hmmsearch error

[avivko]

Some of my sequences result in errors like this:

Traceback (most recent call last):
  File "/scratch/users/X/rhodopsin_heap_2_2025-11-06/.snakemake/scripts/tmpyn2viqts.extract_hmmsearch.py", line 170, in <module>
    data[sequence_name]['domains'] = parse_sequence_data(dom)
                                     ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/scratch/users/X/rhodopsin_heap_2_2025-11-06/.snakemake/scripts/tmpyn2viqts.extract_hmmsearch.py", line 95, in parse_sequence_data
    block = parse_aln_block(fh)
            ^^^^^^^^^^^^^^^^^^^
  File "/scratch/users/X/rhodopsin_heap_2_2025-11-06/.snakemake/scripts/tmpyn2viqts.extract_hmmsearch.py", line 131, in parse_aln_block
    vals['ali_left']  = int(fields[-3])
                        ^^^^^^^^^^^^^^^
ValueError: invalid literal for int() with base 10: '-'

[avivko]

Here's an example of a file that caused this, which has a dash in the parsed position

[avivko]

Seems like some alignment could result in unaligned (gapped) blocks. @alephreish What do you think is the best way to handle this?

For now, see #4