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_00_06_GGTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTGGAAGAAGAAGATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAAGTGGAAGAGAGGAGC
>G9JVYGV01A4910 length=90 xy=0353_0150 region=1 run=R_2011_09_20_15_00_06_GGTGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGAGTGAAGCAACCATCTACAATGCCATGCACC
>G9JVYGV01A0SVP length=70 xy=0302_0163 region=1 run=R_2011_09_20_15_00_06_GCACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGCTGAATGGTGC
>G9JVYGV01A221U length=89 xy=0328_0160 region=1 run=R_2011_09_20_15_00_06_CTGGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGACGTCTCTTCTCCTCCTCCGGACTGGGACA
>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_TCATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGATGTCAATGAGTGTGACAGTGAT
>G9JVYGV01A0JEL length=61 xy=0299_0171 region=1 run=R_2011_09_20_15_00_06_CGAGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTCG