This can be done with a one-liner. See perlrun for the lowdown on the switches used.

c:\test>perl -l -0x3e -ane"@F||next; s/length=//for$F[1]; @F[5]=join''
+,@F[5..99]; $#F=5; print'>',join',',@F" junk.dat
>G9JVYGV01AJE8V,135,xy=0104_0349,region=1,run=R_2011_09_20_15_00_06_,G
+GTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTGGAAGAAGAAG
+ATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAAGTGGAAGAGAGGAGC
>G9JVYGV01A4910,90,xy=0353_0150,region=1,run=R_2011_09_20_15_00_06_,GG
+TGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGAGTGAAGCAACC
+ATCTACAATGCCATGCACC
>G9JVYGV01A0SVP,70,xy=0302_0163,region=1,run=R_2011_09_20_15_00_06_,GC
+ACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGCTGAATGGTGC
>G9JVYGV01A221U,89,xy=0328_0160,region=1,run=R_2011_09_20_15_00_06_,CT
+GGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGACGTCTCTTCTC
+CTCCTCCGGACTGGGACA
>G9JVYGV01BVCPK,46,xy=0650_0134,region=1,run=R_2011_09_20_15_00_06_,GC
+AAGATCGCAAGCCAAGCAACGTTTCACGAACTGGCCAGAATGAG
>G9JVYGV01AOU3I,81,xy=0166_0220,region=1,run=R_2011_09_20_15_00_06_,TC
+ATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGATGTCAATGAGTG
+TGACAGTGAT
>G9JVYGV01A0JEL,61,xy=0299_0171,region=1,run=R_2011_09_20_15_00_06_,CG
+AGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTCG
[download]

Whilst you may not be interested in using a one-liner, especially if you need to do this regularly, it can be instructive to see the code that the one-liner produces when deparsed:

c:\test>perl -MO=Deparse -l -0x3e -ane"@F||next; s/length=//for$F[1]; 
+@F[5]=join'',@F[5..99]; $#F=5; print'>',join',',@F" junk.dat
BEGIN { $/ = ">"; $\ = "\n"; }
LINE: while (defined($_ = <ARGV>)) {
    chomp $_;
    our(@F) = split(' ', $_, 0);
    next unless @F;
    s/length=// foreach ($F[1]);
    @F[5] = join('', @F[5..99]);
    $#F = 5;
    print '>', join(',', @F);
}
-e syntax OK
[download]