Linux awk sed R script python script input variable, awkpython

Linux awk sed R script python script input variable, awkpython

Sed input variable:

1 chrI = "chr2"; sed-n "/$ chrI/p" clippointpos.csv # The variable is represented by $ var. Change the single quotes of sed into double quotes.

Awk input variables:

1 chrI = "chr2"; awk '/' "$ chrI" '/{print $0}' clippointpos.csv # The variable is represented by $ var, and '"is added to both sides of the variable '"

R script input variable:

1 arg <- commandArgs(T)2 filename=arg[1]3 outputfile=arg[2]

Input variable in python script:

1. OptionParser passing Parameters

 1 from optparse import OptionParser 2 def main(): 3     usage = "usage: %prog [options] arg" 4     parser = OptionParser(usage) 5     parser.add_option("-f", "--file", dest="filename", 6                       help="read data from FILENAME") 7     parser.add_option("-v", "--verbose", 8                       action="store_true", dest="verbose") 9     parser.add_option("-q", "--quiet",10                       action="store_false", dest="verbose")11     (options, args) = parser.parse_args()12     if options.verbose:13         print "reading %s..." % options.filename14    15 16 if __name__ == "__main__":17     main()

2. pass variables in the sys module

1 import sys2 print sys. argv [0] # python program name 3 print sys. argv [1] # The first input variable