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Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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trouble connecting to loom file #320

Closed orrzor closed 3 years ago

orrzor commented 5 years ago

Hi scanpy team, I am having trouble reading in a loom file using read_loom. I started a jupyter lab session in a conda environment and tried to read in a loom file from http://scope.aertslab.org/#/Bernard_Thienpont , under the User Uploaded -> Uncategorized tab (Thienpont_T-cell_v4_R_fixed.loom).

Here are the relevant parts of my conda environment

loompy                    2.0.15                    <pip>
python                    3.6.6                h5001a0f_0    conda-forge
anndata                   0.6.11                    <pip>
scanpy                    1.3.2                     <pip>

Here is the error below, I don't know if this is an issue with the latest loompy version? Thanks so much for any help! -Orr

import scanpy.api as sc 
sc.read_loom('./Thienpont_T-cell_v4_R_fixed.loom')

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-2-3e86e297513a> in <module>
      1 import scanpy.api as sc
----> 2 sc.read_loom('./Thienpont_T-cell_v4_R_fixed.loom')

~/miniconda3/envs/scanpy/lib/python3.6/site-packages/anndata/readwrite/read.py in read_loom(filename, sparse, cleanup, X_name, obs_names, var_names)
    142     filename = fspath(filename)  # allow passing pathlib.Path objects
    143     from loompy import connect
--> 144     with connect(filename, 'r') as lc:
    145 
    146         if X_name not in lc.layers.keys(): X_name = ''

~/miniconda3/envs/scanpy/lib/python3.6/site-packages/loompy/loompy.py in connect(filename, mode, validate, spec_version)
   1151                 Note: if validation is requested, an exception is raised if validation fails.
   1152     """
-> 1153         return LoomConnection(filename, mode, validate=validate, spec_version=spec_version)

~/miniconda3/envs/scanpy/lib/python3.6/site-packages/loompy/loompy.py in __init__(self, filename, mode, validate, spec_version)
     82                         lv = loompy.LoomValidator(version=spec_version)
     83                         if not lv.validate(filename):
---> 84                                 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}'")
     85 
     86                 self._file = h5py.File(filename, mode)

