Error when using simulated reads from ecSimulator

[uretaj]

Hi,

I'm getting this error whenever I try to use simulated reads from ecSimulator

$ /CycleViz/CycleViz.py --ref GRCh38 --cycles_file test_amplicon1_BPG_converted_cycles.txt --cycle 1 -g est_amplicon1_graph.txt --rotate_to_min --figure_size_style small

CycleViz 0.1.10 Using resources in CycleViz/resources/ Plots will use reference hg38 Using figure_size_style=small Bar width scaled up 1.5x to 1.05 Gene fontsize scaled up 2x to 14 Tick fontsize scaled up 1.5x to: 6.0 checking adjacency plotting structure Reading genes plotting genes Traceback (most recent call last): File "/CycleViz/CycleViz.py", line 1418, in <module> plot_bpg_connection(ref_placements, total_length, prev_seg_index_is_adj, bpg_dict, seg_end_pos_d) File "/CycleViz/CycleViz.py", line 106, in plot_bpg_connection bpg_dict, seg_end_pos_d) File "/CycleViz/VizUtil.py", line 294, in pair_is_edge rObj1_end = seg_end_pos_d[a_id][-1] if a_dir == "+" else seg_end_pos_d[a_id][0] KeyError: '14'

[jluebeck]

Hi,

Thanks for sending this error. The cause is likely because you shouldn't use the BPG-converted version of the cycles file when using input from ecSimulator, simply use the simulated graph and cycles files as given in that case.

I plan to simplify this process in the future to avoid confusion.

Thanks and sorry for the confusion!
Jens