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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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pySCENIC: use prune2df() ERROR #384

Open peixiaoya opened 4 years ago

peixiaoya commented 4 years ago

my code: df = prune2df(rnkdbs=dbs, modules, MOTIF_ANNOTATIONS_FNAME)

The error is: ValueError: The columns in the computed data do not match the columns in the provided metadata Extra: [] Missing: []

I don't know what are the columns in the computed data and the columns in the provided metadata means. The columns means genes or modules?

my other objects are:

dbs

[FeatherRankingDatabase(name="hg19-500bp-upstream-7species.mc9nr"), FeatherRankingDatabase(name="hg19-tss-centered-10kb-7species.mc9nr")]

MOTIF_ANNOTATIONS_FNAME

'motifs-v9-nr.hgnc-m0.001-o0.0.tbl'

modules

modules is pruduced by last step: modules_from_adjacencies(adjacencies, ex_matrix)

I just show the first element in modules:

modules[1]: Regulon(name='Regulon for AGGF1', gene2weight=<frozendict {'PHF20L1': 5.536453825351042, 'SLTM': 4.784352848021737, 'KLF13': 4.480358355367266, 'CES1': 4.444073983264985, 'HNRNPAB': 3.5097931888215808, 'CLINT1': 3.4154243965394833, 'RPS6KA1': 3.204985779429065, 'HNRNPA1L2': 2.9785526155315423, 'KDM5A': 2.925367952591891, 'PRKCD': 2.8695911440746698, 'CLU': 2.7780233081596144, 'TTC7A': 2.7530113181646167, 'DYNC1I2': 2.68532797822178, 'CDK11A': 2.6815736560396126, 'GTF2I': 2.662046373846452, 'TTC37': 2.4726282993015807, 'ARID4B': 2.4644504945894514, 'ZC3H13': 2.222352963043234, 'CEP350': 2.1117785611349804, 'ATP6V1B2': 2.0694409152149618, 'ACIN1': 1.9974352859669344, 'DNAJC7': 1.9715089415128244, 'SRSF4': 1.815038604270737, 'OSCAR': 1.8043279676926285, 'MAP2K1': 1.6793833301235643, 'EIF3J': 1.6554023912070843, 'PHIP': 1.4856959214510794, 'TRAF3IP3': 1.4656063998347393, 'STAG2': 1.4395589095719783, 'GOPC': 1.418899877232492, 'HSPA1A': 1.3887598149883325, 'WIPF1': 1.3425416753626582, 'EIF4H': 1.3257280199920285, 'BDP1': 1.317071881724102, 'MTDH': 1.3151084420269152, 'MBP': 1.3128931028447586, 'CAPN2': 1.1944260206766693, 'METTL14': 1.1495700895036571, 'ZNF90': 1.1009198912106408, 'SAFB': 1.089580128861544, 'OAS1': 1.063853629371401, 'ATRX': 1.0418632927619078, 'NBPF14': 1.0414393262079236, 'APBB1IP': 1.012628534284406, 'SEPT7': 0.9665785832869574, 'HIST1H4C': 0.9066484037190048, 'SMCHD1': 0.8469815005151253, 'CD93': 0.7946930466478108, 'TRIM38': 0.6447514785457761, 'USP15': 0.6356668374557868, 'MRPL20': 0.6336113487270661, 'EIF3A': 0.631952810070231, 'BPTF': 0.6261021870139323, 'MYADM': 0.6227425212614649, 'SELL': 0.6193514014633118, 'EIF5B': 0.5844943054326748, 'AGGF1': 1.0}>, gene2occurrence=<frozendict {}>, transcription_factor='AGGF1', context=frozenset({'activating', 'weight>75.0%'}), score=0.0, nes=0.0, orthologous_identity=0.0, similarity_qvalue=0.0, annotation='')

rekham1077 commented 4 years ago

I am having this same exact issue

celinesin commented 4 years ago

me too~

celinesin commented 4 years ago

I got it to work with an older docker instance -- following is a non-exhaustive list of packages with different versions (I only included those that I deem to be possible culprits):

dask==1.0.0 (instead of 2.20.0) numba==0.45.1 (instead of 0.48.0) pyscenic==0.10.0 (instead of 0.10.2)

hope this can help someone... i can attach a full requirements.txt if that might help someone :)