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:

## 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