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.