Coordinate "0" in bed file unrecognized by the transform command

[tzxiong]

Hi,

The "transform" command seems to produce errors when coordinate 0 is encountered in the input bed file. For instance:

Here is a simple test.bed:

contig  0       3       +

A simple test.agp:

scaffold        1       100     1       W       contig  1       100     +

If I run:

agptools transform test.bed test.agp > test.transform.bed

The error reads:

Traceback (most recent call last):
  File "/home/tx84/miniconda3/envs/EnvPy3.12/bin/agptools", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/tx84/miniconda3/envs/EnvPy3.12/lib/python3.12/site-packages/agp/agptools.py", line 303, in main
    args.func(args)
  File "/home/tx84/miniconda3/envs/EnvPy3.12/lib/python3.12/site-packages/agp/agptools.py", line 255, in <lambda>
    transform_parser.set_defaults(func=lambda a: transform.run(a.bed, a.agp, a.outfile))
                                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/tx84/miniconda3/envs/EnvPy3.12/lib/python3.12/site-packages/agp/transform.py", line 187, in run
    print(transform_bed_row(bed_row, contig_dict), file=bed_out)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/tx84/miniconda3/envs/EnvPy3.12/lib/python3.12/site-packages/agp/transform.py", line 150, in transform_bed_row
    agp_row_start = find_agp_row(bed_row.chrom, bed_row.start, contig_dict)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/tx84/miniconda3/envs/EnvPy3.12/lib/python3.12/site-packages/agp/transform.py", line 126, in find_agp_row
    raise CoordinateNotFoundError(f"{contig_name}:{coordinate_on_contig}")
agp.transform.CoordinateNotFoundError: contig:0

It seems the problem is caused by any zeros in the bed coordinates, but I think the bed file is 0-based right?

Thanks!

[esrice]

Thanks for catching this! My brain must have been in 1-based mode because AGP is 1-based. I'll fix it ASAP.

[esrice]

I just fixed this on the branch fix-9. Thank you for providing a nice test case; I've added it to the test suite. Feel free to test this commit by doing:

git clone https://github.com/WarrenLab/agptools.git
cd agptools
git checkout fix-9
pip install .
agptools [command]

Otherwise, I'll merge it into main and release a new version in the next few days.

[tzxiong]

Thank you for fixing this! I checked another more tricky example for the fix-9 branch and there still seems to be a bug somewhere. For instance,

test.agp (inverts a 100-bp contig to a scaffold):

scaffold        1       100     1       W       contig  1       100     -

test.bed (an interval containing only the first base of the contig, which should be the last base of the scaffold):

contig  0       1       +

Command is

agptools transform test.bed test.agp > test.transform.bed

This produces:

scaffold        100     101     -

The expected outcome should be scaffold 99 100 - since the last base is 99.

[esrice]

Thanks for finding yet another bug and providing a test case for it. The latest commit to branch fix-9 should fix it.