ukbsearch 0.1.0

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ukbsearch

Search tools to retreive term(s) from UKB HTML files to be downloaded in the local drive.

Installation

pip install https://github.com/danielmsk/ukbsearch/dist/ukbsearch-0.0.1-py3-none-any.whl
pip install ukbsearch

Options

optional arguments:
  -h, --help            show this help message and exit

  -v, --version         show program's version number and exit

  -s, --searchterm      search. terms (ex: age smoking)
                        -s age
                        -s age smoking
                        -s 'smok*'
                        -s '*age' 'smok*'

  -l, --logic           logical operator for multiple terms [or(default), and]
                        -s '*age' 'smok*' -l and
                        -s age 'smok*' -l or

  -o, --out             title of output file
                        -o searchresult_20220322

  -t, --outtype         output type [console(default), csv, udi]
                        -t csv
                        -t console csv
                        -t udi
                        -t console udi

  -p, --path            directory path for data files (.html, .Rdata) (default: ./)
                        -p /other/path/for/ukb/html/.

  -u, --udilist         FileID and UDI list for saving data from RData files
                        -u ukb39003 3536-0.0 3536-1.0 3536-2.0

  -d, --savedata        save data from .Rdata [csv, rdata]
                        -d csv 
                        -d rdata
                        -d csv rdata

Usage

Search result

Search for single term

ukbsearch -s age
ukbsearch --searchterm age
ukbsearch -s 'ag*'
ukbsearch -s '*ge' 

Search for multiple terms

• The logical operators (and or or) are supported.

ukbsearch -s age smoking
ukbsearch -s age smoking -l or
ukbsearch -s age smoking -l and
ukbsearch -s 'ag*' 'smok*' -l and 

Print only html and UDI

ukbsearch -s 'ag*' 'smok*' -l and -t udi

Save the search result as csv file

ukbsearch -s 'ag*' 'rep*' -l and -o test1 -t csv
(= ukbsearch --searchterm 'ag*' 'rep*' --logic and --out test1 --outtype csv)
ukbsearch -s 'ag*' 'rep*' -l and -o test1 -t console csv
ukbsearch -s 'ag*' 'rep*' -l and -o test1 -t console udi csv

Set a particular directory

• The default path is './'.

ukbsearch -s age -p /other/path/for/ukb/html/.

Save data (.csv and .rdata) from .RData

ukbsearch -u ukb39003 3536-0.0 3536-1.0 3536-2.0 -d csv -o test3
(=ukbsearch --udilist ukb39003 3536-0.0 3536-1.0 3536-2.0 --savedata csv --out test3)
ukbsearch -u ukb39003 3536-0.0 3536-1.0 ukb26086 20161-0.0 21003-1.0 -d csv rdata -o test3

ukbsearch -s 'ag*' 'rep*' -l and -d csv -o test3
ukbsearch -s 'ag*' 'rep*' -l and -d rdata -o test3