I assumed the line breaks in the data was unintentional and that each line began with >:
(timtowtdi) 
use strict;
use warnings;

while (<DATA>) {
    chomp;
    my @parts = split /\s+/,$_;
    ## $parts[0] = substr $parts[0],1,-1;
    $parts[1] = $1 if $parts[1] =~ /length=(\d+)/;
    print join(",",@parts),"\n";
}

__DATA__
>G9JVYGV01AJE8V length=135 xy=0104_0349 region=1 run=R_2011_09_20_15_0
+0_06_GGTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTGGAAG
+AAGAAGATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAAGTGGAAGAGAGGA
+GC
>G9JVYGV01A4910 length=90 xy=0353_0150 region=1 run=R_2011_09_20_15_00
+_06_GGTGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGAGTGAA
+GCAACCATCTACAATGCCATGCACC
>G9JVYGV01A0SVP length=70 xy=0302_0163 region=1 run=R_2011_09_20_15_00
+_06_GCACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGCTGAAT
+GGTGC
>G9JVYGV01A221U length=89 xy=0328_0160 region=1 run=R_2011_09_20_15_00
+_06_CTGGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGACGTCT
+CTTCTCCTCCTCCGGACTGGGACA
>G9JVYGV01BVCPK length=46 xy=0650_0134 region=1 run=R_2011_09_20_15_00
+_06_GCAAGATCGCAAGCCAAGCAACGTTTCACGAACTGGCCAGAATGAG
>G9JVYGV01AOU3I length=81 xy=0166_0220 region=1 run=R_2011_09_20_15_00
+_06_TCATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGATGTCAA
+TGAGTGTGACAGTGAT
>G9JVYGV01A0JEL length=61 xy=0299_0171 region=1 run=R_2011_09_20_15_00
+_06_CGAGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTCG

[download]

I like using split instead as it's a little less fragile when it comes to parsing input. Edit: I guess the OP wanted to preserve the ">" at lines' beginning, which I didn't.

mr.nick ...

In reply to Re: Perl script help to convert .txt file to .csv by mr.nick
in thread Perl script help to convert .txt file to .csv by Seabass

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