cliftonlewis
commented
2 years ago After check back over this error again, I think this error may be due to the sc.read having the validate=False flag as it hid the fact that error was in the formatting of the integrated results loom file as just I tested it without and this the error I get.
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-10-861eb679c1d3> in <module>
----> 1 adata = sc.read_loom( f_test_loom)
2 adata.obs.columns
3 # drop the embeddings and extra attributes from the obs object
4 adata.obs.drop( ['Embedding','Embeddings_X','Embeddings_Y','RegulonsAUC'], axis=1, inplace=True )
/home/shared/anaconda3/envs/scenic3/lib/python3.6/site-packages/anndata/compat/__init__.py in inner_f(*args, **kwargs)
251 extra_args = len(args) - len(all_args)
252 if extra_args <= 0:
--> 253 return f(*args, **kwargs)
254
255 # extra_args > 0
/home/shared/anaconda3/envs/scenic3/lib/python3.6/site-packages/anndata/_io/read.py in read_loom(filename, sparse, cleanup, X_name, obs_names, obsm_names, var_names, varm_names, dtype, obsm_mapping, varm_mapping, **kwargs)
259 from loompy import connect
260
--> 261 with connect(filename, "r", **kwargs) as lc:
262 if X_name not in lc.layers.keys():
263 X_name = ""
/home/shared/anaconda3/envs/scenic3/lib/python3.6/site-packages/loompy/loompy.py in connect(filename, mode, validate, spec_version)
1147 Note: if validation is requested, an exception is raised if validation fails.
1148 """
-> 1149 return LoomConnection(filename, mode, validate=validate, spec_version=spec_version)
/home/shared/anaconda3/envs/scenic3/lib/python3.6/site-packages/loompy/loompy.py in __init__(self, filename, mode, validate, spec_version)
83 lv = loompy.LoomValidator(version=spec_version)
84 if not lv.validate(filename):
---> 85 raise ValueError("\n".join(lv.errors) + f"\n{filename} does not appead to be a valid Loom file according to Loom spec version '{spec_version}'")
86
87 self._file = h5py.File(filename, mode)
ValueError: Row attribute 'Regulons' dtype [('Abd-B_(+)', '<i8'), ('Abl_(+)', '<i8'), ('Antp_(+)', '<i8'), ('Argk_(+)', '<i8'), ('Atf3_(+)', '<i8'), ('Atf6_(+)', '<i8'), ('Awh_(+)', '<i8'), ('B-H1_(+)', '<i8'), ('BEAF-32_(+)', '<i8'), ('Bgb_(+)', '<i8'), ('Blimp-1_(+)', '<i8'), ('BtbVII_(+)', '<i8'), ('C15_(+)', '<i8'), ('CG10654_(+)', '<i8'), ('CG12018_(+)', '<i8'), ('CG12605_(+)', '<i8'), ('CG16779_(+)', '<i8'), ('CG17829_(+)', '<i8'), ('CG32532_(+)', '<i8'), ('CG34367_(+)', '<i8'), ('CG44247_(+)', '<i8'), ('CG5245_(+)', '<i8'), ('CG8319_(+)', '<i8'), ('Clk_(+)', '<i8'), ('CrebA_(+)', '<i8'), ('CrebB_(+)', '<i8'), ('D_(+)', '<i8'), ('D19B_(+)', '<i8'), ('Dif_(+)', '<i8'), ('Doc1_(+)', '<i8'), ('Dp_(+)', '<i8'), ('Dref_(+)', '<i8'), ('E_(bx)_(+)', '<i8'), ('E_(spl)m5-HLH_(+)', '<i8'), ('E_(spl)mbeta-HLH_(+)', '<i8'), ('E_(spl)mgamma-HLH_(+)', '<i8'), ('E2f1_(+)', '<i8'), ('E5_(+)', '<i8'), ('EcR_(+)', '<i8'), ('Ets21C_(+)', '<i8'), ('Ets65A_(+)', '<i8'), ('Ets96B_(+)', '<i8'), ('FoxK_(+)', '<i8'), ('H15_(+)', '<i8'), ('HDAC1_(+)', '<i8'), ('HLH3B_(+)', '<i8'), ('Hnf4_(+)', '<i8'), ('Hr3_(+)', '<i8'), ('Hr38_(+)', '<i8'), ('Hr78_(+)', '<i8'), ('Jra_(+)', '<i8'), ('Kdm4B_(+)', '<i8'), ('Kr_(+)', '<i8'), ('Lim1_(+)', '<i8'), ('Max_(+)', '<i8'), ('Mef2_(+)', '<i8'), ('Mitf_(+)', '<i8'), ('Mnt_(+)', '<i8'), ('Myb_(+)', '<i8'), ('Myc_(+)', '<i8'), ('NFAT_(+)', '<i8'), ('Nf-YC_(+)', '<i8'), ('Nf1_(+)', '<i8'), ('Oli_(+)', '<i8'), ('Pdp1_(+)', '<i8'), ('Psi_(+)', '<i8'), ('Ptx1_(+)', '<i8'), ('Rb97D_(+)', '<i8'), ('Rel_(+)', '<i8'), ('Rfx_(+)', '<i8'), ('Rx_(+)', '<i8'), ('SREBP_(+)', '<i8'), ('Sox102F_(+)', '<i8'), ('Sox14_(+)', '<i8'), ('SoxN_(+)', '<i8'), ('Spps_(+)', '<i8'), ('Stat92E_(+)', '<i8'), ('Su_(H)_(+)', '<i8'), ('Tet_(+)', '<i8'), ('TfIIB_(+)', '<i8'), ('Trf2_(+)', '<i8'), ('Trl_(+)', '<i8'), ('Usf_(+)', '<i8'), ('Usp39_(+)', '<i8'), ('Vsx1_(+)', '<i8'), ('Xbp1_(+)', '<i8'), ('Zif_(+)', '<i8'), ('abd-A_(+)', '<i8'), ('acj6_(+)', '<i8'), ('ap_(+)', '<i8'), ('ase_(+)', '<i8'), ('awd_(+)', '<i8'), ('bap_(+)', '<i8'), ('bi_(+)', '<i8'), ('bowl_(+)', '<i8'), ('bru3_(+)', '<i8'), ('bs_(+)', '<i8'), ('bsh_(+)', '<i8'), ('cbt_(+)', '<i8'), ('cnc_(+)', '<i8'), ('croc_(+)', '<i8'), ('crol_(+)', '<i8'), ('dimm_(+)', '<i8'), ('dpn_(+)', '<i8'), ('ems_(+)', '<i8'), ('en_(+)', '<i8'), ('eve_(+)', '<i8'), ('ey_(+)', '<i8'), ('fd96Ca_(+)', '<i8'), ('fkh_(+)', '<i8'), ('foxo_(+)', '<i8'), ('gcm_(+)', '<i8'), ('gcm2_(+)', '<i8'), ('grh_(+)', '<i8'), ('h_(+)', '<i8'), ('ham_(+)', '<i8'), ('hth_(+)', '<i8'), ('inv_(+)', '<i8'), ('kay_(+)', '<i8'), ('kn_(+)', '<i8'), ('l_(1)sc_(+)', '<i8'), ('l_(3)neo38_(+)', '<i8'), ('lbl_(+)', '<i8'), ('lola_(+)', '<i8'), ('luna_(+)', '<i8'), ('maf-S_(+)', '<i8'), ('mid_(+)', '<i8'), ('mirr_(+)', '<i8'), ('mor_(+)', '<i8'), ('nej_(+)', '<i8'), ('opa_(+)', '<i8'), ('otp_(+)', '<i8'), ('pad_(+)', '<i8'), ('pan_(+)', '<i8'), ('pb_(+)', '<i8'), ('pnr_(+)', '<i8'), ('pnt_(+)', '<i8'), ('repo_(+)', '<i8'), ('ro_(+)', '<i8'), ('scro_(+)', '<i8'), ('sd_(+)', '<i8'), ('slou_(+)', '<i8'), ('slp1_(+)', '<i8'), ('sna_(+)', '<i8'), ('so_(+)', '<i8'), ('sqz_(+)', '<i8'), ('sr_(+)', '<i8'), ('srl_(+)', '<i8'), ('srp_(+)', '<i8'), ('svp_(+)', '<i8'), ('teq_(+)', '<i8'), ('tj_(+)', '<i8'), ('tll_(+)', '<i8'), ('toe_(+)', '<i8'), ('trx_(+)', '<i8'), ('tsu_(+)', '<i8'), ('tup_(+)', '<i8'), ('unc-4_(+)', '<i8'), ('usp_(+)', '<i8'), ('wor_(+)', '<i8'), ('z_(+)', '<i8'), ('zfh2_(+)', '<i8')] is not allowed
