Error occurred when Plotting Genes #68
Description
Hello, Xiaotao, It's a wonderful tool for enhancer-hijack analysis.
Here is an issue when plot contact maps.
When I plot a contact map using script below:
##########################################################################################
from neoloop.visualize.core import *
import cooler
clr = cooler.Cooler('/public/GongLab/dongy/SV_project/HiC_related_analysis/1.data_shift/Cell/neoloop/Cell_5000.cool')
assembly = 'C28 deletion,12,27127893,+,12,27639555,- 12,26555000 12,28310000'
vis = Triangle(clr, assembly, n_rows=6, figsize=(7, 5.3), track_partition=[5, 0.2, 0.8, 0.8, 0.8,0.8], correct='weight', span=600000, space=0.03)
vis.matrix_plot(vmin=0, vmax=0.08, cbr_fontsize=9)
vis.plot_chromosome_bounds(linewidth=2)
vis.plot_loops('Cell.neo-loops.txt', face_color='none', marker_size=40, cluster=False, filter_by_res=False, onlyneo=True)
vis.plot_genes(filter_=['PPFIBP1'],label_aligns={'PPFIBP1'}, fontsize=9)
vis.plot_signal('H3K27ac', '/public/GongLab/dongy/SV_project/Enhancer/neoloopfinder/3.showcase/Cell/Cell_H3K27ac.bw', label_size=10, data_range_size=9, max_value=20, color='#6A3D9A')
vis.plot_signal('RNA-Seq', '/public/GongLab/dongy/SV_project/Enhancer/neoloopfinder/3.showcase/Cell/Cell_RNA_seq.bw', label_size=10, data_range_size=9, max_value=20, color='#E31A1C')
vis.plot_arcs(lw=1.5, cutoff='top', gene_filter=['PPFIBP1'], arc_color='#666666') # ETV1-related neo-loops
vis.plot_chromosome_bar(name_size=13, coord_size=10, color_by_order=['#1F78B4','#33A02C'])
vis.outfig('Cell_PPFIBP1.png', dpi=300)
##########################################################################################
An error occurred, which was showed below. Can you help me fix this issue? Thanks a lot
##########################################################################################
INFO:pyensembl.download_cache:Fetching /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.97.gtf.gz from URL https://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz
INFO:datacache.download:Downloading https://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz to /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.97.gtf.gz
INFO:pyensembl.download_cache:Fetching /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.cdna.all.fa.gz from URL https://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
INFO:datacache.download:Downloading https://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz to /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.cdna.all.fa.gz
INFO:pyensembl.download_cache:Fetching /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.ncrna.fa.gz from URL https://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz
INFO:datacache.download:Downloading https://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz to /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.ncrna.fa.gz
INFO:pyensembl.download_cache:Fetching /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.pep.all.fa.gz from URL https://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz
INFO:datacache.download:Downloading https://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz to /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.pep.all.fa.gz
INFO:pyensembl.database:Creating database: /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.97.gtf.db
INFO:pyensembl.database:Reading GTF from /public/groups/dongy/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.97.gtf.gz
INFO:root:Extracted GTF attributes: ['gene_id', 'gene_version', 'gene_name', 'gene_source', 'gene_biotype', 'transcript_id', 'transcript_version', 'transcript_name', 'transcript_source', 'transcript_biotype', 'tag', 'transcript_support_level', 'exon_number', 'exon_id', 'exon_version', 'protein_id', 'protein_version', 'ccds_id']
Traceback (most recent call last):
File "/public/GongLab/dongy/SV_project/Enhancer/neoloopfinder/2.get_neoloop/3.TGS_HiC_NGS_RNA_seq_no_filter/OSRC2/plot_figure/2.target_gene/1.plot_PPFIBP1.py", line 10, in
vis.plot_genes(filter_=['PPFIBP1'],label_aligns={'PPFIBP1'}, fontsize=9)
File "/public/groups/dongy/software/miniconda3/envs/neoloop/lib/python3.10/site-packages/neoloop/visualize/core.py", line 485, in plot_genes
genes = Genes(self.bounds, self.orients, self.res, species=species, release=release,
File "/public/groups/dongy/software/miniconda3/envs/neoloop/lib/python3.10/site-packages/neoloop/visualize/bed.py", line 116, in init
ref.index()
File "/public/groups/dongy/software/miniconda3/envs/neoloop/lib/python3.10/site-packages/pyensembl/genome.py", line 280, in index
self.db.connect_or_create(overwrite=overwrite)
File "/public/groups/dongy/software/miniconda3/envs/neoloop/lib/python3.10/site-packages/pyensembl/database.py", line 286, in connect_or_create
return self.create(overwrite=overwrite)
File "/public/groups/dongy/software/miniconda3/envs/neoloop/lib/python3.10/site-packages/pyensembl/database.py", line 239, in create
self._connection = datacache.db_from_dataframes_with_absolute_path(
File "/public/groups/dongy/software/miniconda3/envs/neoloop/lib/python3.10/site-packages/datacache/database_helpers.py", line 176, in db_from_dataframes_with_absolute_path
tables = build_tables(
File "/public/groups/dongy/software/miniconda3/envs/neoloop/lib/python3.10/site-packages/datacache/database_helpers.py", line 136, in build_tables
table = DatabaseTable.from_dataframe(
File "/public/groups/dongy/software/miniconda3/envs/neoloop/lib/python3.10/site-packages/datacache/database_table.py", line 56, in from_dataframe
column_db_type = db_type(values.dtype)
File "/public/groups/dongy/software/miniconda3/envs/neoloop/lib/python3.10/site-packages/datacache/database_types.py", line 96, in db_type
raise ValueError("Failed to find sqlite3 column type for %s" % (
ValueError: Failed to find sqlite3 column type for category