From jillian.maddoxalumni.unimelb.edu.au  Tue Jan 17 18:09:14 2012
From: Jill Maddox <jillian.maddoxalumni.unimelb.edu.au>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: Update: Bash shell script for parsing chrompic files to show
  only phase lines with highest recombinations
Date: Tue, 17 Jan 2012 18:09:14 -0600

Hi again

Sorry, I cut and pasted the script into my mail program and had Unix rather
than DOS carriage returns so that the lines in the script got wrapped and
truncated in the wrong places. For those of you now familiar with scripts
the \ should be at the end of a line and should be preceded by a space.

Here is the corrected script

======================================================================== 
#!/bin/bash 
# chrompic_recomb_ord.sh 
# sort lines containing more than recombinants and order from lowest 
# to highest 
# Input: chrompic filename, minimum number of recombinations 
# Output: chrompic filename with .recomb suffix 
if [ $# -ne 2 ]; then 
      echo 1>&2 Usage: $0 chrompic_filename min_num_recomb 
      exit 127 
fi 
if ! [ -a ./${1} ]; then 
     echo "file ${1} not found" 
     exit 127 
fi 
if ! [[ "$2" =~ ^[0-9]+$ ]]; then 
      echo "$2 is not a suitable number" 
      exit 127 
fi 

egrep " [-0o1i]{10} " $1 | sed 's/ \([0-9]*\)$/\t\1/g' | \
  gawk -v var=$2 'BEGIN{FS=OFS="\t"; line1=0; minrec=var;} \
  {if (line1 == 0) {line1 = 1;num_in_line=split($1, lineinfo, " "); \
         ind = lineinfo[1]; \ 
      if ($2 >= minrec){ for (i=2; i <= num_in_line; i++) \ 
          printf "%s", lineinfo[i];printf "\t%d\t%d\n", $2, ind;} \ 
      else next;} \ 
   else {line1 = 0; if ($2 >= minrec) \ 
     {num_in_line=split($1, lineinfo, " ");  \ 
     for (i=2; i <= num_in_line; i++) printf "%s", lineinfo[i]; \ 
     printf "\t%d\t%d\n", $2, ind;}}}' | \ 
sort -n -k2 -n -k3 > ${1}.recomb 
exit 
==================================================================================  

 
Regards 

 
Jill 

 
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Jill Maddox 16 Park Square Port Melbourne, 3207 Australia phone: 03 9646
0428 E-mail: jillian.maddoxalumni.unimelb.edu.au

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