From zhuiastate.edu  Tue Jan 17 18:47:13 2012
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: Re: Update: Bash shell script for parsing chrompic files to
  show only phase lines with highest recombinations
Date: Tue, 17 Jan 2012 18:47:13 -0600

Hi Jill,

Sorry it's not your copy and paste problem but I have a line wrapper script
to "watch" for long lines for breaks. I have manually corrected your post
on the archive and they should look fine:
http://www.animalgenome.org/tools/share/crimap/forum/

A small trick to keep raw text format on this list is to precede each line
with a space/spaces or "bullet" symbols (eg. "o ", "- ", "# ", etc).

I have some old perl scripts to "clean" the crimap output for easier visual
evaluations or direct copy to a table. Perhaps I should contribute them as
well :-)

Zhiliang
/on PAG @ san diego 

 
On Jan 17, 2012, at 04:09 PM, Jill Maddox wrote: 

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