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Extract specific content from data and rename its header problem asking

 
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Old 03-23-2010
Extract specific content from data and rename its header problem asking
Input file 1:
Code:
>pattern_5
GAATTCGTTCATGTAGGTTGASDASFGDSGRTYRYGHDGSDFGSDGGDSGSDGSDFGSDF
ATTTAATTATGATTCATACGTCATATGTTATTATTCAATCGTATAAAATTATGTGACCTT
SDFSDGSDFKSDAFLKJASLFJASKLFSJAKJFHASJKFHASJKFHASJKFHSJAKFHAW
>pattern_1
AAGTCTTAAGATATCACCGTCGATTAGGTTTATACAGCTTTTGTGTTATTTAAATTTGAC
ASDASRFSARFASFEDEGSDGHSDHWDYTQATWQRQOPTPEOTPWRIYRHIRGOPEIWRA
.
.

Input file 2:
Code:
pattern_5    5   15
pattern_5    18  25 
pattern_1    10  19
pattern_1    22  27
.
.

Desired output:
Code:
>pattern_5_0.01
TCGTTCATGTA
>pattern_5_0.02
TTGASDAS
>pattern_1_0.01
GATATCACCG
>pattern_1_0.02
GATTAG
.
.

I got a long list of input file 1 and input file 2. Input file 1 is the raw data while input file 2 is the range of input file 1 data that I'm interested to extract and generate the output result file. The column 2 and column 3 of input file 2 is the position that I interested to extract from the data of input file 1. The output file I will rename with the header like "pattern_*_0.0*"
It seems like awk or perl scripts able to archive these goal.
Thanks a lot for any advice.
Last edited by patrick87; 03-23-2010 at 06:31 AM.. Reason: further explaining of my question
 
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