Cool, thanks for the reply!

Using your example, I found out there is no need for the header part at all. I removed that part of the code, and then used the s//g; to get rid of the rest of the field names.

Here is the code:

use strict; 
use warnings; 

print "\n Running script for Jiggs \n";
my $infile = "foot.txt";                   

open my $in,  "<", $infile     or die $!;  
open my $out, ">", "foot1.txt" or die $!;

while (<$in>) {
    
    s/\s+\Z/\n/;
    s/ +/,/g;
    s/,length=/,/g;
    s/,xy=/,/g;
    s/,region=/,/g;
    s/,run=/,/g;
    
    print $out $_;
    }

close $in; 
close $out; 
 
print "\n Done!\n";
[download]

Here is the output:

>G9JVYGV01AJE8V,135,0104_0349,1,R_2011_09_20_15_00_06_
GGTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTG
GAAGAAGAAGATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAA
GTGGAAGAGAGGAGC
>G9JVYGV01A4910,90,0353_0150,1,R_2011_09_20_15_00_06_
GGTGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGA
GTGAAGCAACCATCTACAATGCCATGCACC
>G9JVYGV01A0SVP,70,0302_0163,1,R_2011_09_20_15_00_06_
GCACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGC
TGAATGGTGC
>G9JVYGV01A221U,89,0328_0160,1,R_2011_09_20_15_00_06_
CTGGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGA
CGTCTCTTCTCCTCCTCCGGACTGGGACA
>G9JVYGV01BVCPK,46,0650_0134,1,R_2011_09_20_15_00_06_
GCAAGATCGCAAGCCAAGCAACGTTTCACGAACTGGCCAGAATGAG
>G9JVYGV01AOU3I,81,0166_0220,1,R_2011_09_20_15_00_06_
TCATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGAT
GTCAATGAGTGTGACAGTGAT
>G9JVYGV01A0JEL,61,0299_0171,1,R_2011_09_20_15_00_06_
CGAGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTC
G
>G9JVYGV01AUKIG,119,0231_0198,1,R_2011_09_20_15_00_06_
GGCCACCAGGGCTTAACTTCCTGTGCCTCACCATCACGCAGTTGTCAGAGGATCCACATT
GAACAAAGTAGCAATTCTTTCCACTCTGTGACACACCAACATTCTTATACAGCACCAGG
>G9JVYGV01AJ8F7,29,0113_1333,1,R_2011_09_20_15_00_06_
CTGCTTCCAAGCCTCCAACCTCTAACCAG
>G9JVYGV01AMQ87,79,0142_0233,1,R_2011_09_20_15_00_06_
AGAGTCTCCTCATTGTTCTTTCCAAGTCCTCTATTGCTGAGCCTGGTTTCGTACCTTCTC
AGCTAGGCCCTCTTTCTCT
>G9JVYGV01A4W45,85,0348_3895,1,R_2011_09_20_15_00_06_
GCTTCACATCTCAGAAATATAACCGCTAATGATCTGAAACAAGTTACAATCTGACATTCT
GAAACCAAATGAAAGCAGCATAAAC
>G9JVYGV01A7TPA,66,0382_0140,1,R_2011_09_20_15_00_06_
ATGGCTTACCTCACTGTCGATGGAGATCGAATGCAAGCGATGTCCATCGACAGTGAGGTA
AGCCAT
[download]

Almost there, but I need to put a comma after the last field before the sequence. Then remove the returns within the sequence.

If each entry starts with a carot, then I need 6 fields seperated by commas and then the new line: the opening entry, the length=, xy=, region=, run=, AAGGTTGGCC /n).

Apologies for not being clearer, but thanks for the help so far.