Re: Command Line MsatCommander

[Brant Faircloth]

On Mar 17, 2007, at 5:10 PM, <> wrote:

> Hi Brant,
>
> Using the source code you posted on Google I was trying to run
> msatcommander from the command line, but I get an error. The "from
> Bio.SeqIO import SequenceIterator" seems to be depreciated. At
> least I think that is what is happening. Do you know anything
> about this?

nick,

the SeqIO module is not really deprecated - it should eventually be
replacing the fasta module in the new release of biopython (when it
is finally released). anyway, you can follow the instructions here:

http://code.google.com/p/msatcommander/wiki/UnicesNotes

to get biopython from cvs. you then will need to build it similar to
the method used for any python module, i,e.:

% sudo python setup.py install

then, you should be all set to go, provided the other dependencies
are installed. see this link for more info on SeqIO and biopython
1.43 (or biopython from CVS which is what you must currently use
since 1.43 has not been released):

http://biopython.org/wiki/SeqIO#Sequence_Input

cheers,
b

Brant Faircloth
fair...@gmail.com
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