Utils

ColumnExtractor

Receives a file with several columns and writes one of the columns to another file.

Execution

java -cp target/PathwayMatcher-1.0/PathwayMatcher-1.0.jar no.uib.pathwaymatcher.tools.ColumnExtractor -i ../ERC/zBMI3-autosome.result [other options] [-pvc 18 -pvt 0.005]

Command line parameters

Parameter names	Required	Default value	Description
`-i,--input`	Yes	(empty)	File to parse
`-o,--output`	No	"./output.csv"	Output file path and name
`-c,--column`	No	1	Index of the desired column. Count starting with 0,1,2...
`-s,--separator`	No	" "	The string used as field separator. For example: space, tab, coma
`-p,--pattern`	No	"^rs\d*"	The regular expression pattern that the rows must follow
`-pvc,--pValueColumn`	No	18	p-value column index
`-pvt,--pValueThreshold`	No	0.005	p-value threshold. Only rows with this value or more will be sent to the output