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Top Forums UNIX for Dummies Questions & Answers Reporting characters after string Post 302970665 by Scrutinizer on Sunday 10th of April 2016 06:51:57 AM
Old 04-10-2016
Something like this?

Code:
awk -v len=4 -v string=AATTCCGG '
  BEGIN {
    FS=RS; RS=">"; OFS=""
    C["A"]="T"; C["T"]="A"; C["C"]="G"; C["G"]="C"  
  }
  function reverse_complement(s,	t,i) {
    for(i=1;i<=length(s);i++)
      t=C[substr(s,i,1)] t
    return t
  } 
  FNR==1{
    split(FILENAME, F, ".")
    next
  } 
  { 
    label=$1
    $1=""
    rec=$0 FS reverse_complement($0)
    while(match(rec,string)) { 
      print F[1] ":" label ":" substr(rec,RSTART+RLENGTH, len)
      rec=substr(rec, RSTART+1)
    }
  }
' file

Output:
Code:
file1:ID 1:ATCG
file2:ID 2:AACG


Last edited by Scrutinizer; 04-10-2016 at 09:37 AM..
This User Gave Thanks to Scrutinizer For This Post:
 

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IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME
igawk - gawk with include files SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ... igawk [ all gawk options ] [ -- ] program-text file ... DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1). AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like @include getopt.awk in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path. OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports. EXAMPLES
cat << EOF > test.awk @include getopt.awk BEGIN { while (getopt(ARGC, ARGV, "am:q") != -1) ... } EOF igawk -f test.awk SEE ALSO
gawk(1) Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995. AUTHOR
Arnold Robbins (arnold@skeeve.com). Free Software Foundation Nov 3 1999 IGAWK(1)
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