add crabs/dbimport from readsimulator pipeline

[famosab]

PR checklist

Closes #5532

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
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[famosab]

CRABS has changed a lot of its functionality when updating to version 1.0.0. This needs to be taken care of!

[famosab]

Unfortunately I get

java.lang.OutOfMemoryError: Required array size too large  

when I try to use the downloadtaxonomy module (see PR #7423).

I asked if there is a way to only download a fraction of the data here: gjeunen/reference_database_creator#83

We can then either do that or try to downsample the data, load it into test_datasets and continue from there. In any case, the downloadtaxonomy module is needed to properly run crabs.

[famosab]

There is downsampled test data available in the test-datasets repository. Unfortunately I run into the following error:

│   Command executed:                                                                                                                                                   │
│                                                                                                                                                                       │
│     if [ "false" == "true" ]; then                                                                                                                                    │
│         gzip -c -d genome.fasta > genome.fasta                                                                                                                        │
│     fi                                                                                                                                                                │
│                                                                                                                                                                       │
│     crabs --import \                                                                                                                                                  │
│         --input genome.fasta \                                                                                                                                        │
│         --output test.crabsdb.fa \                                                                                                                                    │
│         --acc2tax nucl_gb.accession2taxid \                                                                                                                           │
│         --names names.dmp \                                                                                                                                           │
│         --nodes nodes.dmp \                                                                                                                                           │
│         --import-format embl --ranks 'superkingdom;phylum;class;order;family;genus;species' \                                                                         │
│                                                                                                                                                                       │
│     rm genome.fasta                                                                                                                                                   │
│                                                                                                                                                                       │
│     cat <<-END_VERSIONS > versions.yml                                                                                                                                │
│     "CRABS_DBIMPORT":                                                                                                                                                 │
│         crabs: $(crabs --help | grep 'CRABS |' | sed 's/.*CRABS | \(v[0-9.]*\).*/\1/')                                                                                │
│     END_VERSIONS                                                                                                                                                      │
│                                                                                                                                                                       │
│   Command exit status:                                                                                                                                                │
│     1                                                                                                                                                                 │
│                                                                                                                                                                       │
│   Command output:                                                                                                                                                     │
│     | Read data to memory |                                       0% -:--:-- 0:00:00                                                                                  │
│                                                                                                                                                                       │
│   Command error:                                                                                                                                                      │
│     /usr/local/lib/python3.12/site-packages/function/crabs_functions.py:775: SyntaxWarning: invalid escape sequence '\.'                                              │
│       for item in ['_sp\.','_SP\.','_indet.', '_sp.', '_SP.']:                                                                                                        │
│     /usr/local/lib/python3.12/site-packages/function/crabs_functions.py:775: SyntaxWarning: invalid escape sequence '\.'                                              │
│       for item in ['_sp\.','_SP\.','_indet.', '_sp.', '_SP.']:                                                                                                        │
│     Matplotlib created a temporary cache directory at /tmp/matplotlib-am3lbtwt because the default path (/.config/matplotlib) is not a writable directory; it is      │
│ highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support     │
│ multiprocessing.                                                                                                                                                      │
│                                                                                                                                                                       │
│     /// CRABS | v1.0.7                                                                                                                                                │
│                                                                                                                                                                       │
│     |            Function | Import sequence data into CRABS format                                                                                                    │
│     | Read data to memory |                                       0% -:--:-- 0:00:00                                                                                  │
│     Traceback (most recent call last):                                                                                                                                │
│       File "/usr/local/bin/crabs", line 847, in <module>                                                                                                              │
│         crabs()                                                                                                                                                       │
│       File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1157, in __call__                                                                            │
│         return self.main(*args, **kwargs)                                                                                                                             │
│                ^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                                                                             │
│       File "/usr/local/lib/python3.12/site-packages/rich_click/rich_command.py", line 152, in main                                                                    │
│         rv = self.invoke(ctx)                                                                                                                                         │
│              ^^^^^^^^^^^^^^^^                                                                                                                                         │
│       File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1434, in invoke                                                                              │
│         return ctx.invoke(self.callback, **ctx.params)                                                                                                                │
│                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                                                                │
│       File "/usr/local/lib/python3.12/site-packages/click/core.py", line 783, in invoke                                                                               │
│         return __callback(*args, **kwargs)                                                                                                                            │
│                ^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                                                                            │
│       File "/usr/local/bin/crabs", line 561, in crabs                                                                                                                 │
│         seq_input_dict, initial_seq_number = input_to_memory(task, progress_bar, input_)                                                                              │
│                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                                                              │
│       File "/usr/local/lib/python3.12/site-packages/function/crabs_functions.py", line 393, in embl_to_memory                                                         │
│         seq_name = line.split('|')[1]                                                                                                                                 │
│                    ~~~~~~~~~~~~~~~^^^                                                                                                                                 │
│     IndexError: list index out of range