In [1]:

    

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
from collections import Counter
import sys
from scipy import signal
from collections import defaultdict


    

In [2]:

    

data = pd.read_table("/mnt/scratch5/avi/alevin/testing/salmonData/quant/alevin/counts.tsv", header=None)


    

In [3]:

    

alevin = []
for row in data.itertuples():
    alevin.append(np.mean(list(row[:-1])))


    

In [ ]:

    




    

In [28]:

    

import csv
import os
import scipy.io
 
genome = "GRCh38"
matrices_dir = "/mnt/scratch5/avi/alevin/data/10x/human/filtered_gene_bc_matrices"
human_matrix_dir = os.path.join(matrices_dir, genome)
mat = scipy.io.mmread(os.path.join(human_matrix_dir, "matrix.mtx")).toarray()
 
genes_path = os.path.join(human_matrix_dir, "genes.tsv")
gene_ids = [row[0] for row in csv.reader(open(genes_path), delimiter="\t")]
gene_names = [row[1] for row in csv.reader(open(genes_path), delimiter="\t")]
 
barcodes_path = os.path.join(human_matrix_dir, "barcodes.tsv")
barcodes = [row[0][:-2] for row in csv.reader(open(barcodes_path), delimiter="\t")]


    

In [ ]:

    




    

In [ ]: