hivnetworkannotate

HIV Network Annotator

This script takes the JSON file output by hivnetworkcsv and adds the data dictionary for subject attributes to create an annotated JSON suitable for rendering by hivtrace-viz (https://github.com/veg/hivtrace-viz)

Usage

Example command

python3 scripts/hivnetworkannotate -t examples/lanl.tsv -n examples/network.json -f "Country" "Country" "String" "x: 'N/A' f x=='-' else x" -f "Year" "Year" "Number" "x: 'N/A' if x=='-' else x" -f "RiskFactor" "Risk factor" "enum" '{"SG" : "homosexual", "SB" : "bisexual", "SM" : "male sex with male", "SH" : "heterosexual", "SW" : "sex worker", "SU" : "sexual transmission, unspecified type", "PH" : "hemophiliac", "PB" : "Blood transfusion", "PI" : "IV drug use", "MB" : "Mother-baby", "NO" : "Nosocomial", "EX" : "Experimental", "NR" : "not recorded (or unknown)", "OT" : "other", "-" : "N/A"}'

Arguments

-o, --output: Output the annotated JSON network file to. If not specified, the output will be written to standard output.
-n, --network: The input network file to process. If not specified, the input will be read from standard input.
-x, --missing: If desired, provide a value to inject for nodes that do not have an attribute value specified
-X, --clear: Flush existing attributes
-i, --index: The name of the column that indexes records (patient ID); default is to index on the first column.
-r, --inplace: Write attributes to the input file (cannot be stdin)
-a, --attributes: The JSON file with node attributes
-t, --tab: A TSV file with node attributes
-c, --csv: A CSV file with node attributes
-f, --field: Describe an argument to be added to invididual nodes as "name" "label" "type" "transform"; currently supported types are "String", "enum", "Date", "Number"; transform must be specified as a lambda, an empty string to use an identity map, or a python style dict to specify an enum; "fulldate" is a predefined option to reformat the date using the default hivtrace-viz format
-g, --fields-file: Read in fields from a JSON file

Author

Sergei L Kosakovsky Pond ([email protected])

Version

v1.0.0 (2017-05-09) v1.1.0 (2017-09-04) : added support for 'enums', fixed bugs Note

This script requires the hivclustering library to be installed.