From fe67888f00d35fdfd4c0ba2a1961d535e1ab83b8 Mon Sep 17 00:00:00 2001 From: Manuel Rueda Date: Wed, 6 Nov 2024 12:15:38 +0100 Subject: [PATCH] Update docs --- README.md | 4 ++-- bin/pheno-ranker | 4 ++-- docs/csv-import.md | 8 +++++++- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 1cab129..e00ef45 100644 --- a/README.md +++ b/README.md @@ -51,10 +51,10 @@ pheno-ranker: A script that performs semantic similarity in PXF/BFF data structu -config 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 Exclude BFF/PXF terms (e.g., --exclude-terms sex, id) + -exclude-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 Include BFF/PXF terms (e.g., --include-terms diseases) + -include-terms Include BFF/PXF terms (e.g., --include-terms diseases) or CSV column names in JSON-derived from CSV -max-number-var Maximum variables for binary string [default: 10000] -max-out Print only N comparisons [default: 50] -o, --out-file Output file path [default: -r matrix.txt | -t rank.txt] diff --git a/bin/pheno-ranker b/bin/pheno-ranker index 0853e63..7f4862d 100755 --- 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 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 Exclude BFF/PXF terms (e.g., --exclude-terms sex, id) + -exclude-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 Include BFF/PXF terms (e.g., --include-terms diseases) + -include-terms Include BFF/PXF terms (e.g., --include-terms diseases) or CSV column names in JSON-derived from CSV -max-number-var Maximum variables for binary string [default: 10000] -max-out Print only N comparisons [default: 50] -o, --out-file Output file path [default: -r matrix.txt | -t rank.txt] diff --git a/docs/csv-import.md b/docs/csv-import.md index c12699a..649419f 100644 --- 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!