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Shell Programming and Scripting

Add headerline to the values

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Top Forums Shell Programming and Scripting Add headerline to the values
# 1  
Old 10-03-2010
Add headerline to the values
if header line starts with chr1 and span 10 print chr1 and the original values and ov+10 and viceversa

input
Code:
variableStep chrom=chr1 span=10
191     1
201     18
211     1
variableStep chrom=chr2 span=10
191     11
201     1
211     12

output
Code:
 
chr1 191 201     1
chr1 201 211     18
chr1 211 221     1
chr2 191 201     11
chr2 201 211     1
chr2 211 221     12

# 2  
Old 10-03-2010
something like this,

Code:
 perl -nle 'if (/variableStep chrom=(.+?)\sspan=(\d+)/) { $a=$1;} elsif (/(\d+)\s+(\d+)/) {print "$a\t$1\t", $1+10 ,"\t$2";}' inputfile

# 3  
Old 10-03-2010
bash code:
  1. #!/bin/bash
  2. while read A B C
  3. do
  4.    if [ "$A" = variableStep ]
  5.    then eval "$B; $C"
  6.    else echo -e "$chrom $A $((A+span))\t$B"
  7.    fi
  8. done <infile
Which can also be written
bash code:
  1. #!/bin/bash
  2. while read A B C
  3. do &#91; "$A" = variableStep ] && eval "$B; $C" || echo -e "$chrom $A $((A+span))\t$B"
  4. done <infile
maybe the test condition can be [ -n "$C" ] in state of [ "$A" = variableStep ]
# 4  
Old 10-03-2010
With awk...

Code:
 
awk -F" |=" '/variableStep/{chrom=$3;span=$NF;next}{print chrom,$1,$1+span,$NF}' infile

# 5  
Old 10-03-2010
Code:
awk '/^var/ {split($2,a,"=");split($3,b,"=");next}{print a[2],$1,$1+b[2],$2}' infile

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