Shell Programming and Scripting

Hi all,
I am very new in programming.
Can anyone please help me in the matter below?

I have one raw file like:
gi|77|ref|NC_002971.3| Coxiella burnetii RSA 493, complete genome 6371 ATCGTGGT[GC]TG[AG]TGGTTCAT 5032 P 2 12
gi|71|ref|NC_005773.3| Pseudomonas syringae pv. phaseolicola 1448A, complete genome 6280 ATC[AG]G[CG]TTTCAT 5032 P 2 12
gi|19|ref|NW_002063157.1| Streptomyces pristinaespiralis ATCC 25486 supercont1.24, whole genome shotgun sequence 47242 CACC[TG]CAGGACCG 6071 P 1 4
gi|17|ref|NW_002062785.1| Streptomyces sp. Mg1 supercont1.3, whole genome shotgun sequence 249645 CACC[TG]GACCG 6071 P 1 4
gi|32|ref|NC_003888.3| Streptomyces coelicolor A3(2), complete genome 139563 CACCC[GC] 6071 P 1 4

gi is the starting of a new line.

I need one out put like :
Coxiella burnetii RSA 493, 5032, 50
Pseudomonas syringae pv. phaseolic, 5032, 50
Streptomyces pristinaespiralis ATC, 6071, 50
Streptomyces sp. Mg1 supercont1.3, 6071, 50
Streptomyces coelicolor A3(2), 6071,

where
1st column is 5th column of raw file
2nd column is 9th column of raw file
last column 50 is an arbitary number added as a column.

My main problem is there are several separators as: pipe, comma, space, tab in the file. ore over the names like 'Coxiella burnetii RSA 493' and descriptors 'complete genome ' should be treated as one column.

Can any body help me?
Thanks in advance,
Mitra.

nawk -f ia.awk myRawFile

ia.awk:

Code:

BEGIN {
  SEP=FS
  FS="|"
  OFS=","

  arb=50
}
{
  f1=substr($NF,2,index($NF, ",")-2)
  n=split($NF, tmp, SEP)
  f2=tmp[n-3]
  print f1, f2, arb
}

In the future please use the BB code tags when posting code/data samples.

Try this

Code:

awk -F "," '{match($1,/[|] [A-Z]+/);n=split($2,a," ");print substr($1,RSTART+2,length($1)-(RSTART+1)),a[n-3],50}' OFS="," filename

cheers,
Devaraj Takhellambam

Thank you very much. It works...
Thanks a lot...
Best,
Mitra.

Code:

open $fh,"<","a.txt";
while(<$fh>){
	chomp;
	my @tmp=split("[||,]",$_);
	my @t=split(" ",$tmp[5]);
	print $tmp[4],",",$t[$#t-3],",50\n";
}
close $fh;