inputfile: 

>1_1 geneid1 34 45 len=10 
AGTCGA 
GCAA 
>1_2 geneid1 54 75 len=21 
AGTCGAAGTCGA 
ACAAACAAT 
>2_1 geneid1 78 83 len=5 
CGTCG 
>1_1 geneid2 14 25 len=11 
AGTCGAA 
GCAA 
>2_1 geneid2 4 12 len=8 
AGTCGAAT 
>2_3 geneid2 19 27 len=8 
AGTC 
GCAA 
>2_2 geneid2 89 95 len=6 
AAAAAA 

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facts: 
1) this is just a sample. but the real file will be 2 GB in size. the AGTC bases wil be in 1000's to millions. 

problem: 
1) i have to join the sequences belonging to the same number and also same geneid. 
2) the output file wil be a list of sequences (each sequence wil be a set of numbers joined together but have one header {which is my problem now that i am not able to print it} ). 

--------------------------------- 
sample output file: 

>1 gid1 
AGTCGA 
GCAA 
AGTCGAAGTCGA 
ACAAACAAT 
>2 gid1 
CGTCG 
>1 gid2 
AGTCGAA 
GCAA 
>2 gid2 
AGTCGAAT 
AAAAAA 
AGTC 
GCAA