I see. Maybe 'v' should be changed to 'orgstr' then?
On Mon, May 25, 2009 at 5:17 AM, Namshin Kim <deepr...@gmail.com> wrote:
> I think wiki page is correct. seqlist is only list of genome assembly names
> and seqdict (in your term) it genomes (= {}).
>
>
> On Mon, May 25, 2009 at 4:13 PM, Jenny Qing Qian <jqian....@gmail.com>wrote:
>
>> Hi,
>>
>> To build a pairwise assembly alignments, do I need to go through all the
>> steps as if I was building a msa? Or, is there a simpler way to do this?
>> More specifically, can I skip the ref_assembly_self alignment?
>>
>> BTW, I think there is a minor mistake on the
>> http://code.google.com/p/pygr/wiki/NlmsaFromAxtPairwise wiki page.
>>
>> Shouldn't the seqlist be a seqdict?
>>
>> # a dictionary of genomic sequences
>> seqdict = {'hg18':hg18, 'panTro2':panTro2, 'mm8':mm8, 'rn4':rn4,
>> 'canFam2':canFam2}
>>
>>
>> for k, v in seqdict.iteritems():
>> genomes[k] = seqdb.SequenceFileDB(v)
>>
>>
>> Best wishes,
>> Jenny
>>
>>
>>
>>
>>
>
> >
>
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