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

In case no pvc and pvt are provided, all the rows are considered.