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Full Discussion: awk to adjust coordinates in field based on sequential numbers in another field
Top Forums Shell Programming and Scripting awk to adjust coordinates in field based on sequential numbers in another field Post 302990535 by MadeInGermany on Friday 27th of January 2017 04:59:03 PM
Old 01-27-2017
If I run your awk on your input then I do not get your output.
But maybe I have understood your description.
If your file is sorted by $4 and $6 (so $6 sequences are in adjacent lines),
then the following can do it:
Code:
awk '
# print from stored values
function prt(){
  print p1 ":" (p6start==1 ? p2 : p2+p6start) "-" p2+p6, p5
}
($4!=p4 || $6!=p6+1) {
# new sequence, print the previous sequence
  if (NR>1) prt()
  p6start=$6  
}
{
# store the values that we need later
  p1=$1
  p2=$2
  p4=$4
  p5=$5
  p6=$6
}
END { prt() }
' file

A problem is the "late" end-of-sequence detection. This is solved with storing the previous values, and an END section, and a print function.
This User Gave Thanks to MadeInGermany For This Post:
cmccabe
 

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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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