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to move in a line

Posted by revtopo (revtopo), 4 October 2007
hi there,

I have got a very large sequence, in which I have to move every 500bp a time and do some processing there.

I read that Bio::Location::Simple could help to define the start and the end position. but I would like to continue the walk through out the length of the sequence.

is there any effective way of doing this in simple perl?
thanks



Posted by admin (Graham Ellis), 4 October 2007
Potentially, yes.   How is the sequences stored?  Is it in a file where you need to move forward 500 bytes at a time?     If so, you can use seek to move to a new location in the file and read to read a certain number of bytes.

Posted by revtopo (revtopo), 4 October 2007
Yes, it is  stored in a file. the sequence are around  30432563 basepairs long.

Posted by KevinAD (KevinAD), 5 October 2007
bioperl has may many modules and methods, I would think there would be one already written to do what you want, but you can certainly try reading the line in 500 byte chunks and process as desired. read() is the function you want to look at.



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