Utilities

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This section is for various utilities 

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

To see how a script is used, run it without any inputs.

Otherwise, assuming that the scripts are extracted into your home directory, the standard usage is

module load perl; perl ~/SSN_TOOLS/script_name.pl <input_xgmml_full_or_rep> <OUTPUT>

OUTPUT may be to STDOUT or to a directory containing a list of files.

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 how to download the scripts.




GNN and COLORED SSNS

extract_node_color_acc_gnn_of_many_pfams.pl

  • Description: Extracts lists of uniprot
  • INPUT: [inputFileName] [a colored GNN network ]
  • OUTPUT: [a directory called inputFileName followed by _MSA]
  • created this script using 2056_gnn.xgmml

filter_full_xgmml.pl

  • Description: Extracts Node ID, Color, and Accessions, and prints to STDOUT
  • INPUT: [inputFileName] [ a colored FULL Network xgmml]
  • OUTPUT: STDOUT
  • created this script using PF05544.repnode-1.00.1978_color.xgmml

filter_xgmml_repnode.pl

  • Description: Extracts Node ID, Color, and Accessions, and prints to STDOUT
  • INPUT: [inputFileName] [ a colored REPNODE Network xgmml]
  • OUTPUT: STDOUT
  • created this script using PF05544.full-1.00.1978_color.xgmml

SSN

parse_full_ssn.pl

  • Description: Script to extract uniprot sequence ids for multiple sequence alignment from full SSNS that have been colored
  • INPUT=[inputFileName] [a colored full network ssn]
  • OUTPUT=[a directory called inputFileName followed by _MSA]
  • Created with full.2148_color.xgmml

parse_repnode_ssn.pl

  • Description: Script to extract uniprot sequence ids for multiple sequence alignment from REPNODE SSNS that have been colored
  • INPUT=[inputFileName] [a colored REPNODE network ssn]
  • OUTPUT=[a directory called inputFileName followed by _MSA]
  • Created with repnodel.2149_color.xgmml