We don't have default motifs for your species, Please specify motif data by yourself.

[Roger-GOAT]

Thank you for the wonderful tool! When I want to make my own GRN, get error. My network can't download ref_genome so I manual download https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.fa.gz and

ref_genome = ".mm39.fa.gz"

get error and follow the tips

gunzip mm39.fa.gz; bgzip mm39.fa

then again

ref_genome = ".mm39.fa.gz"
peaks = pd.read_csv(".processed_peak_file.csv", index_col=0) #my own peak make before
peaks.head()
peak_id gene_short_name
0   chr12_102758077_102758127   Ubr7
1   chr12_102758083_102758133   Ubr7
2   chr12_102758115_102758165   Ubr7
3   chr12_102758292_102758342   Ubr7
4   chr12_102758366_102758416   Ubr7
peaks = ma.check_peak_format(peaks, ref_genome, genomes_dir=None)
Peaks before filtering:  1331636
Peaks with invalid chr_name:  0
Peaks with invalid length:  0
Peaks after filtering:  1331636
tfi = ma.TFinfo(peak_data_frame=peaks,
                ref_genome=ref_genome,
                genomes_dir=None)
tfi
<celloracle.motif_analysis.tfinfo_core.TFinfo at 0x7fb7a2e8e6e0>
tfi.scan(fpr=0.02,
         motifs=None,  # If you enter None, default motifs will be loaded.
         verbose=True,
        n_cpus=20,
        )
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File <timed exec>:2

File ~/.local/lib/python3.10/site-packages/celloracle/motif_analysis/tfinfo_core.py:386, in TFinfo.scan(self, background_length, fpr, n_cpus, verbose, motifs, TF_evidence_level, TF_formatting, batch_size, divide)
    382 self.background_length = background_length
    384 ## 1. initialilze scanner  ##
    385 # set motif
--> 386 self.set_motifs(motifs=motifs, TF_formatting=TF_formatting, verbose=verbose)
    388 self.dic_motif2TFs = _get_dic_motif2TFs(species=self.species, motifs=self.motifs, TF_evidence_level=TF_evidence_level, formatting=self.TF_formatting)
    389 self.TF_evidence_level = TF_evidence_level

File ~/.local/lib/python3.10/site-packages/celloracle/motif_analysis/tfinfo_core.py:338, in TFinfo.set_motifs(self, motifs, TF_formatting, verbose)
    335             print(f" Default motif for {self.species}: {self.motif_db_name}. \n For more information about the motif data, please see https://gimmemotifs.readthedocs.io/en/master/overview.html \n")
    337     else:
--> 338         raise ValueError(f"We don't have default motifs for your species, Please specify motif data by yourself.")
    340 else:
    341     # Check format
    342     if isinstance(motifs, list):

ValueError: We don't have default motifs for your species, Please specify motif data by yourself.

when I set the ref_genome = "mm39" before tfi.scan still get same error. Would you and some one give some tips? thanks a lot!

[Roger-GOAT]

anybody get same issue?