An error trying to plot the rna004

[hasindu2008]

Got an an error trying to plot the rna004.

plot region: 1-234      read_id: e8d52b46-e829-464a-a9d0-23223c7756d4
BokehUserWarning: ColumnDataSource's columns must be of the same length. Current lengths: ('line_color', 6095), ('x', 6094), ('y', 6094)
BokehUserWarning: ColumnDataSource's columns must be of the same length. Current lengths: ('hatch_color', 6095), ('line_color', 6095), ('x', 6094), ('y', 6094)
BokehUserWarning: ColumnDataSource's columns must be of the same length. Current lengths: ('fill_color', 6095), ('hatch_color', 6095), ('line_color', 6095), ('x', 6094), ('y', 6094)
Traceback (most recent call last):
  File "/home/hasindu/squigualiser-v0.5.1/bin/squigualiser", line 8, in <module>
    sys.exit(main())
  File "/home/hasindu/squigualiser-v0.5.1/lib/python3.8/site-packages/src/__init__.py", line 56, in main
    args.func(args)
  File "/home/hasindu/squigualiser-v0.5.1/lib/python3.8/site-packages/src/plot.py", line 710, in run
    layout_ = plot_function(p=p, read_id=read_id, signal_tuple=signal_tuple, sig_algn_data=sig_algn_dic, fasta_sequence=fasta_seq, base_limit=base_limit, draw_data=draw_data)
  File "/home/hasindu/squigualiser-v0.5.1/lib/python3.8/site-packages/src/plot.py", line 207, in plot_function
    plot_title = f'{sig_algn_data["tag_name"]}[{sig_algn_data["ref_end"]:,}-{sig_algn_data["ref_end"] - base_index+1:,}]{indt}signal: [{int(x_real[0])}-{int(x_real[x_coordinate - 1])}]{indt}deletions(bases): {num_Ds} insertions(samples): {num_Is}{indt}{read_id}{indt}signal dir:{draw_data["sig_dir"]}'
IndexError: index 6094 is out of bounds for axis 0 with size 6094
[12:27](https://genometech2.slack.com/archives/D02M0JVQ78C/p1708176434566439)
command:
~/squigualiser-v0.5.1/squigualiser plot  -f test/uhr_rna004_1k/PNXRXX240011_reads_1k.fastq -s test/uhr_rna004_1k/PNXRXX240011_reads_1k.blow5 -a test/uhr_rna004_1k/resquiggle.paf  -o plot1/ --rna
[12:27](https://genometech2.slack.com/archives/D02M0JVQ78C/p1708176476263939)

from f5c v1.4 run:

 test/test_rsq.sh -z

to generate the necessary files.

[hiruna72]

Thanks for sharing this.

In resquiggle.paf file PAF records for the following readids are wrong.
They should not have the first insertion at the very beginning of the ss string (it is already reflected in the start raw value - third column).

I manually edited the ss strings to remove that part.
For example ss:Z:221I8,20,17... was updated as ss:Z:8,20,17...
Then the above squigualiser command worked (dev branch).

[hasindu2008]

Did this not happen in R9 reads?

[hiruna72]

f5c rna r9 data also has this bug. but it did not cause squigualiser to error out. example,
16d22568-4ed8-4966-8f12-bb77b57f670f 119493 49 119303 + 16d22568-4ed8-4966-8f12-bb77b57f670f 1089 1087 0 1081 1089 255 sc:f:1.021642 sh:f:12.343329 ss:Z:49I23,53,7,643,8814,...

[hiruna72]

please check the PR hasindu2008/f5c#156 when you get time.
thanks!

[hasindu2008]

Merged that and it should work. Thanks for the fix. We should update the recommended f5c version for squigualiser when the new f5c version is released