replacing xdformat with formatdb in prok. annotation pipeline

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replacing xdformat with formatdb in prok. annotation pipeline

Chris Hemmerich

Hi,

  The new prok. annotation pipeline replaces wu-blastp with ncbi-blastx,
but still uses xdformat rather than formatdb to process the results of
bsml2fasta.pre_overlap_analysis for ber. I performed a quick test of
replacing this with formatdb, and ber appears to still work.

I'm pretty clueless about the intricies of ber though, is there a reason
to stick with xdformat over formatdb?

Thanks,
  Chris

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Re: replacing xdformat with formatdb in prok. annotation pipeline

Joshua Orvis
Chris -

Did you ever notice anything awry here?  If you can test that there's no change here either way (and Kevin doesn't have any strong feelings about it) this change should probably be made in the code.

Joshua



On Tue, Feb 22, 2011 at 3:22 AM, Chris Hemmerich <[hidden email]> wrote:

Hi,

 The new prok. annotation pipeline replaces wu-blastp with ncbi-blastx,
but still uses xdformat rather than formatdb to process the results of
bsml2fasta.pre_overlap_analysis for ber. I performed a quick test of
replacing this with formatdb, and ber appears to still work.

I'm pretty clueless about the intricies of ber though, is there a reason
to stick with xdformat over formatdb?

Thanks,
 Chris

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Collect, index and harness all the fast moving IT data generated by your
applications, servers and devices whether physical, virtual or in the cloud.
Deliver compliance at lower cost and gain new business insights.
Free Software Download: http://p.sf.net/sfu/splunk-dev2dev
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Re: replacing xdformat with formatdb in prok. annotation pipeline

Chris Hemmerich


Joshua,

We haven't seen any problems using formatdb on our test data or running it
in production for a few weeks. We were worried about formatdb being picky
about sequence headers, but this hasn't manifested as a problem yet and we
see a wide mix of header styles.

  Chris

On Sat, 12 Mar 2011, Joshua Orvis wrote:

> Chris -
>
> Did you ever notice anything awry here?  If you can test that there's no
> change here either way (and Kevin doesn't have any strong feelings about it)
> this change should probably be made in the code.
>
> Joshua
>
>
>
> On Tue, Feb 22, 2011 at 3:22 AM, Chris Hemmerich
> <[hidden email]>wrote:
>
>>
>> Hi,
>>
>>  The new prok. annotation pipeline replaces wu-blastp with ncbi-blastx,
>> but still uses xdformat rather than formatdb to process the results of
>> bsml2fasta.pre_overlap_analysis for ber. I performed a quick test of
>> replacing this with formatdb, and ber appears to still work.
>>
>> I'm pretty clueless about the intricies of ber though, is there a reason
>> to stick with xdformat over formatdb?
>>
>> Thanks,
>>  Chris
>>
>>
>> ------------------------------------------------------------------------------
>> Index, Search & Analyze Logs and other IT data in Real-Time with Splunk
>> Collect, index and harness all the fast moving IT data generated by your
>> applications, servers and devices whether physical, virtual or in the
>> cloud.
>> Deliver compliance at lower cost and gain new business insights.
>> Free Software Download: http://p.sf.net/sfu/splunk-dev2dev
>> _______________________________________________
>> Ergatis-users mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>

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