[Biojava-l] How to combine multiple Sequence objects into a singleSequence object?

Keith James kdj at sanger.ac.uk
Sun Oct 19 06:24:34 EDT 2003

>>>>> "Mark" == Schreiber, Mark <mark.schreiber at agresearch.co.nz> writes:

    Mark> Hi - We get asked this a lot. Unfortunately there isn't an
    Mark> easy solution. If you have access to all of the files
    Mark> referenced in the main EMBL file then you could write a
    Mark> simple program to retrieve and open them all and then use
    Mark> something like Edit functions to join them together.

Is this the purpose of Assembly and ComponentFeature? I haven't used
these, but it looks like you can create an aggregate sequence. I had a
brief look at the code and it seems that a current limitation is that
new features cannot be created on the component sequences.

See NewSimpleAssemblyTest in tests which creates a SimpleAssembly
(which isa Sequence) from 6 smaller Sequences.



- Keith James <kdj at sanger.ac.uk> Microarray Facility, Team 65 -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -

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