ValueError: Row attribute 'Gene' dtype object is not allowed
Row attribute 'Regulons' dtype [('SPI1_extended_(1805g)', 'u1'), ('SPI1_(1756g)', 'u1'), ('KLF5_extended_(1521g)', 'u1'), ('EHF_extended_(1513g)', 'u1'), ('STAT1_extended_(1443g)', 'u1'), ('ELF3_extended_(1249g)', 'u1'), ('STAT1_(1212g)', 'u1'), ('CEBPB_extended_(1162g)', 'u1'), ('CEBPB_(1045g)', 'u1'), ('KLF5_(1038g)', 'u1'), ('ELF1_extended_(987g)', 'u1'), ('ETS2_extended_(932g)', 'u1'), ('IRF8_extended_(923g)', 'u1'), ('JUND_extended_(789g)', 'u1'), ('EHF_(762g)', 'u1'), ('ELF1_(753g)', 'u1'), ('TFEC_extended_(694g)', 'u1'), ('ETS2_(688g)', 'u1'), ('IRF7_extended_(688g)', 'u1'), ('IRF8_(687g)', 'u1'), ('XBP1_extended_(669g)', 'u1'), ('IRF1_extended_(662g)', 'u1'), ('ETS1_extended_(647g)', 'u1'), ('IRF1_(617g)', 'u1'), ('IRF7_(616g)', 'u1'), ('XBP1_(587g)', 'u1'), ('ETS1_(577g)', 'u1'), ('UQCRB_(573g)', 'u1'), ('PRDM1_extended_(538g)', 'u1'), ('RUNX3_extended_(532g)', 'u1'), ('CREM_extended_(507g)', 'u1'), ('REL_extended_(497g)', 'u1'), ('TFEC_(483g)', 'u1'), ('CREM_(442g)', 'u1'), ('FOSL2_extended_(442g)', 'u1'), ('FOS_extended_(436g)', 'u1'), ('REL_(434g)', 'u1'), ('TEAD1_extended_(417g)', 'u1'), ('RUNX3_(414g)', 'u1'), ('TEAD1_(413g)', 'u1'), ('FOSB_extended_(403g)', 'u1'), ('RFX3_extended_(391g)', 'u1'), ('RFX3_(380g)', 'u1'), ('CREB3L2_extended_(372g)', 'u1'), ('FOSL1_extended_(360g)', 'u1'), ('IRF9_extended_(358g)', 'u1'), ('FOXP1_extended_(334g)', 'u1'), ('ATF3_extended_(333g)', 'u1'), ('CEBPD_extended_(330g)', 'u1'), ('SOX4_extended_(320g)', 'u1'), ('IRF9_(302g)', 'u1'), ('CREB3L2_(289g)', 'u1'), ('STAT2_extended_(287g)', 'u1'), ('FOXP1_(286g)', 'u1'), ('EGR1_extended_(284g)', 'u1'), ('MAFK_extended_(280g)', 'u1'), ('JUND_(274g)', 'u1'), ('ATF3_(265g)', 'u1'), ('ATF4_extended_(261g)', 'u1'), ('SOX4_(260g)', 'u1'), ('ELF3_(260g)', 'u1'), ('FOSL1_(253g)', 'u1'), ('NFE2L2_extended_(253g)', 'u1'), ('BCL3_extended_(250g)', 'u1'), ('RFX2_extended_(248g)', 'u1'), ('PIR_(247g)', 'u1'), ('RFX2_(241g)', 'u1'), ('CEBPD_(241g)', 'u1'), ('YY1_extended_(240g)', 'u1'), ('PPARG_extended_(235g)', 'u1'), ('SF1_(234g)', 'u1'), ('STAT2_(234g)', 'u1'), ('EOMES_extended_(223g)', 'u1'), ('YBX1_extended_(212g)', 'u1'), ('NR1H3_extended_(208g)', 'u1'), ('FOSB_(207g)', 'u1'), ('NR1H3_(207g)', 'u1'), ('BCL11A_extended_(207g)', 'u1'), ('HIF1A_extended_(207g)', 'u1'), ('HIF1A_(206g)', 'u1'), ('SPIB_extended_(207g)', 'u1'), ('BCL3_(201g)', 'u1'), ('EGR1_(199g)', 'u1'), ('IRF2_extended_(196g)', 'u1'), ('SPIB_(195g)', 'u1'), ('FOXO3_extended_(191g)', 'u1'), ('YY1_(188g)', 'u1'), ('ELK3_extended_(186g)', 'u1'), ('IRF2_(179g)', 'u1'), ('HTATIP2_(179g)', 'u1'), ('NR2F6_extended_(176g)', 'u1'), ('ATF4_(168g)', 'u1'), ('EOMES_(168g)', 'u1'), ('FOXO3_(168g)', 'u1'), ('NFIL3_extended_(163g)', 'u1'), ('NFKB1_extended_(156g)', 'u1'), ('NFKB1_(146g)', 'u1'), ('BCL11A_(142g)', 'u1'), ('TFDP2_extended_(141g)', 'u1'), ('MYBL2_extended_(141g)', 'u1'), ('MYBL2_(140g)', 'u1'), ('CREB5_extended_(139g)', 'u1'), ('CREB3_extended_(137g)', 'u1'), ('GABPB1_extended_(134g)', 'u1'), ('MYC_extended_(128g)', 'u1'), ('TFEB_extended_(128g)', 