$ echo ">G9JVYGV01AJE8V length=135 xy=0104_0349 region=1 run=R_2011_09_20_15_00_06_
GGTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTG
GAAGAAGAAGATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAA
GTGGAAGAGAGGAGC
>G9JVYGV01A4910 length=90 xy=0353_0150 region=1 run=R_2011_09_20_15_00_06_
GGTGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGA
GTGAAGCAACCATCTACAATGCCATGCACC
>G9JVYGV01A0SVP length=70 xy=0302_0163 region=1 run=R_2011_09_20_15_00_06_
GCACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGC
TGAATGGTGC
>G9JVYGV01A221U length=89 xy=0328_0160 region=1 run=R_2011_09_20_15_00_06_
CTGGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGA
CGTCTCTTCTCCTCCTCCGGACTGGGACA
>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_
TCATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGAT
GTCAATGAGTGTGACAGTGAT
>G9JVYGV01A0JEL length=61 xy=0299_0171     region=1     run=R_2011_09_20_15_00_06_
CGAGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTC
G
" | perl -e'
my $line;     
while ( <> ) {
    chomp;
    s/length=//;
    tr/ /,/s;
    if ( /^>/ ) {
        print "$line\n" if $line;
        $line = $_;
        }
    else {
        $line .= $_;
        }
    }           
print "$line\n";
'
>G9JVYGV01AJE8V,135,xy=0104_0349,region=1,run=R_2011_09_20_15_00_06_GGTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTGGAAGAAGAAGATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAAGTGGAAGAGAGGAGC
>G9JVYGV01A4910,90,xy=0353_0150,region=1,run=R_2011_09_20_15_00_06_GGTGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGAGTGAAGCAACCATCTACAATGCCATGCACC
>G9JVYGV01A0SVP,70,xy=0302_0163,region=1,run=R_2011_09_20_15_00_06_GCACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGCTGAATGGTGC
>G9JVYGV01A221U,89,xy=0328_0160,region=1,run=R_2011_09_20_15_00_06_CTGGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGACGTCTCTTCTCCTCCTCCGGACTGGGACA
>G9JVYGV01BVCPK,46,xy=0650_0134,region=1,run=R_2011_09_20_15_00_06_GCAAGATCGCAAGCCAAGCAACGTTTCACGAACTGGCCAGAATGAG
>G9JVYGV01AOU3I,81,xy=0166_0220,region=1,run=R_2011_09_20_15_00_06_TCATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGATGTCAATGAGTGTGACAGTGAT
>G9JVYGV01A0JEL,61,xy=0299_0171,region=1,run=R_2011_09_20_15_00_06_CGAGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTCG