kolossus-test 0.0.5
Predict kinase-substrate interactions. TEST VERSION!!! JUNK OUTPUT!!!

# p_KolossuS_test

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Currently under development. Right now all results are junk since data input is randomly generated, 
but the basic coding functionality is working. See example data and usage in the `example/toy` folder.

Main function you would use is `kolossus`. Function works as follows: 

```
Input:
  - fasta file of all sequences (or .h5 file of embeddings)
  - pair file of format '<kinase_id>\t<substrate_id>\t<substrate_phosphorylation_site>'

Output:
  - pairs (kinase_id, substrate_id, substrate_phosphorylation_site, predicted_probability)
```

Over here, `<substrate_phosphorylation_site>` is the offset of the phosphorylated residue. 
So for example, if the substrate has sequence 'GGRGSDD', and the serine (5th amino acid)
is the phosphorylated residue, then `substrate_phosphorylation_site=5`.

Note that the fasta file should contain **all** of the sequences (including the full substrate sequences). 
We'll get the appropriate windows from the pairs file. 

Usage:

``` python
## on the command line
kinase_file="kinases.fasta"
substrate_file="substrates.fasta"

cat $kinase_file $substrate_file > seqs.fasta

## in python
from kolossus import kolossus

# define inputs to function
seqs_file = 'seqs.fasta' 
pairs_file = 'pairs_with_phosphorylation_sites.txt'

# returns a dictionary (kinase, substrate, site): probability
pairs_and_probs = kolossus(pairs_file, fseqs=seqs_file, device='cpu')

# to get kolossus embeddings: use the return_projections parameter
pairs_and_probs, projections = kolossus(pairs_file, fseqs=seqs_file, device='cpu', return_projections=True)
```

There is also a command-line interface which can be called on the terminal: `kolossus-cli`.

```
usage: kolossus-cli [-h] --pairs PAIRS [--seqs SEQS] [--embeddings EMBEDDINGS] [--dtype DTYPE] [--projections PROJECTIONS]
                    [--device DEVICE] [--batch_size BATCH_SIZE] -o OUTPUT

optional arguments:
  -h, --help            show this help message and exit
  --pairs PAIRS         format: <kinase_id> <substrate_id> <substrate_phosphorylation_site>
  --seqs SEQS           fasta formatted file of sequences, either seqs or embeddings must be provided
  --embeddings EMBEDDINGS
                        h5 file of sequence embeddings, either seqs or embeddings must be provided
  --dtype DTYPE         data type of sequence embeddings (usually float32)
  --projections PROJECTIONS
                        name of .h5 files for kolossus projections
  --device DEVICE       default device on which to run model
  --batch_size BATCH_SIZE
                        Number of pairs at a time on which to run model
  -o OUTPUT, --output OUTPUT
                        desired file path for output
```

To get esm embeddings, you can use the `kolossus-extract` command. 

```
usage: kolossus-extract [-h] -i I [--model MODEL] [--device DEVICE] -o O

optional arguments:
  -h, --help       show this help message and exit
  -i I             name of input fasta file
  --model MODEL    name of model to extract embeddings
  --device DEVICE  cpu or gpu device to use
  -o O             name of output .h5 file
```