'u1'), ('ELF2_extended_(123g)', 'u1'), ('NR2F6_(121g)', 'u1'), ('MAF_extended_(119g)', 'u1'), ('MAFK_(117g)', 'u1'), ('LUZP1_(111g)', 'u1'), ('FLI1_extended_(111g)', 'u1'), ('FOSL2_(109g)', 'u1'), ('BCLAF1_extended_(109g)', 'u1'), ('NFKB2_extended_(107g)', 'u1'), ('RXRA_extended_(107g)', 'u1'), ('BHLHE41_extended_(106g)', 'u1'), ('MEF2C_extended_(106g)', 'u1'), ('TFDP1_extended_(106g)', 'u1'), ('HDAC2_(105g)', 'u1'), ('GATA2_extended_(103g)', 'u1'), ('KLF3_extended_(102g)', 'u1'), ('CREB3_(99g)', 'u1'), ('GATA2_(99g)', 'u1'), ('BHLHE41_(97g)', 'u1'), ('MEF2C_(95g)', 'u1'), ('NFKB2_(95g)', 'u1'), ('HES1_extended_(95g)', 'u1'), ('MAZ_extended_(96g)', 'u1'), ('NR3C1_extended_(94g)', 'u1'), ('RELB_extended_(94g)', 'u1'), ('ATF5_(94g)', 'u1'), ('TFDP1_(93g)', 'u1'), ('TFEB_(92g)', 'u1'), ('PPARG_(90g)', 'u1'), ('ETV7_extended_(90g)', 'u1'), ('SMARCC2_extended_(91g)', 'u1'), ('SMARCC2_(90g)', 'u1'), ('RELB_(88g)', 'u1'), ('KLF7_extended_(88g)', 'u1'), ('GLIS3_extended_(87g)', 'u1'), ('ELF2_(85g)', 'u1'), ('FOXO1_extended_(85g)', 'u1'), ('POLE4_extended_(86g)', 'u1'), ('JUNB_extended_(84g)', 'u1'), ('MAX_extended_(83g)', 'u1'), ('POLE4_(83g)', 'u1'), ('CREB1_extended_(81g)', 'u1'), ('MAX_(80g)', 'u1'), ('ATF2_extended_(80g)', 'u1'), ('GABPA_extended_(79g)', 'u1'), ('RXRA_(78g)', 'u1'), ('POU2F2_extended_(78g)', 'u1'), ('BHLHE40_extended_(77g)', 'u1'), ('FOXP3_extended_(76g)', 'u1'), ('ZNF683_extended_(75g)', 'u1'), ('FOXO1_(72g)', 'u1'), ('ELK1_extended_(72g)', 'u1'), ('TFAP2A_(70g)', 'u1'), ('BDP1_extended_(70g)', 'u1'), ('KLF10_extended_(70g)', 'u1'), ('TBX21_extended_(69g)', 'u1'), ('MYB_extended_(68g)', 'u1'), ('GABPA_(67g)', 'u1'), ('POU2F2_(66g)', 'u1'), ('ELK3_(65g)', 'u1'), ('MAFG_extended_(64g)', 'u1'), ('POU2AF1_extended_(64g)', 'u1'), ('ELK1_(63g)', 'u1'), ('ETV7_(63g)', 'u1'), ('MYB_(63g)', 'u1'), ('NR3C1_(63g)', 'u1'), ('BACH1_extended_(63g)', 'u1'), ('ERF_extended_(63g)', 'u1'), ('JUN_extended_(62g)', 'u1'), ('CREB1_(61g)', 'u1'), ('ATF6B_extended_(61g)', 'u1'), ('NFIX_extended_(59g)', 'u1'), ('SP1_extended_(59g)', 'u1'), ('ATF2_(58g)', 'u1'), ('TBX21_(58g)', 'u1'), ('HES4_extended_(59g)', 'u1'), ('NFIX_(57g)', 'u1'), ('ETV6_extended_(56g)', 'u1'), ('MSC_extended_(56g)', 'u1'), ('MLX_extended_(53g)', 'u1'), ('POLE3_extended_(54g)', 'u1'), ('MYC_(53g)', 'u1'), ('ARNT_extended_(52g)', 'u1'), ('CLOCK_extended_(52g)', 'u1'), ('PPARD_extended_(52g)', 'u1'), ('TCF7_extended_(52g)', 'u1'), ('FLI1_(51g)', 'u1'), ('MYLK_(52g)', 'u1'), ('RORA_(51g)', 'u1'), ('ELK4_extended_(50g)', 'u1'), ('ETV3_extended_(50g)', 'u1'), ('HOXB2_extended_(50g)', 'u1'), ('SMC3_extended_(50g)', 'u1'), ('ELF4_extended_(49g)', 'u1'), ('IRF4_extended_(49g)', 'u1'), ('ERF_(49g)', 'u1'), ('NFIL3_(47g)', 'u1'), ('TCF7_(47g)', 'u1'), ('ATF6_extended_(47g)', 'u1'), ('HSF1_extended_(47g)', 'u1'), ('HES1_(45g)', 'u1'), ('BATF3_extended_(45g)', 'u1'), ('SETDB1_extended_(46g)', 'u1'), ('E2F3_extended_(42g)', 'u1'), ('KLF7_(42g)', 'u1'), ('ZEB1_(42g)', 'u1'), ('SOX2_extended_(41g)', 'u1'), ('USF2_extended_(41g)', 'u1'), ('SETDB1_(41g)', 'u1'), ('CEBPG_extended_(40g)', 