[Bioperl-l] Deprecating

Stefan Kirov skirov at utk.edu
Sat Oct 16 11:41:29 EDT 2004


Brian Osborne wrote:

>I took a look at AlignIO/meme.pm and fixed some obvious problems but I think
>it's possible that the file used in the tests, t/data/meme.dat, may not have
>all the information I need to debug the module (and I don't have meme
I don't think there were tests for AlignIO/meme.pm. Anyway id there are 
I am not able to find these. t/data/meme.dat is a test file for 
Bio/Matrix/PSM/IO/meme.pm. But as this is presumably the same format 
AlignIO/meme.pm should read....

> Question: is "strand" ever stipulated in the meme output file?
>There's no "+" or "-" indicated in meme.dat. This file is the result of an
>analysis of DNA, so I'm a bit surprised not to see some indication of strand
>(and the code, before I modified it, was using a regexp that attempted to
>capture strand information). Can you enlighten me here? Here's one of the
>relevant sections:
>Sequence name             Start   P-value                      Site
>-------------             ----- ---------            -----------------------
>6603                       1311  2.59e-15 GGCGCATTGA
>83796                      1284  2.59e-15 GGAGGATTGA
>20218                       938  6.34e-12 TTTTTGGTAA
>10657                      1685  8.70e-12 GGCCCGCGCG
>Perhaps when one runs meme with DNA one can tell it to just do 1 strand,
>rather than both?
You are quite right on this. I had somewhere an example with strands... 
I'll find it (or regenrate it) ASAP and send it to you. I will try to 
rewrite the tests for meme (other one) for the new test file.

> This would explain the absence of strand information, but
>it means the regexp changes depending on this mode. Again, I don't have meme
>or use meme, so you're going to have to tell me, or send me output files
>with and without strand stipulation.
>Brian O.
>-----Original Message-----
>From: Stefan Kirov [mailto:skirov at utk.edu]
>Sent: Friday, October 15, 2004 6:33 PM
>To: Brian Osborne
>Cc: bioperl-l at bioperl.org
>Subject: Re: [Bioperl-l] Deprecating
>I wonder if anyone uses *Bio::AlignIO::meme*. Last time (year ago) it
>did not work for me and I have not seen anyone committing changes....
>Brian Osborne wrote:
>>Any objections to my adding Bio::Tools::RestrictionEnzyme to the DEPRECATED
>>file? It was replaced by Bio::Restriction a while ago.
>>Along the same lines, is there anything else that should be deprecated?
>>Brian O.
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>Stefan Kirov, Ph.D.
>University of Tennessee/Oak Ridge National Laboratory
>5700 bldg, PO BOX 2008 MS6164
>Oak Ridge TN 37831-6164
>tel +865 576 5120
>fax +865-576-5332
>e-mail: skirov at utk.edu
>sao at ornl.gov
>"And the wars go on with brainwashed pride
>For the love of God and our human rights
>And all these things are swept aside"

Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

"And the wars go on with brainwashed pride
For the love of God and our human rights
And all these things are swept aside"

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