pirovc / dudes Goto Github PK

Due to the recent update to v0.10.0, promising results with metaproteomics data (thanks to @rababerladuseladim) and the potential to use of the core methodology from DUDes in different applications, I suggest a couple of changes and features for this repository:

• code refactoring
  • simplification in many areas, removal of unnecessary classes and better structure
  • use of multitax to handle taxonomy. This will simplify a good part of the code and allow usage of the method with many other existing and custom taxonomies (e.g. GTDB)
  • removal of GI support for genomic data, since it is long outdated
  • properly parse acc2txid files similar to this.
  • re-evaluate the role and necessity of having a dudesdb
• generalization of the deepest uncommon descendant (DUD) method
  • independence of input data type
  • standardize the inputs and outputs for the core method
  • create standard modules for specific data types, for example the parse_sam.py for metagenomics and parse_diamond_blast.py for metaproteomics, which could be easily extended to other types
  • possibility to input raw text data
• infrastructure
  • increase and improve testing and CI
  • documentation

Hi Vitor,

I tried to run with the sample data, and had this error:

DUDes.py -s sampledata/hiseq_accuracy_k60.sam -d sampledata/arc-bac_refseq-cg_201503.npz -o sampledata/dudes_profile_output

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|		DUDes v0.08		|
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Output prefix = sampledata/dudes_profile_output
SAM (format) = sampledata/hiseq_accuracy_k60.sam (nm)
Database = sampledata/arc-bac_refseq-cg_201503.npz
Threads = 1
TaxID Start/Last rank = 1/species
Max. Read Matches = 0.000000
Min. Ref. Matches = 0.001000
Bin size = 0.250000
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Loading database file ...Traceback (most recent call last):
  File "DUDes.py", line 645, in <module>
    main()
  File "DUDes.py", line 119, in main
    refids_lookup = npzfile["refids_lookup"].item()
  File "/<path-to-python>/lib/python3.7/site-packages/numpy/lib/npyio.py", line 262, in __getitem__
    pickle_kwargs=self.pickle_kwargs)
  File "/<path-to-python>/lib/python3.7/site-packages/numpy/lib/format.py", line 692, in read_array
    raise ValueError("Object arrays cannot be loaded when "
ValueError: Object arrays cannot be loaded when allow_pickle=False

The numpy version I am using: python '3.7.3' numpy '1.16.3'.

Thanks,
Coax,