'u1'), ('HIVEP2_extended_(40g)', 'u1'), ('SREBF2_extended_(39g)', 'u1'), ('TAF1_extended_(39g)', 'u1'), ('ELK4_(38g)', 'u1'), ('SREBF2_(38g)', 'u1'), ('MAFB_extended_(39g)', 'u1'), ('SOX7_extended_(39g)', 'u1'), ('TGIF2_extended_(38g)', 'u1'), ('E2F6_extended_(37g)', 'u1'), ('NR2C2_extended_(37g)', 'u1'), ('NRF1_extended_(37g)', 'u1'), ('TGIF2_(36g)', 'u1'), ('FOXJ1_extended_(37g)', 'u1'), ('KLF12_extended_(36g)', 'u1'), ('KLF16_extended_(36g)', 'u1'), ('NR2F2_extended_(36g)', 'u1'), ('ETV3_(35g)', 'u1'), ('JUNB_(35g)', 'u1'), ('BATF_extended_(35g)', 'u1'), ('BRF1_(35g)', 'u1'), ('E2F3_(34g)', 'u1'), ('PBX1_(34g)', 'u1'), ('ESRRA_extended_(34g)', 'u1'), ('USF2_(33g)', 'u1'), ('ARNTL2_extended_(33g)', 'u1'), ('RELA_extended_(33g)', 'u1'), ('CEBPG_(32g)', 'u1'), ('KLF2_(32g)', 'u1'), ('TEAD4_(33g)', 'u1'), ('TFAP2C_(32g)', 'u1'), ('TBX3_extended_(32g)', 'u1'), ('FOS_(31g)', 'u1'), ('KLF12_(31g)', 'u1'), ('SP1_(31g)', 'u1'), ('MYEF2_extended_(32g)', 'u1'), ('NFIC_(31g)', 'u1'), ('NRF1_(30g)', 'u1'), ('MSC_(30g)', 'u1'), ('CEBPA_extended_(30g)', 'u1'), ('CENPB_(29g)', 'u1'), ('HIVEP2_(28g)', 'u1'), ('CEBPA_(28g)', 'u1'), ('ESRRA_(27g)', 'u1'), ('TCF7L2_(27g)', 'u1'), ('IRF5_extended_(27g)', 'u1'), ('JUN_(26g)', 'u1'), ('ZBTB7B_extended_(26g)', 'u1'), ('MAFG_(25g)', 'u1'), ('NR2C2_(25g)', 'u1'), ('RAD21_(26g)', 'u1'), ('GATA3_extended_(25g)', 'u1'), ('STAT5A_extended_(24g)', 'u1'), ('DDIT3_extended_(23g)', 'u1'), ('MXI1_extended_(23g)', 'u1'), ('NFYC_extended_(23g)', 'u1'), ('FOXP3_(23g)', 'u1'), ('HOXB2_(23g)', 'u1'), ('MAF_(22g)', 'u1'), ('ZNF143_extended_(22g)', 'u1'), ('BATF_(21g)', 'u1'), ('CREB5_(21g)', 'u1'), ('MLX_(21g)', 'u1'), ('NFYC_(21g)', 'u1'), ('ETV1_extended_(21g)', 'u1'), ('FOXK1_extended_(22g)', 'u1'), ('MAFF_extended_(22g)', 'u1'), ('LEF1_(20g)', 'u1'), ('MECOM_(21g)', 'u1'), ('TAF1_(20g)', 'u1'), ('ZNF143_(20g)', 'u1'), ('DDIT3_(19g)', 'u1'), ('FOXJ1_(20g)', 'u1'), ('IRF4_(20g)', 'u1'), ('KLF4_(20g)', 'u1'), ('NR2F2_(19g)', 'u1'), ('PPARD_(20g)', 'u1'), ('SOX2_(19g)', 'u1'), ('RUNX2_extended_(19g)', 'u1'), ('THAP1_extended_(19g)', 'u1'), ('HES4_(19g)', 'u1'), ('ZBTB33_(19g)', 'u1'), ('BCL6_extended_(18g)', 'u1'), ('GATA3_(18g)', 'u1'), ('ZNF664_(18g)', 'u1'), ('HOXC9_extended_(18g)', 'u1'), ('BCL6_(16g)', 'u1'), ('BHLHE40_(16g)', 'u1'), ('HINFP_(16g)', 'u1'), ('HOXA5_(16g)', 'u1'), ('KLF3_(16g)', 'u1'), ('MEF2A_(16g)', 'u1'), ('ASCL2_extended_(16g)', 'u1'), ('RARA_extended_(16g)', 'u1'), ('ARNT_(16g)', 'u1'), ('PRDM1_(15g)', 'u1'), ('BACH1_(14g)', 'u1'), ('CREBZF_(15g)', 'u1'), ('POU2AF1_(14g)', 'u1'), ('RELA_(14g)', 'u1'), ('ZNF100_(15g)', 'u1'), ('ZNF254_(15g)', 'u1'), ('FOXP4_extended_(14g)', 'u1'), ('IRF6_extended_(14g)', 'u1'), ('NFE2L3_extended_(15g)', 'u1'), ('RFX5_extended_(14g)', 'u1'), ('SRF_extended_(14g)', 'u1'), ('HOXC9_(14g)', 'u1'), ('HSF1_(14g)', 'u1'), ('IKZF2_(13g)', 'u1'), ('RFX5_(13g)', 'u1'), ('SRF_(13g)', 'u1'), ('FOXM1_extended_(14g)', 'u1'), ('NKX2-1_extended_(14g)', 'u1'), ('NR1D2_extended_(13g)', 'u1'), ('POU2F1_extended_(13g)', 'u1'), ('CLOCK_(13g)', 'u1'), ('CTCF_(13g)', 'u1'), ('MAFF_(13g)', 