell_groupings, num_force_iter, output_spring, precomputed_pca, gene_filter, custom_colors, exclude_corr_genes_list, exclude_corr_genes_minCorr, dist_metric, use_approxnn, run_doub_detector, dd_k, dd_frac, dd_approx, tot_counts_final)
113 save_spring_dir_sparse_hdf5(E, [], 0, gene_list, save_path,
114 custom_colors = custom_colors, edges=list(links),
--> 115 cell_groupings = cell_groupings)
116 else:
117 save_spring_dir_sparse_hdf5(E, [], 0, gene_list, save_path,

TypeError: save_spring_dir_sparse_hdf5() got multiple values for keyword argument 'custom_colors'

how can i fix this issue?
Any advices would be appreciated.
Best,
Hanhuihong

calebweinreb commented

Can you send the data and notebook that led to the error? (calebsw@gmail.com)

honghh2018 commented

Hi @calebweinreb ,
The ipynb file and the data had been sent to you from the 939869915@qq.com email.
Hope the reply.
Best
Hanhuihong

honghh2018 commented

Hi @calebweinreb ,
Had any advices for this circumstance?

Best,
Hanhuihong

honghh2018 commented

Hi @calebweinreb
Is data had received ?
Had anyone feedback this issue? if having any question please let me know. I am be glad to help.

honghh2018 commented

Had anyone hear this circumstance？

calebweinreb commented
honghh2018 commented

Very grateful for the reply.
I have carefully checked the spring_example_pbmc4k.ipynb but found the weird question,
It can not found the spring_helper directory when Running the header of the notebook with from spring_helper import * .
It is strange that download the spring_dev software, because of the module of spring_helper can not be imported properly with conda environment.

%pylab inline
File "", line 1
%pylab inline
^
SyntaxError: invalid syntax
from spring_helper import *
Traceback (most recent call last):
File "", line 1, in
ImportError: No module named spring_helper
from doublet_detector import *
Traceback (most recent call last):
File "", line 1, in
ImportError: No module named doublet_detector
from collections import defaultdict

the spring setup following you github project workflow

Best,
Hanhuihong

calebweinreb commented
honghh2018 commented

Hi @calebweinreb ,
Thanks the advices, The issue have be solved by your alert. I manually create a prep_data dir and bring the helper_funciton.py into it and then import it.
This way can work well.
Hope the Best for you
My friends