kmh-dbgap-utils

Some helpers for dealing with dbgap xmls.

Install

1. git clone git@github.com:kmhernan/kmh-dbgap-utils.git
2. pip install kmh-dbgap-utils

You should be on python>=3.5 and it is recommended to install within a virtual environment. Only standard libraries are used.

Usage

Download data dictionary XMLs and create TSV

$ kmh-dbgap-utils extractdatadict --help
2020-01-28 19:34:24,281 - kmh-dbgap-utils.main - INFO - ---------------------------------------------------------------------------
2020-01-28 19:34:24,281 - kmh-dbgap-utils.main - INFO - Program Args: kmh-dbgap-utils extractdatadict --help
2020-01-28 19:34:24,281 - kmh-dbgap-utils.main - INFO - Date/time: 2020-01-28 19:34:24.281374
2020-01-28 19:34:24,281 - kmh-dbgap-utils.main - INFO - ---------------------------------------------------------------------------
2020-01-28 19:34:24,281 - kmh-dbgap-utils.main - INFO - ---------------------------------------------------------------------------
usage: KMH dbGap Helpers extractdatadict [-h] --phs PHS --outdir OUTDIR

Download phenotype dictionaries and make TSV.

optional arguments:
  -h, --help       show this help message and exit
  --phs PHS        phsid of the project you want to extract
  --outdir OUTDIR  The directory to put results in

Download variable report XMLs and create TSV

$ kmh-dbgap-utils extractvariablereport --help
2020-01-28 19:35:27,726 - kmh-dbgap-utils.main - INFO - ---------------------------------------------------------------------------
2020-01-28 19:35:27,726 - kmh-dbgap-utils.main - INFO - Program Args: kmh-dbgap-utils extractvariablereport --help
2020-01-28 19:35:27,726 - kmh-dbgap-utils.main - INFO - Date/time: 2020-01-28 19:35:27.726958
2020-01-28 19:35:27,727 - kmh-dbgap-utils.main - INFO - ---------------------------------------------------------------------------
2020-01-28 19:35:27,727 - kmh-dbgap-utils.main - INFO - ---------------------------------------------------------------------------
usage: KMH dbGap Helpers extractvariablereport [-h] --phs PHS --outdir OUTDIR

Download variable reports and make TSV.

optional arguments:
 -h, --help       show this help message and exit
 --phs PHS        phsid of the project you want to extract
 --outdir OUTDIR  The directory to put results in

Note Currently I only extract variable reports for enumerated valued. Will do others in future.