Column attribute 'Clusterings' dtype [('0', '<i8')] is not allowed
Column attribute 'Embedding' dtype [('_X', '<f4'), ('_Y', '<f4')] is not allowed
Column attribute 'Embeddings_X' dtype [('1', '<f4'), ('2', '<f4'), ('3', '<f8'), ('4', '<f8')] is not allowed
Column attribute 'Embeddings_Y' dtype [('1', '<f4'), ('2', '<f4'), ('3', '<f8'), ('4', '<f8')] is not allowed
Column attribute 'RegulonsAUC' dtype [('Abd-B_(+)', '<f8'), ('Abl_(+)', '<f8'), ('Antp_(+)', '<f8'), ('Argk_(+)', '<f8'), ('Atf3_(+)', '<f8'), ('Atf6_(+)', '<f8'), ('Awh_(+)', '<f8'), ('B-H1_(+)', '<f8'), ('BEAF-32_(+)', '<f8'), ('Bgb_(+)', '<f8'), ('Blimp-1_(+)', '<f8'), ('BtbVII_(+)', '<f8'), ('C15_(+)', '<f8'), ('CG10654_(+)', '<f8'), ('CG12018_(+)', '<f8'), ('CG12605_(+)', '<f8'), ('CG16779_(+)', '<f8'), ('CG17829_(+)', '<f8'), ('CG32532_(+)', '<f8'), ('CG34367_(+)', '<f8'), ('CG44247_(+)', '<f8'), ('CG5245_(+)', '<f8'), ('CG8319_(+)', '<f8'), ('Clk_(+)', '<f8'), ('CrebA_(+)', '<f8'), ('CrebB_(+)', '<f8'), ('D_(+)', '<f8'), ('D19B_(+)', '<f8'), ('Dif_(+)', '<f8'), ('Doc1_(+)', '<f8'), ('Dp_(+)', '<f8'), ('Dref_(+)', '<f8'), ('E_(bx)_(+)', '<f8'), ('E_(spl)m5-HLH_(+)', '<f8'), ('E_(spl)mbeta-HLH_(+)', '<f8'), ('E_(spl)mgamma-HLH_(+)', '<f8'), ('E2f1_(+)', '<f8'), ('E5_(+)', '<f8'), ('EcR_(+)', '<f8'), ('Ets21C_(+)', '<f8'), ('Ets65A_(+)', '<f8'), ('Ets96B_(+)', '<f8'), ('FoxK_(+)', '<f8'), ('H15_(+)', '<f8'), ('HDAC1_(+)', '<f8'), ('HLH3B_(+)', '<f8'), ('Hnf4_(+)', '<f8'), ('Hr3_(+)', '<f8'), ('Hr38_(+)', '<f8'), ('Hr78_(+)', '<f8'), ('Jra_(+)', '<f8'), ('Kdm4B_(+)', '<f8'), ('Kr_(+)', '<f8'), ('Lim1_(+)', '<f8'), ('Max_(+)', '<f8'), ('Mef2_(+)', '<f8'), ('Mitf_(+)', '<f8'), ('Mnt_(+)', '<f8'), ('Myb_(+)', '<f8'), ('Myc_(+)', '<f8'), ('NFAT_(+)', '<f8'), ('Nf-YC_(+)', '<f8'), ('Nf1_(+)', '<f8'), ('Oli_(+)', '<f8'), ('Pdp1_(+)', '<f8'), ('Psi_(+)', '<f8'), ('Ptx1_(+)', '<f8'), ('Rb97D_(+)', '<f8'), ('Rel_(+)', '<f8'), ('Rfx_(+)', '<f8'), ('Rx_(+)', '<f8'), ('SREBP_(+)', '<f8'), ('Sox102F_(+)', '<f8'), ('Sox14_(+)', '<f8'), ('SoxN_(+)', '<f8'), ('Spps_(+)', '<f8'), ('Stat92E_(+)', '<f8'), ('Su_(H)_(+)', '<f8'), ('Tet_(+)', '<f8'), ('TfIIB_(+)', '<f8'), ('Trf2_(+)', '<