'u1'), ('POU2F1_(12g)', 'u1'), ('RUNX2_(12g)', 'u1'), ('SMAD3_(13g)', 'u1'), ('ETV5_extended_(12g)', 'u1'), ('FOXJ3_extended_(12g)', 'u1'), ('FOXN3_extended_(12g)', 'u1'), ('NFATC1_extended_(13g)', 'u1'), ('ELF4_(12g)', 'u1'), ('ETV1_(11g)', 'u1'), ('FOXP4_(11g)', 'u1'), ('SP2_(11g)', 'u1'), ('TCF3_(12g)', 'u1'), ('ZBTB41_(12g)', 'u1'), ('ZNF503_(12g)', 'u1'), ('HIVEP1_extended_(11g)', 'u1'), ('NPDC1_extended_(12g)', 'u1'), ('RXRB_extended_(11g)', 'u1'), ('FOXK2_(11g)', 'u1'), ('FOXM1_(11g)', 'u1'), ('HDAC1_(10g)', 'u1'), ('MELK_(11g)', 'u1'), ('RARA_(10g)', 'u1'), ('RXRB_(11g)', 'u1'), ('TP53_(10g)', 'u1'), ('ZNF260_(11g)', 'u1'), ('MEF2D_extended_(10g)', 'u1'), ('MLXIP_extended_(11g)', 'u1')] is not allowed
Column attribute 'CellID' dtype object is not allowed
Column attribute 'ClusterName' dtype object is not allowed
Column attribute 'Clusterings' dtype [('0', '<i4')] is not allowed
Column attribute 'Embedding' dtype [('_X', '<f8'), ('_Y', '<f8')] is not allowed
Column attribute 'Embeddings_X' dtype [('0', '<f8')] is not allowed
Column attribute 'Embeddings_Y' dtype [('0', '<f8')] is not allowed
Column attribute 'RegulonsAUC' dtype [('TBX21_extended (69g)', '<f8'), ('TBX21 (58g)', '<f8'), ('ELF1_extended (987g)', '<f8'), ('ELF1 (753g)', '<f8'), ('EOMES_extended (223g)', '<f8'), ('EOMES (168g)', '<f8'), ('RUNX3_extended (532g)', '<f8'), ('RUNX3 (414g)', '<f8'), ('PRDM1_extended (538g)', '<f8'), ('ETS1_extended (647g)', '<f8'), ('ETS1 (577g)', '<f8'), ('ZNF683_extended (75g)', '<f8'), ('IRF1_extended (662g)', '<f8'), ('IRF1 (617g)', '<f8'), ('JUN_extended (62g)', '<f8'), ('JUN (26g)', '<f8'), ('IRF7_extended (688g)', '<f8'), ('IRF7 (616g)', '<f8'), ('IRF9_extended (358g)', '<f8'), ('IRF9 (302g)', '<f8'), ('MAFB_extended (39g)', '<f8'), ('NR1H3_extended (208g)', '<f8'), ('NR1H3 (207g)', '<f8'), ('CEBPB_extended (1162g)', '<f8'), ('CEBPB (1045g)', '<f8'), ('ETS2_extended (932g)', '<f8'), ('ETS2 (688g)', '<f8'), ('YBX1_extended (212g)', '<f8'), ('SPI1_extended (1805g)', '<f8'), ('SPI1 (1756g)', '<f8'), ('ATF5 (94g)', '<f8'), ('TFEC_extended (694g)', '<f8'), ('TFEC (483g)', '<f8'), ('BHLHE41_extended (106g)', '<f8'), ('BHLHE41 (97g)', '<f8'), ('PPARG_extended (235g)', '<f8'), ('PPARG (90g)', '<f8'), ('MEF2C_extended (106g)', '<f8'), ('MEF2C (95g)', '<f8'), ('REL_extended (497g)', '<f8'), ('REL (434g)', '<f8'), ('SPIB_extended (207g)', '<f8'), ('SPIB (195g)', '<f8'), ('IRF8_extended (923g)', '<f8'), ('IRF8 (687g)', '<f8'), ('RORA (51g)', '<f8'), ('NR3C1_extended (94g)', '<f8'), ('NR3C1 (63g)', '<f8'), ('TCF7_extended (52g)', '<f8'), ('TCF7 (47g)', '<f8'), ('SF1 (234g)', '<f8'), ('GABPB1_extended (134g)', '<f8'), ('FOXP1_extended (334g)', '<f8'), ('FOXP1 (286g)', '<f8'), ('CREM_extended (507g)', '<f8'), ('CREM (442g)', '<f8'), ('FOS_extended (436g)', '<f8'), ('JUNB_extended (84g)', '<f8'), ('JUNB (35g)', '<f8'), ('IKZF2 (13g)', '<f8'), ('BATF_extended (35g)', '<f8'), ('BATF (21g)', '<f8'), ('FOXP3_extended (76g)', '<f8'), ('FOXP3 (23g)', '<f8'), ('PRDM1 (15g)', '<f8'), ('MAF_extended (119g)', '<f8'), ('MAF (22g)', '<f8'), ('UQCRB (573g)', '<f8'), ('LEF1 (20g)', '<f8'), ('GATA3_extended (25g)', '<f8'), ('GATA3 (18g)', '<f8'), ('IRF4_extended (49g)', '<f8'), ('IRF4 (20g)', '<f8'), ('KLF2 (32g)', '<f8'), ('CEBPD_extended (330g)', '<f8'), ('CEBPD (241g)', '<f8'), ('FOSL2 (109g)', '<f8'), ('FOSL2_extended (442g)', '<f8'), ('JUND_extended (789g)', '<f8'), ('JUND (274g)', '<f8'), ('IRF6_extended (14g)', '<f8'), ('NR2F6_extended (176g)', '<f8'), ('NR2F6 (121g)', '<f8'), ('MAFK_extended (280g)', '<f8'), ('MAFK (117g)', '<f8'), ('ELF3 (260g)', '<f8'), ('HTATIP2 (179g)', '<f8'), ('PIR (247g)', '<f8'), ('XBP1_extended (669g)', '<f8'), ('XBP1 (587g)', '<f8'), ('KLF5_extended (1521g)', '<f8'), ('KLF5 (1038g)', '<f8'), ('NR2F2_extended (36g)', '<f8'), ('NR2F2 (19g)', '<f8'), ('GLIS3_extended (87g)', '<f8'), ('MYLK (52g)', '<f8'), ('HOXA5 (16g)', '<f8'), ('FOXO1_extended (85g)', '<f8'), ('FOXO1 (72g)', '<f8'), ('ZEB1 (42g)', '<f8'), ('MSC_extended (56g)', '<f8'), ('MSC (30g)', '<f8'), ('ZNF503 (12g)', '<f8'), ('HOXB2_extended (50g)', '<f8'), ('HOXB2 (23g)', '<f8'), ('FOS (31g)', '<f8'), ('FOSB_extended (403g)', '<f8'), ('FOSB (207g)', '<f8'), ('EGR1_extended (284g)', '<f8'), ('EGR1 (199g)', '<f8'), ('ATF3_extended (333g)', '<f8'), ('ATF3 (265g)', '<f8'), ('NFKB2_extended (107g)', '<f8'), ('NFKB2 (95g)', '<f8'), ('NFKB1_extended (156g)', '<f8'), ('NFKB1 (146g)', '<f8'), ('GATA2_extended (103g)', '<f8'), ('GATA2 (99g)', '<f8'), ('RELB_extended (94g)', '<f8'), ('RELB (88g)', '<f8'), ('NKX2-1_extended (14g)', '<f8'), ('BCL3_extended (250g)', '<f8'), ('BCL3 (201g)', '<f8'), ('FOSL1_extended (360g)', '<f8'), ('FOSL1 (253g)', '<f8'), ('KLF4 (20g)', '<f8'), ('KLF10_extended (70g)', '<f8'), ('RFX2_extended (248g)', '<f8'), ('RFX2 (241g)', '<f8'), ('ETV1_extended (21g)', '<f8'), ('ETV1 (11g)', '<f8'), ('ETV5_extended (12g)', '<f8'), ('NFIX_extended (59g)', '<f8'), ('NFIX (57g)', '<f8'), ('KLF7_extended (88g)', '<f8'), ('KLF7 (42g)', '<f8'), ('FLI1_extended (111g)', '<f8'), ('FLI1 (51g)', '<f8'), ('HES1_extended (95g)', '<f8'), ('HES1 (45g)', '<f8'), ('TEAD1_extended (417g)', '<f8'), ('TEAD1 (413g)', '<f8'), ('ELK3_extended (186g)', '<f8'), ('ELK3 (65g)', '<f8'), ('MECOM (21g)', '<f8'), ('LUZP1 (111g)', '<f8'), ('SOX7_extended (39g)', '<f8'), ('BCL6_extended (18g)', '<f8'), ('BCL6 (16g)', '<f8'), ('NFIL3_extended (163g)', '<f8'), ('NFIL3 (47g)', '<f8'), ('CREB5_extended (139g)', '<f8'), ('CREB5 (21g)', '<f8'), ('NFE2L2_extended (253g)', '<f8'), ('HIF1A_extended (207g)', '<f8'), ('HIF1A (206g)', '<f8'), ('FOXO3_extended (191g)', '<f8'), ('FOXO3 (168g)', '<f8'), ('MYC_extended (128g)', '<f8'), ('MYC (53g)', '<f8'), ('TFAP2A (70g)', '<f8'), ('TFAP2C (32g)', '<f8'), ('HOXC9_extended (18g)', '<f8'), ('HOXC9 (14g)', '<f8'), ('SOX4_extended (320g)', '<f8'), ('SOX4 (260g)', '<f8'), ('ELF3_extended (1249g)', '<f8'), ('EHF_extended (1513g)', '<f8'), ('EHF (762g)', '<f8'), ('HES4 (19g)', '<f8'), ('HES4_extended (59g)', '<f8'), ('PBX1 (34g)', '<f8'), ('TFDP2_extended (141g)', '<f8'), ('HDAC2 (105g)', '<f8'), ('CREB3_extended (137g)', '<f8'), ('CREB3 (99g)', '<f8'), ('CREB3L2_extended (372g)', '<f8'), ('CREB3L2 (289g)', '<f8'), ('ATF4_extended (261g)', '<f8'), ('ATF4 (168g)', '<f8'), ('DDIT3_extended (23g)', '<f8'), ('DDIT3 (19g)', '<f8'), ('CEBPG_extended (40g)', '<f8'), ('CEBPG (32g)', '<f8'), ('BDP1_extended (70g)', '<f8'), ('SMARCC2_extended (91g)', '<f8'), ('SMARCC2 (90g)', '<f8'), ('RFX3_extended (391g)', '<f8'), ('RFX3 (380g)', '<f8'), ('BCLAF1_extended (109g)', '<f8'), ('YY1_extended (240g)', '<f8'), ('YY1 (188g)', '<f8'), ('ATF2_extended (80g)', '<f8'), ('ATF2 (58g)', '<f8'), ('ERF_extended (63g)', '<f8'), ('ERF (49g)', '<f8'), ('ELK4_extended (50g)', '<f8'), ('ELK4 (38g)', '<f8'), ('ELF2_extended (123g)', '<f8'), ('ELF2 (85g)', '<f8'), ('GABPA_extended (79g)', '<f8'), ('GABPA (67g)', '<f8'), ('TAF1_extended (39g)', '<f8'), ('TAF1 (20g)', '<f8'), ('KLF3_extended (102g)', '<f8'), ('KLF3 (16g)', '<f8'), ('FOXP4_extended (14g)', '<f8'), ('FOXP4 (11g)', '<f8'), ('NR2C2_extended (37g)', '<f8'), ('NR2C2 (25g)', '<f8'), ('CEBPA_extended (30g)', '<f8'), ('CEBPA (28g)', '<f8'), ('ZNF143_extended (22g)', '<f8'), ('ZNF143 (20g)', '<f8'), ('RUNX2_extended (19g)', '<f8'), ('RUNX2 (12g)', '<f8'), ('SOX2_extended (41g)', '<f8'), ('SOX2 (19g)', '<f8'), ('FOXJ1_extended (37g)', '<f8'), ('FOXJ1 (20g)', '<f8'), ('RARA_extended (16g)', '<f8'), ('RARA (10g)', '<f8'), ('RELA_extended (33g)', '<f8'), ('RELA (14g)', '<f8'), ('MAFF_extended (22g)', '<f8'), ('MAFF (13g)', '<f8'), ('MYBL2_extended (141g)', '<f8'), ('MYBL2 (140g)', '<f8'), ('FOXM1_extended (14g)', '<f8'), ('FOXM1 (11g)', '<f8'), ('POLE4_extended (86g)', '<f8'), ('POLE4 (83g)', '<f8'), ('TFDP1_extended (106g)', '<f8'), ('TFDP1 (93g)', '<f8'), ('NRF1_extended (37g)', '<f8'), ('NRF1 (30g)', '<f8'), ('ELK1_extended (72g)', '<f8'), ('ELK1 (63g)', '<f8'), ('SP1_extended (59g)', '<f8'), ('SP1 (31g)', '<f8'), ('RXRB_extended (11g)', '<f8'), ('RXRB (11g)', '<f8'), ('NFYC_extended (23g)', '<f8'), ('NFYC (21g)', '<f8'), ('TGIF2_extended (38g)', '<f8'), ('TGIF2 (36g)', '<f8'), ('ESRRA_extended (34g)', '<f8'), ('ESRRA (27g)', '<f8'), ('POU2F1_extended (13g)', '<f8'), ('POU2F1 (12g)', '<f8'), ('RXRA_extended (107g)', '<f8'), ('RXRA (78g)', '<f8'), ('MAFG_extended (64g)', '<f8'), ('MAFG (25g)', '<f8'), ('SRF_extended (14g)', '<f8'), ('SRF (13g)', '<f8'), ('HIVEP2_extended (40g)', '<f8'), ('HIVEP2 (28g)', '<f8'), ('ZBTB41 (12g)', '<f8'), ('SETDB1_extended (46g)', '<f8'), ('SETDB1 (41g)', '<f8'), ('ETV3_extended (50g)', '<f8'), ('ETV3 (35g)', '<f8'), ('HSF1_extended (47g)', '<f8'), ('HSF1 (14g)', '<f8'), ('E2F3_extended (42g)', '<f8'), ('E2F3 (34g)', '<f8'), ('USF2_extended (41g)', '<f8'), ('USF2 (33g)', '<f8'), ('MYB_extended (68g)', '<f8'), ('MYB (63g)', '<f8'), ('CREB1_extended (81g)', '<f8'), ('CREB1 (61g)', '<f8'), ('MAX_extended (83g)', '<f8'), ('MAX (80g)', '<f8'), ('KLF12_extended (36g)', '<f8'), ('KLF12 (31g)', '<f8'), ('RFX5_extended (14g)', '<f8'), ('RFX5 (13g)', '<f8'), ('CLOCK_extended (52g)', '<f8'), ('CLOCK (13g)', '<f8'), ('SREBF2_extended (39g)', '<f8'), ('SREBF2 (38g)', '<f8'), ('ARNT_extended (52g)', '<f8'), ('ARNT (16g)', '<f8'), ('MLX_extended (53g)', '<f8'), ('MLX (21g)', '<f8'), ('SP2 (11g)', '<f8'), ('BACH1_extended (63g)', '<f8'), ('BACH1 (14g)', '<f8'), ('BHLHE40_extended (77g)', '<f8'), ('BHLHE40 (16g)', '<f8'), ('NFATC1_extended (13g)', '<f8'), ('NPDC1_extended (12g)', '<f8'), ('CREBZF (15g)', '<f8'), ('ZNF100 (15g)', '<f8'), ('PPARD_extended (52g)', '<f8'), ('PPARD (20g)', '<f8'), ('ELF4_extended (49g)', '<f8'), ('ELF4 (12g)', '<f8'), ('TEAD4 (33g)', '<f8'), ('NFIC (31g)', '<f8'), ('HDAC1 (10g)', '<f8'), ('CTCF (13g)', '<f8'), ('SMC3_extended (50g)', '<f8'), ('RAD21 (26g)', '<f8'), ('BRF1 (35g)', '<f8'), ('HINFP (16g)', '<f8'), ('MLXIP_extended (11g)', '<f8'), ('ATF6B_extended (61g)', '<f8'), ('ZNF260 (11g)', '<f8'), ('MEF2A (16g)', '<f8'), ('FOXK1_extended (22g)', '<f8'), ('FOXN3_extended (12g)', '<f8'), ('ASCL2_extended (16g)', '<f8'), ('MXI1_extended (23g)', '<f8'), ('SMAD3 (13g)', '<f8'), ('CENPB (29g)', '<f8'), ('NFE2L3_extended (15g)', '<f8'), ('ZNF664 (18g)', '<f8'), ('TBX3_extended (32g)', '<f8'), ('MEF2D_extended (10g)', '<f8'), ('BATF3_extended (45g)', '<f8'), ('TCF7L2 (27g)', '<f8'), ('FOXJ3_extended (12g)', '<f8'), ('ATF6_extended (47g)', '<f8'), ('ZNF254 (15g)', '<f8'), ('E2F6_extended (37g)', '<f8'), ('ZBTB33 (19g)', '<f8'), ('MYEF2_extended (32g)', '<f8'), ('THAP1_extended (19g)', '<f8'), ('IRF5_extended (27g)', '<f8'), ('STAT5A_extended (24g)', '<f8'), ('NR1D2_extended (13g)', '<f8'), ('HIVEP1_extended (11g)', '<f8'), ('TCF3 (12g)', '<f8'), ('MELK (11g)', '<f8'), ('TP53 (10g)', '<f8'), ('ETV6_extended (56g)', '<f8'), ('POLE3_extended (54g)', '<f8'), ('ZBTB7B_extended (26g)', '<f8'), ('MAZ_extended (96g)', '<f8'), ('ARNTL2_extended (33g)', '<f8'), ('KLF16_extended (36g)', '<f8'), ('FOXK2 (11g)', '<f8'), ('TFEB_extended (128g)', '<f8'), ('TFEB (92g)', '<f8'), ('POU2AF1_extended (64g)', '<f8'), ('POU2AF1 (14g)', '<f8'), ('POU2F2_extended (78g)', '<f8'), ('POU2F2 (66g)', '<f8'), ('BCL11A_extended (207g)', '<f8'), ('BCL11A (142g)', '<f8'), ('ETV7_extended (90g)', '<f8'), ('ETV7 (63g)', '<f8'), ('STAT1_extended (1443g)', '<f8'), ('STAT1 (1212g)', '<f8'), ('IRF2_extended (196g)', '<f8'), ('IRF2 (179g)', '<f8'), ('STAT2_extended (287g)', '<f8'), ('STAT2 (234g)', '<f8')] is not allowed
For help, see http://linnarssonlab.org/loompy/format/
./Thienpont_T-cell_v4_R_fixed.loom does not appead to be a valid Loom file according to Loom spec version '2.0.1'
falexwolf commented 5 years ago

That seems to be a loompy issue. Doesn't updating loompy help?

orrzor commented 5 years ago

Hi Alex, thank you for your quick response! I contacted Sten over at loompy and he just pushed an update that allows for a little more flexibility when reading in loom files. It now works for me. The change he applied only applies to the loompy function loompy.connect, so I think I would still get this same problem when using scanpy function read_loom. I have the latest version of loompy. I don't think this is something that necessarily needs to be fixed on your end. It sounds like the loom format has changed a little bit, and maybe the people who made the loom file I was using did not follow all the rules when making the file. Thank you!