CAFA SwissProt Targets This is a part of the CAFA project.

A collection of functionality related to identifying proteins with limited GO annotation from SwissProt files.

Running the code:

Install the package:

python -m pip install -e "git+https://github.com/CAFA-Challenge/cafa-swissprot#egg=cafa-swissprot"

Download one or more SwissProt files. The most recent release is available here: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz

The uniprot.org *.gz files contain several files, only the ...sprot-only... files are relevant here.

The package exposes a couple of command-line entrypoints:

1. Identify low-annotation candidate proteins in a SwissProt file:

   • create a yaml-formatted configuration file (see yaml/filter_sprot_species_example.yml)

   • run CAFA_generate_no_exp_files <YOUR YAML FILE>

   • results are written to output_directory specified in your yaml file

     Output:

     • sp_species.[taxon_id].tfa FASTA file containing all the proteins in [taxon_id] (replaced by an actual number, e.g. sp_species.9606.tfa for human.)
     • sp_species.[taxon_id].MFO.noexp.tfa Assuming MFO is specified in config, FASTA file for proteins that are not experimentally annotated in the MFO namespace.
     • sp_species.[taxon_id].BPO.noexp.tfa See above.
     • sp_species.[taxon_id].CCO.noexp.tfa See above.
     • sp_species.[taxon_id].all.noexp.tfa FASTA file containing proteins that are not experimentally annotated in any GO ontology.

2. Count proteins

   • create a yaml-formatted configuration file (see yaml/sprot_growth_example.yml). Please note that this yaml file is different from the one used above for CAFA_generate_no_exp_files
   • run CAFA_experimental_growth <YOUR YAML FILE>
   • results are written to stdout:

     $ CAFA_experimental_growth sprot_growth_example.yml
       filename	taxon	CCO	BPO	MFO
       /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2019_01/uniprot_sprot.dat	9606	9905	8786	7539
       /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2019_06/uniprot_sprot.dat	9606	9996	8960	7533
       /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2020_01/uniprot_sprot.dat	9606	10153	9091	7638
       /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2020_05/uniprot_sprot.dat	9606	10294	9282	8175
       /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2019_01/uniprot_sprot.dat	4577	65	94	80
       /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2019_06/uniprot_sprot.dat	4577	73	111	95
       /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2020_01/uniprot_sprot.dat	4577	73	115	101
       /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2020_05/uniprot_sprot.dat	4577	73	116	102
       

3. Count proteins with annotation (grouped by ontology namespace) in one or more SwissProt files:

   • create a yaml-formatted configuration file (see yaml/swissprot_counts_example.yml). Please note that this yaml file is different from the one used above for CAFA_generate_no_exp_files

   • run CAFA_print_annotation_counts <YOUR YAML FILE>

   • results are written to stdout:

       $ CAFA_print_annotation_counts swissprot_counts_example.yml
       ---------------------------------------------------------------------------------------------------------------------------------------
       | COUNTS OF PROTEINS WITH ANNOTATION                                                                                                  |
       ---------------------------------------------------------------------------------------------------------------------------------------
       | FILE                                                                                    | TAXON | CCO    | BPO    | MFO    | GROWTH |
       ---------------------------------------------------------------------------------------------------------------------------------------
       | /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2019_01/uniprot_sprot_truncated.dat | 9606  |  9,905 |  8,786 |  7,539 |        |
       ---------------------------------------------------------------------------------------------------------------------------------------
       | /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2019_06/uniprot_sprot_truncated.dat | 9606  |  9,996 |  8,960 |  7,533 |   +259 |
       ---------------------------------------------------------------------------------------------------------------------------------------
       | /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2020_01/uniprot_sprot_truncated.dat | 9606  | 10,153 |  9,091 |  7,638 |   +393 |
       ---------------------------------------------------------------------------------------------------------------------------------------
       | /home/scott/virtualenvs/cafa_swissprot/code/uniprot/2020_05/uniprot_sprot_truncated.dat | 9606  | 10,294 |  9,282 |  8,175 |   +869 |
       ---------------------------------------------------------------------------------------------------------------------------------------