'2-uninfected',
'3-mock',
'4-mock',
'5-low',
'6-low',
'7-high',
'8-high',
]
print('Get counts from single samples')
data = []
cells = []
n_cells = 0
for sn in samplenames:
print(sn)
fn = get_count_filenames(expname, sn, fmt='dataframe')
df = read_dataframe(fn)
n_cells += df.shape[1]
n_genes = df.shape[0]
genes = df.index
cells.extend([sn + '_' + bc for bc in df.columns])
data.append(df.values)
print('{:}, n. genes: {:}, n. cells: {:}'.format(
sn,
df.shape[0],
df.shape[1],
))
print('Merge into a single matrix')
counts = np.zeros((n_genes, n_cells), float)
i = 0
def from_10X(cls, expname, samplename):
from mCMV.filenames import get_count_filenames
fdict = get_count_filenames(expname, samplename, fmt='10X')
return cls.from_10X_filenames(fdict)