On Mon, Mar 30, 2009 at 11:02 PM, Christopher Lee <l...@chem.ucla.edu> wrote:
>
>
> On Mar 30, 2009, at 5:54 PM, Brent Pedersen wrote:
>
>> all goes well until the 2nd to last line. where i get an error:
>> KeyError: "no key 'b11' in database <SequenceFileDB
>> '/home/bpederse/work/learn_pygr/data/b.fasta'>"
>>
>> where 'b11' is the name of the fake gene in the variable b_gene. but
>> apparently, it's looking for the keys in b.fasta which
>> has the chromsomal fasta headers of 'chr1' ... 'chr3'
>
> Hi Brent,
> I looked at your load_simple_msa.py, and I think I see the problem:
> you are specifying seqDict=a_seq when you construct the NLMSA, but
> that's not right. Remember, the NLMSA seqDict needs to contain *all*
> the objects that are being mapped from / to. In this case that is not
> only the sequences in a_seq, but also the annotations in a_anno (this
> is why seqDict is almost invariably a union like PrefixUnionDict,
> unless all the source and destination sequences being aligned are from
> a single "sequence database").
>
> The easiest solution is just not give any seqDict argument, which will
> make the NLMSA construct a seqDict for you automatically (based on the
> object pairs you tell it to align). So just build your NLMSA like this:
>
> a_gene_msa = cnestedlist.NLMSA('/tmp/agenes', mode='w',
> pairwiseMode=True, bidirectional=False)
>
> bidirectional=False is recommended because you will never need the
> reverse mapping (from annotation --> sequence), since the annotation
> object automatically provides that via its own "sequence" attribute).
> bidirectional=False will prevent NLMSA from wasting space storing the
> reverse mapping.
>
> Here's an example of how we usually build such a sequence -->
> annotation mapping:
> http://www.doe-mbi.ucla.edu/~leec/newpygrdocs/tutorials/annotation.html#constructing-an-annotation-database
>
> It seems we need to add an error message that will catch this problem
> and give you a clear explanation of what to do. And of course we need
> to update all the docs to reflect the new 0.8 features and tutorials.
>
> By the way, importing AnnotationDB from seqdb is deprecated in 0.8;
> annotation functionality has been moved to a separate module called
> (unsurprisingly) pygr.annotation.
>
> -- Chris
>
> >
>
makes sense. i got this working and actually have it going on real data now too.
i didnt use ManyToMany, but it looks like i should try that in the
future to simplify things.
thanks for the help.
-brent
-brent
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