ilevantis/dvorfs

Tool for mining endogenous viral elements from eukaryotic genomes.

dvorfs's Issues

Fix sed inplace edit error on MacOS

error caused by GNU vs BSD sed handling of -i during hmmer_pre_search

Error when using the --full-search flag

Hi,

I have been using dvorfs successfully with exciting results. But when I wanted to try the --full-search, I got a problem with GeneWise with the following error:

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Converted HMM databases already present, skipping step.
Windowing genome...
GeneWise outfile already present, skipping step.
Processing GeneWise hits...
Traceback (most recent call last):
  File "/n/home06/ftermignonigarcia/.conda/envs/MAMBA/envs/snakemake2/envs/DVORFS/bin/dvorfs", line 33, in <module>
    sys.exit(load_entry_point('dvorfs==1.0.1', 'console_scripts', 'dvorfs')())
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/n/home06/ftermignonigarcia/.conda/envs/MAMBA/envs/snakemake2/envs/DVORFS/lib/python3.12/site-packages/dvorfs/dvorfs.py", line 434, in main
    run_dvorfs(args)
  File "/n/home06/ftermignonigarcia/.conda/envs/MAMBA/envs/snakemake2/envs/DVORFS/lib/python3.12/site-packages/dvorfs/dvorfs.py", line 310, in run_dvorfs
    gw_tsv, gw_alidir = process_genewise_output(windowed_fasta, gw_out, windowed=True,
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/n/home06/ftermignonigarcia/.conda/envs/MAMBA/envs/snakemake2/envs/DVORFS/lib/python3.12/site-packages/dvorfs/dvorfs.py", line 208, in process_genewise_output
    df, alis = process_genewise(gw_out, sefasta,
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/n/home06/ftermignonigarcia/.conda/envs/MAMBA/envs/snakemake2/envs/DVORFS/lib/python3.12/site-packages/dvorfs/process_genewise.py", line 256, in process_genewise
    .sort_values(['query','bits'],ascending=[True,False])
     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/n/home06/ftermignonigarcia/.conda/envs/MAMBA/envs/snakemake2/envs/DVORFS/lib/python3.12/site-packages/pandas/core/frame.py", line 6930, in sort_values
    keys = [self._get_label_or_level_values(x, axis=axis) for x in by]
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/n/home06/ftermignonigarcia/.conda/envs/MAMBA/envs/snakemake2/envs/DVORFS/lib/python3.12/site-packages/pandas/core/generic.py", line 1844, in _get_label_or_level_values
    raise KeyError(key)
KeyError: 'query'

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I would like to use the --full-search version.
I have tried to use smaller chunks of the genome, databases, and genomes. It seems it is getting more hits than expected than with the presearch but cannot process them?