f8'), ('Trl_(+)', '<f8'), ('Usf_(+)', '<f8'), ('Usp39_(+)', '<f8'), ('Vsx1_(+)', '<f8'), ('Xbp1_(+)', '<f8'), ('Zif_(+)', '<f8'), ('abd-A_(+)', '<f8'), ('acj6_(+)', '<f8'), ('ap_(+)', '<f8'), ('ase_(+)', '<f8'), ('awd_(+)', '<f8'), ('bap_(+)', '<f8'), ('bi_(+)', '<f8'), ('bowl_(+)', '<f8'), ('bru3_(+)', '<f8'), ('bs_(+)', '<f8'), ('bsh_(+)', '<f8'), ('cbt_(+)', '<f8'), ('cnc_(+)', '<f8'), ('croc_(+)', '<f8'), ('crol_(+)', '<f8'), ('dimm_(+)', '<f8'), ('dpn_(+)', '<f8'), ('ems_(+)', '<f8'), ('en_(+)', '<f8'), ('eve_(+)', '<f8'), ('ey_(+)', '<f8'), ('fd96Ca_(+)', '<f8'), ('fkh_(+)', '<f8'), ('foxo_(+)', '<f8'), ('gcm_(+)', '<f8'), ('gcm2_(+)', '<f8'), ('grh_(+)', '<f8'), ('h_(+)', '<f8'), ('ham_(+)', '<f8'), ('hth_(+)', '<f8'), ('inv_(+)', '<f8'), ('kay_(+)', '<f8'), ('kn_(+)', '<f8'), ('l_(1)sc_(+)', '<f8'), ('l_(3)neo38_(+)', '<f8'), ('lbl_(+)', '<f8'), ('lola_(+)', '<f8'), ('luna_(+)', '<f8'), ('maf-S_(+)', '<f8'), ('mid_(+)', '<f8'), ('mirr_(+)', '<f8'), ('mor_(+)', '<f8'), ('nej_(+)', '<f8'), ('opa_(+)', '<f8'), ('otp_(+)', '<f8'), ('pad_(+)', '<f8'), ('pan_(+)', '<f8'), ('pb_(+)', '<f8'), ('pnr_(+)', '<f8'), ('pnt_(+)', '<f8'), ('repo_(+)', '<f8'), ('ro_(+)', '<f8'), ('scro_(+)', '<f8'), ('sd_(+)', '<f8'), ('slou_(+)', '<f8'), ('slp1_(+)', '<f8'), ('sna_(+)', '<f8'), ('so_(+)', '<f8'), ('sqz_(+)', '<f8'), ('sr_(+)', '<f8'), ('srl_(+)', '<f8'), ('srp_(+)', '<f8'), ('svp_(+)', '<f8'), ('teq_(+)', '<f8'), ('tj_(+)', '<f8'), ('tll_(+)', '<f8'), ('toe_(+)', '<f8'), ('trx_(+)', '<f8'), ('tsu_(+)', '<f8'), ('tup_(+)', '<f8'), ('unc-4_(+)', '<f8'), ('usp_(+)', '<f8'), ('wor_(+)', '<f8'), ('z_(+)', '<f8'), ('zfh2_(+)', '<f8')] is not allowed
For help, see http://linnarssonlab.org/loompy/format/
drosophilalarval_scenic_integrated-output_test.loom does not appead to be a valid Loom file according to Loom spec version '2.0.1'I'm still unsure how I would go about fixing the error even though I seem to manage to work through it by following the alternative path suggested at the start of the tutorial
cflerin
Describe the bug A clear and concise description of what the bug is.
Steps to reproduce the behavior
drop the embeddings and extra attributes from the obs object
adata.obs.drop( ['Embedding','Embeddings_X','Embeddings_Y','RegulonsAUC'], axis=1, inplace=True )
Expected behavior A clear and concise description of what you expected to happen. I was hoping someone could explain this error to me as I can't seem to understand why I have gotten this. Cheers Please complete the following information: