[Bioperl-l] Help needed urgently

Sayali sayali_salodkar at persistent.co.in
Wed Nov 15 09:15:52 EST 2006


I wish to fetch consensus sequence and the names of the trace (chromat)
files used in the assembly from the .ace file

For this purpose, I am using Bio::Assembly::IO. But I am unable to find the
appropriate methods which would enable me to fetch this information.

 

Note: 

The BS line (base segment) in the .ace file indicates which read phrap has
chosen to be the consensus at a particular position.

For example: 

BS 1 515 K26-572c gives 

BS <padded start consensus position> <padded end consensus position> <read
name> respectively.

      

How do I retrieve this information contig wise?

Kindly help.

Regards,

Sayali D Salodkar


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