svndigest - svndigest

Rev	Date	Author	Line
6675	13 Apr 22	nicklas	1	#!/bin/sh
6675	13 Apr 22	nicklas	2
6675	13 Apr 22	nicklas	3	# $Id$
6675	13 Apr 22	nicklas	4
6675	13 Apr 22	nicklas	5	# Nicklas Nordborg, 2014
6675	13 Apr 22	nicklas	6	#
6675	13 Apr 22	nicklas	7	# Replaces tracking_id and gene_id values in Cufflinks
6675	13 Apr 22	nicklas	8	# *.fpkm_tracking files
6675	13 Apr 22	nicklas	9	#
6675	13 Apr 22	nicklas	10	# The values to search for and their replacement values must
6675	13 Apr 22	nicklas	11	# be defined in the file given as a parameter to this script.
6675	13 Apr 22	nicklas	12	# This file must have at least two columns. The second column
6675	13 Apr 22	nicklas	13	# contain the values to look for and the first column is the
6675	13 Apr 22	nicklas	14	# replacement values.
6675	13 Apr 22	nicklas	15	#
6675	13 Apr 22	nicklas	16	# The script then read stdin, perform the replacement and
6675	13 Apr 22	nicklas	17	# write the result to stdout
6675	13 Apr 22	nicklas	18	#
6675	13 Apr 22	nicklas	19	# Script inspired by post on http://www.unix.com/302448486-post6.html
6675	13 Apr 22	nicklas	20	#
6675	13 Apr 22	nicklas	21	# run ./fix_cufflinks_tracking_id.sh path/to/map-file < infile > outfile
6675	13 Apr 22	nicklas	22	#
6675	13 Apr 22	nicklas	23
6675	13 Apr 22	nicklas	24	awk 'NR==FNR {a[$2]=$1;next} {for (i in a) gsub(i,a[i])}1' $1 /dev/stdin