/SSN_TOOLS

Primary LanguagePerl

SSN Tools

A collection of scripts to extract lists from existing XGMML Files.

  • To see how a script is used, run it without any inputs. It will display what the script requires.

  • You do not need to be in the same directory as the script or the input file or the output file.

  • See install file for instructions on how to install the scripts.

SNN

Create a list of uniprot accession ids for MSA , by cluster for a given colored SSN

Example Usage:

~/EFI_TOOLS/SSN_TOOLS/ssn_to_msa.pl -repnode_network ~/PF05544.SSN-GNN.repnode/repnode.2149_color.xgmml

~/EFI_TOOLS/SSN_TOOLS/ssn_to_msa.pl -full_network ~/PF05544.SSN-GNN.full/full.2148_color.xgmml

  • Script Name: ssn_to_msa.pl
  • Usage: -full_network<colored ssn> or -repnode_network<colored ssn> -dir<optional>
  • Output: A directory , which by default is called 'ssn_filename-msa'.
  • Creates a file for each cluster, each containing a list of uniprot accession ids.

Create a list of ids, colors and cluster#s for MSA, for a given colored SSN

Example Usage:

~/EFI_TOOLS/SSN_TOOLS/filter_colored_ssn.pl -repnode_network ~/PF05544.SSN-GNN.repnode/repnode.2149_color.xgmml

~/EFI_TOOLS/SSN_TOOLS/filter_colored_ssn.pl -full_network ~/PF05544.SSN-GNN.full/full.2148_color.xgmml

  • Script Name: filter_colored_ssn.pl
  • Usage: -full_network<colored xgmml> or -repnode_network<colored xgmml> -output<optional>
  • Output: A file, which by default is called 'ssn_filename-filtered' which contains the following fields
  • Repnode Network Fields: ID, Color, Cluster#, Seed Sequence
  • Full Network Fields: ID, Color, Cluster#

GNN

To create a directory for a GNN that contains a tab file for each PFAM.

Example Usage:

~/EFI_TOOLS/GNN_TOOLS/gnn_filter.pl -gnn ~/PF05544.SSN-GNN.full/full.2148_gnn.xgmml

~/EFI_TOOLS/GNN_TOOLS/gnn_filter.pl -gnn ~/PF05544.SSN-GNN.repnode/repnode.2149_gnn.xgmml

  • Script name: gnn_filter.pl
  • Usage: -gnn<gnn file> -dir<optional>
  • Output: A directory, which by default is called 'ssn_filename-mapping'. with tab files titled by PFAM.
  • Fields: Query, Neighbor, Distance, Cluster# , Color