Integrate with 10x genomics output

[olgabot]

10X genomics has examples in Python and R for how to read their outputs, and we should integrate these into flotilla

import csv
import os
import scipy.io

genome = "hg19"
matrices_dir = "/opt/sample345/outs/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"))

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] for row in csv.reader(open(barcodes_path), delimiter="\t")]