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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
...
>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

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
...
}
-e syntax OK