[Bioperl-l] Indexing HMMER reports
cjfields at illinois.edu
Tue Mar 10 10:22:42 EDT 2009
I wouldn't say it's not useful; just depends on your purpose. The
similar Bio::Index::Blast was very useful when I ran MCL clustering
and needed to pull out a single BLAST report (out of a very large
concatenated BLAST file) via the query ID.
Saying that, it would be nice to come up with a way to index the hit
ID but that may require reconfiguring how parsed IDs are stored.
On Mar 10, 2009, at 8:49 AM, Toni Hermoso Pulido wrote:
> Thanks Mauricio. I will take a look at your script and I will adapt my
> own ones.
> As Jason commented before, as this module is documented, it only
> reports (not their contents) and so it's not very useful in the
> En/na Mauricio Herrera Cuadra ha escrit:
>> I've been kind of disconnected from this stuff for a while but I
>> you could use (or take ideas from) a script of mine in the core
>> If you give the script a file with the list of reports to parse, it
>> print out most of the useful data from them. `bp_parse_hmmsearch.pl
>> will provide more help about its use.
>> Toni Hermoso Pulido wrote:
>>> I'm trying to index HMMER reports using:
>>> However, I have not found enough information in the module code
>>> examples for being able to index and get info from those reports.
>>> I would like to get HSP alignments associated to hit accession codes
>>> from reports distributed in several files.
>>> Does anyone have experience on this?
>>> After dumping variables, I think I'm just indexing report files, but
>>> not its contents.
>>> Best regards,
> Toni Hermoso Pulido
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