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CNAG-Biomedical-Informatics · Nov 6, 2024 · fe67888 · fe67888
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diff --git a/README.md b/README.md
@@ -51,10 +51,10 @@ pheno-ranker: A script that performs semantic similarity in PXF/BFF data structu
         -config <file>                   YAML config file to modify default parameters [default: share/conf/config.yaml]
         -cytoscape-json [file]           Serializes the pairwise comparison matrix as an undirected graph in JSON, compatible with Cytoscape [default: graph.json]
         -e, --export [path/basename]     Export miscellaneous JSON files. If not specified, default filenames are used [default: export.*]
-        -exclude-terms <terms>           Exclude BFF/PXF terms (e.g., --exclude-terms sex, id)
+        -exclude-terms <terms>           Exclude BFF/PXF terms (e.g., --exclude-terms sex, id) or CSV column names in JSON-derived from CSV 
         -graph-stats [file]              Generates a text file with key graph metrics, for use with <-cytoscape-json> [default: graph_stats.txt]
         -include-hpo-ascendants          Include ascendant terms from the Human Phenotype Ontology (HPO)
-        -include-terms <terms>           Include BFF/PXF terms (e.g., --include-terms diseases)
+        -include-terms <terms>           Include BFF/PXF terms (e.g., --include-terms diseases) or CSV column names in JSON-derived from CSV
         -max-number-var <number>         Maximum variables for binary string [default: 10000]
         -max-out <number>                Print only N comparisons [default: 50]
         -o, --out-file <file>            Output file path [default: -r matrix.txt | -t rank.txt]

diff --git a/bin/pheno-ranker b/bin/pheno-ranker
@@ -244,10 +244,10 @@ pheno-ranker: A script that performs semantic similarity in PXF/BFF data structu
      -config <file>                   YAML config file to modify default parameters [default: share/conf/config.yaml]
      -cytoscape-json [file]           Serializes the pairwise comparison matrix as an undirected graph in JSON, compatible with Cytoscape [default: graph.json]
      -e, --export [path/basename]     Export miscellaneous JSON files. If not specified, default filenames are used [default: export.*]
-     -exclude-terms <terms>           Exclude BFF/PXF terms (e.g., --exclude-terms sex, id)
+     -exclude-terms <terms>           Exclude BFF/PXF terms (e.g., --exclude-terms sex, id) or CSV column names in JSON-derived from CSV 
      -graph-stats [file]              Generates a text file with key graph metrics, for use with <-cytoscape-json> [default: graph_stats.txt]
      -include-hpo-ascendants          Include ascendant terms from the Human Phenotype Ontology (HPO)
-     -include-terms <terms>           Include BFF/PXF terms (e.g., --include-terms diseases)
+     -include-terms <terms>           Include BFF/PXF terms (e.g., --include-terms diseases) or CSV column names in JSON-derived from CSV
      -max-number-var <number>         Maximum variables for binary string [default: 10000]
      -max-out <number>                Print only N comparisons [default: 50]
      -o, --out-file <file>            Output file path [default: -r matrix.txt | -t rank.txt]

diff --git a/docs/csv-import.md b/docs/csv-import.md
@@ -96,7 +96,13 @@
         ```bash
         pheno-ranker -r example.json --config example_config.yaml
         ```
-        
+
+        If you want to exclude or include columns (i.e., terms) you can use the corresponding flag:
+
+        ```bash
+        pheno-ranker -r example.json --exclude-terms Id Foo --config example_config.yaml
+        ```
+
         Remember to always use `--config example_config.yaml`.
         
         Good luck!