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Full Discussion: Replacing part of a delimited string
Top Forums Shell Programming and Scripting Replacing part of a delimited string Post 302900413 by LMHmedchem on Tuesday 6th of May 2014 04:11:25 PM
Old 05-06-2014
I am sorry for the very long delay, one of my servers has been acting up and I needed to get it fixed.

I always seem to forget that regex is not the same as using a wildcard in bash. I guess it doesn't help that there are some many flavors of regex. I spent a few days a while ago trying to decipher some regex in ruby.

Quote:
Originally Posted by SriniShoo
Code:
awk -F "\t" '{split($2, a, ";"); $2 = a[2]}1' file

Could you provide an interpretation of this? Is there a difference between -F "" and FS=""? It looks like you used -F "\t" to indicate that it is a tab delimited file, but then split on ; to split column 2. Is that right? That would be at least three different ways to specify a delimiter.

As indicated, this works properly,
sed 's/;cpd;[0-9]*;line;[0-9]*//g' | \

LMHmedchem
 

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LEARN ABOUT DEBIAN

csv2mipe

CSV2MIPE(1)						User Contributed Perl Documentation					       CSV2MIPE(1)

NAME

       csv2mipe.pl - Generates MIPE file based on 3 tab-delimited files
	 based on MIPE version v1.1
	 arguments: * tab-delimited file with PCR-level data
		    * tab-delimited file with SNP-level data
		    * tab-delimited file with assay-level data

	 Columns in file with PCR-level data:
	   pcr_id
	   pcr_modified (might be multiple, divided by semi-colon ";")
	   pcr_project (might be multiple, divided by semi-colon ";")
	   pcr_researcher (might be multiple, divided by semi-colon ";")
	   pcr_species
	   source_type
	   source_id
	   design_seq
	   primer1_oligo
	   primer1_seq
	   primer1_tm
	   primer2_oligo
	   primer2_seq
	   primer2_tm
	   design_remark (might be multiple, divided by semi-colon ";")
	   use_seq
	   use_revcomp
	   use_remark (might be multiple, divided by semi-colon ";")
	   pcr_remark (might be multiple, divided by semi-colon ";")

	 Columns in file with SNP-level data:
	   pcr_id
	   snp_id
	   snp_pos
	   snp_amb
	   snp_remark (might be multiple, divided by semi-colon ";")

	 Columns in file with assay-level data:
	   pcr_id
	   snp_id
	   assay_id
	   assay_type
	   assay_enzyme
	   assay_oligo
	   assay_specific
	   assay_tail
	   assay_strand
	   assay_remark (might be multiple, divided by semi-colon ";")

SYNOPSIS

       csv2mipe.pl <pcr_file.csv> <snp_file.csv> <assay_file.csv>

ADDITIONAL INFO

       See http://mipe.sourceforge.net

AUTHOR

       Jan Aerts (jan.aerts@bbsrc.ac.uk)

perl v5.14.2							    2005-07-20							       CSV2MIPE(1)
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