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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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generating figure has error #38

Closed yangfeizZZ closed 1 year ago

yangfeizZZ commented 1 year ago

Hi: I plot the figure following your Github,it has an error.

My code: from neoloop.visualize.core import * import cooler clr = cooler.Cooler("M2_5000.cool") assembly = "C2 translocation,7,152075000,-,21,11095000,+ 7,152110000 21,11055000" vis = Triangle(clr, assembly, n_rows=3, figsize=(7, 4.2), track_partition=[5, 0.4, 0.5], correct='sweight') vis.matrix_plot(vmin=0,vmax=0.015) vis.plot_chromosome_bounds(linewidth=2.5) vis.plot_loops('M1.neo-loop_0.8.txt', face_color='none', marker_size=40, cluster=True) vis.plotgenes(filter=['PRIM2',"TP53"],label_aligns={'PRI':'right'} ,fontsize=9) vis.plot_chromosome_bar(name_size=10, coord_size=4.8) vis.outfig('test.pdf')

The error : INFO:pyensembl.sequence_data:Loaded sequence dictionary from /home/yangfei/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.cdna.all.fa.gz.pickle INFO:pyensembl.sequence_data:Loaded sequence dictionary from /home/yangfei/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.ncrna.fa.gz.pickle INFO:pyensembl.sequence_data:Loaded sequence dictionary from /home/yangfei/.cache/pyensembl/GRCh38/ensembl97/Homo_sapiens.GRCh38.pep.all.fa.gz.pickle Traceback (most recent call last): File "plot.py", line 11, in vis.plotgenes(filter=['PRIM2',"TP53"],label_aligns={'PRI':'right'} ,fontsize=9) File "/home/yangfei/.conda/envs/neoloop/lib/python3.7/site-packages/neoloop/visualize/core.py", line 484, in plot_genes style=style, global_max_row=global_max_row) File "/home/yangfei/.conda/envs/neoloop/lib/python3.7/site-packages/neoloop/visualize/bed.py", line 321, in init self.interval_tree, min_score, max_score = self._process_bed() File "/home/yangfei/.conda/envs/neoloop/lib/python3.7/site-packages/neoloop/visualize/bed.py", line 326, in _process_bed bed_fileh = ReadBed(self.properties['file']) File "/home/yangfei/.conda/envs/neoloop/lib/python3.7/site-packages/coolbox/utilities/bed.py", line 122, in init fields = self.get_no_comment_line() File "/home/yangfei/.conda/envs/neoloop/lib/python3.7/site-packages/coolbox/utilities/bed.py", line 154, in get_no_comment_line line = next(self.file_handle) StopIteration