START option and LINEBREAK error?

[abs-yy]

I've been trying use sangerseq_viewer to visualize my Sanger sequence alignments. From what I understand, I have two errors when I use the -rs and -l options.

First of all, when I try a single ab1 file it works, producing a beautiful figure out.png. The plasmid is about 9000bp and the alignment starts from the position 5774 up to 6476.

% sangerseq_viewer  -s plasmid.gbk -q abis/seq.ab1 -o out.png  --dpi 300 -l 150
module 'pyarrow' has no attribute '__version__'

But when I add --start 5774, which is the start position for the above alignment, it fails. The only difference is using the --start option.

% sangerseq_viewer  -s plasmid.gbk -q abis/seq.ab1 -o out.png  --dpi 300 -l 150 --start 5774
module 'pyarrow' has no attribute '__version__'
Traceback (most recent call last):
  File "/Users/yoshida/micromamba/envs/general/bin/sangerseq_viewer", line 27, in <module>
    ax_all = view_sanger(gbkpath, abipath, start, end, linebreak=linebreak, output=output, display_quality=quality, dpi=dpi)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/sangerseq_viewer/sangerseq_viewer.py", line 823, in view_sanger
    ax_all = visualize(template_aligned, abidata, query_aligned, abiname=abipath.split("/")[-1], start=i, end=i+linebreak if i+linebreak < len(template_aligned.seq) else len(template_aligned.seq),
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/sangerseq_viewer/sangerseq_viewer.py", line 474, in visualize
    axmap   = visualizemap(subject, seq=True, start=start, end=end, linebreak=end-start, tick_interval=10, title="", height_scale=0.8, fontsize_nucl=10, fontsize=10)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/QUEEN/qfunction.py", line 3535, in visualizemap
    figo, ax = vl.visualize(dna, start=start, end=end, feature_list=feature_list, wrap_width=linebreak, annotation_loc=label_location, unvisible_types=["source"],
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/QUEEN/visualize_linear_dna.py", line 684, in visualize
    patch = pw.Bricks(patch_dict)
            ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/patchworklib/patchworklib.py", line 1532, in __init__
    x0, x1, y0, y1 = self.get_middle_corner()
                     ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/patchworklib/patchworklib.py", line 2112, in get_middle_corner
    return min(x0_list), max(x1_list), min(y0_list), max(y1_list)
           ^^^^^^^^^^^^
ValueError: min() arg is an empty sequence

Next, I tried to change the line width to increase visuability. First of all, I can produce a multiple alignment using four AB1 files like this.

% sangerseq_viewer  -s plasmid.gbk -q abis -o out.png  --dpi 300 -l 150
module 'pyarrow' has no attribute '__version__'

But when I choose -l 120, it fails.

% sangerseq_viewer  -s plasmid.gbk -q abis -o out.png  --dpi 300 -l 120
module 'pyarrow' has no attribute '__version__'
Traceback (most recent call last):
  File "/Users/abs/micromamba/envs/general/bin/sangerseq_viewer", line 27, in <module>
    ax_all = view_sanger(gbkpath, abipath, start, end, linebreak=linebreak, output=output, display_quality=quality, dpi=dpi)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/sangerseq_viewer/sangerseq_viewer.py", line 720, in view_sanger
    ax_all = visualize(template_aligned, new_abidata_list, query_aligned_list, abiname=abifile_path_list, start=i, end=i+linebreak if i+linebreak < len(template_aligned.seq) else len(template_aligned.seq),
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/sangerseq_viewer/sangerseq_viewer.py", line 474, in visualize
    axmap   = visualizemap(subject, seq=True, start=start, end=end, linebreak=end-start, tick_interval=10, title="", height_scale=0.8, fontsize_nucl=10, fontsize=10)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/QUEEN/qfunction.py", line 3535, in visualizemap
    figo, ax = vl.visualize(dna, start=start, end=end, feature_list=feature_list, wrap_width=linebreak, annotation_loc=label_location, unvisible_types=["source"],
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/QUEEN/visualize_linear_dna.py", line 549, in visualize
    ax, y_list, ty_list = map_feat(fig, ax, sub_brick.dnafeatures, len(sub_brick.seq), head_length, unvisible_types=unvisible_types, visible_types=visible_types, enlarge_w=enlarge_w, enlarge_h=enlarge_h, annotation_loc=annotation_loc, label_visible=label_visible, fontsize=fontsize, project=sub_brick.project, title_visible=title_visible, axis_visible=axis_visible, labelcolor=labelcolor, titlename=titlename)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/abs/micromamba/envs/general/lib/python3.11/site-packages/QUEEN/visualize_linear_dna.py", line 330, in map_feat
    text_position_matrix[t][j] = 1
    ~~~~~~~~~~~~~~~~~~~~~~~^^^
IndexError: list assignment index out of range