I was running stereoscope look and got this error:
Traceback (most recent call last):
File "foo/bar/stereoscope/bin/stereoscope", line 33, in
sys.exit(load_entry_point('stereoscope==0.3.1', 'console_scripts', 'stereoscope')())
File "foo/bar/python3.9/site-packages/stereoscope-0.3.1-py3.9.egg/stsc/main.py", line 16, in main
look(args)
File "foo/bar/python3.9/site-packages/stereoscope-0.3.1-py3.9.egg/stsc/look.py", line 436, in look
crdlist = [get_crd(w,as_he = args.image_orientation) for w in wlist]
File "foo/bar/python3.9/site-packages/stereoscope-0.3.1-py3.9.egg/stsc/look.py", line 436, in
crdlist = [get_crd(w,as_he = args.image_orientation) for w in wlist]
File "foo/bar/python3.9/site-packages/stereoscope-0.3.1-py3.9.egg/stsc/look.py", line 362, in get_crd
crd = np.array(crd).astype(float)
ValueError: could not convert string to float: 'AAACAAGTATCTCCCA-1'
I checked test data and found the rownames were like 4.83x31.08,19.98x24.93, and
def get_crd(w,as_he = False):
crd = [x.replace('X','').split('x') for x in w.index.values]
crd = np.array(crd).astype(float)
if as_he:
crd = crd[:,[1,0]]
crd[:,1] = crd[:,1].max() - crd[:,1] + crd[:,1].min()
return crd
seems specially deal with these rownames.
How could I use stereoscope look with 10X visium barcodes?
I was running stereoscope look and got this error:
Traceback (most recent call last): File "foo/bar/stereoscope/bin/stereoscope", line 33, in
sys.exit(load_entry_point('stereoscope==0.3.1', 'console_scripts', 'stereoscope')())
File "foo/bar/python3.9/site-packages/stereoscope-0.3.1-py3.9.egg/stsc/main.py", line 16, in main
look(args)
File "foo/bar/python3.9/site-packages/stereoscope-0.3.1-py3.9.egg/stsc/look.py", line 436, in look
crdlist = [get_crd(w,as_he = args.image_orientation) for w in wlist]
File "foo/bar/python3.9/site-packages/stereoscope-0.3.1-py3.9.egg/stsc/look.py", line 436, in
crdlist = [get_crd(w,as_he = args.image_orientation) for w in wlist]
File "foo/bar/python3.9/site-packages/stereoscope-0.3.1-py3.9.egg/stsc/look.py", line 362, in get_crd
crd = np.array(crd).astype(float)
ValueError: could not convert string to float: 'AAACAAGTATCTCCCA-1'
I checked test data and found the rownames were like 4.83x31.08,19.98x24.93, and
seems specially deal with these rownames.
How could I use stereoscope look with 10X visium barcodes?