SSNpipe directories and file structures - ahvdk/SSNpipe GitHub Wiki

1.1 Main results directory

The main results folder, named with a date-time stamp (YYYYMMDD_HHMMSS). Created when the user runs: 2.1: “Create SSNs”.

1.1.1 Log file

  • Every run in SSNpipe generates a log file with a corresponding date-time stamp.

1.1.2 Error file

  • Every run in SSNpipe, even if no errors or warnings occur, generates an error log file with a corresponding date-time stamp.

1.1.3 MASTER.txt file

  • The MASTER.txt file is a modified BLASTP output file created during 2.1: “Create SSNs”.
  • It can be used to speed-up the refinement of SSNs during 2.2: “Refine SSNs”.

1.1.4 NodeTable_ff.txt file

  • This files contains translation from the SSNpipe generated numerical IDs to the original sequence headers (Labels).
  • Created during 2.1: “Create SSNs”.
  • ff = visualization software; cs = Cytoscape, gp = Gephi or Tulip.

1.2 “networks” subfolder

The networks subfolder is created when the user runs: 2.1: “Create SSNs”.

1.2.1 NETWORK_ff_pp_n_.txt files

  • These are the network files, which can visualized in a network viewer.
  • ff = visualization software; cs = Cytoscape, gp = Gephi or Tulip, pj = Pajek
  • pp = threshold parameter; ev = E-value, bs = Bitscore.
  • n = network threshold.

1.3 “metanodes” subfolder

The metanodes subfolder is created from: 2.3: “Create Metanodes”.

1.3.1 Metanodes_n_m_Info.txt file

  • This file contains information about which sequence represents the metanode, the size, and which sequences are merged into it.
  • n = Network threshold.
  • m = Metanode threshold.

1.3.2 METANODES-NETWORKS_ff_pp_n_m_.txt file

  • These are metanode-network files, which can visualized in a network viewer.
  • ff = visualization software; cs = Cytoscape, gp = Gephi or Tulip, pj = Pajek
  • pp = threshold parameter; ev = E-value, bs = Bitscore.
  • n = Network threshold.
  • m = Metanode threshold.

1.4 “analysis” subfolder

The analysis subfolder is created when the user runs: 2.4: “Group Analysis”

1.4.1 GROUPS_n_Info.txt file

  • This file contains information about which sequences belong to which group.
  • n = Network threshold.