Some issues with the pipelines

[simonbray]

While wrapping some of the python pipelines for Galaxy we discovered some of the following issues:

• Two of the scripts (show_feats.py and constrained_conf_gen.py) don't have main() functions defined; this would be handy for defining entry points to the scripts, as in the conda recipe we wrote here: https://github.com/bioconda/bioconda-recipes/pull/22348/files#diff-a937f0d7f1f974a955b3aac5cbef8db1R16. The same issue would arise with a PyPI package, I expect.
• The meta flag does not work in pbf_ev.py (maybe deliberate)
• The screen.py returns the number of screened molecules as the exit code. Maybe the intention is to pass this information to the next pipeline somehow, but surely there's a better way of doing it? It should return 0 as long as the script completes successfully.
• Running gzip on the output of constrained_conf_gen.py gives an unexpected end of file error.

[tdudgeon]

@simonbray Thanks for pointing out those problems.
I fixed some of them in the commits mentioned above.
What is not fixed is:

1. show_feats.py not changed yet - this is not a pipeline, just seems to be a file that was committed by mistake. I need to double check this
2. pbv_ev.py was written by someone else and doesn't follow the normal patterns for IO. I need to spend time of refactoring this.
3. Don't understand the problem with gzip, but haven't looked at this yet.

[simonbray]

From @lorrainealisha75:

File "/Users/lorraine/PycharmProjects/PubChem/rxn_selector.py", line 75, in <module>
main()
File "/Users/lorraine/PycharmProjects/PubChem/rxn_selector.py", line 55, in main
count = filter_to_use.perform_reaction(mol,args.reaction,reagent_suppl,writer,count)
File "/Users/lorraine/PycharmProjects/PubChem/poised_filter.py", line 238, in perform_reaction
if reactant_mol.HasProp('uuid'):
AttributeError: 'ForwardSDMolSupplier' object has no attribute 'HasProp'.

Only rdkit.Chem.rdchem.Mol object has attribute 'HasProp'. 'ForwardSDMolSupplier' contains the Mol objects.