Highlight subsets of protein sequences from a larger superset on a Sequence Similarity Network (SSN).
The only requirements are Nextflow and Docker.
--seqs : File containing protein sequences in FASTA format.
--subset : File containing the subset of sequences to highlight - one Sequence ID per line.
*MUST* match the IDs in `--seqs`
--threshold : Threshold to use for building the SSN.
Should be paired with `--seqs` to run 'from scratch'.
--outdir : Directory to store the results in.
--ini_ssn : Sequence Similarity Network from a previous run 'from scratch'.
This workflow can be run with two different sets of inputs:
If you run this workflow from scratch, you need three inputs:
- A FASTA file containing the protein sequences you want to create an SSN for using
--seqs. - A threshold for the SSN using
--threshold. - A subset file containing the list of sequences to highlight on the SSN using
--subset, with one sequence name per line. These names should match the headers provided in the--seqsinput.
nextflow run intbio-ncl/seq-sublight --seqs test_seqs.fasta --threshold 0.4 --subset test_subset.txt --outdir Test
With these inputs, the workflow will produce an initial ssn called 'ini_ssn.gml' that can be reused in 'reruns'.
The initial SSN can be reused in a new run. As the SSN can take a long time to produce, we recommend you use the 'rerun' set of inputs if you want to highlight a subset of nodes on the same sequences, but with different other inputs.
In this case, the parameters --seqs and --threshold should be replaced with one input: --ini_ssn for the initial SSN.
nextflow run intbio-ncl/seq-sublight --ini_ssn ini_ssn.gml --subset test_subset.txt --outdir Test
You can find the ini_ssn.gml file necessary for reruns in the output directory after your initial run.
This workflow produces two main outputs:
- ssn.gml : A .gml file of the SSN with the subset highlighted, to be used in interactive network software like Cytoscape.
- ssn.png : A picture file of the SSN with the subset highlighted.