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Sebastian Bassi | 1 Feb 2004 05:51

[BioPython] DNALinux

I've just uploaded DNALinux. A Live Linux distro with Bioinformatics 
software bundled (based on Slackware). EMBOSS, Primer3 and other 
bioiformatic software is included. This version does not include 
BioPython (it doesn't even include C++ compiler), but I'll do my best to 
put it in the next version (about April). I do use BioPython a lot, so I 
will try to put on the LiveCD.
I also need mirrors for the iso. If anybody is interested just email me.
The project page is www.dnalinux.com

--

-- 
Best regards,

//=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ   //=\
\=// IT Manager Advanta Seeds - Balcarce Research Center -      \=//
//=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\
\=// E-mail: sbassi <at> genesdigitales.com - ICQ UIN: 3356556 -     \=//

                 http://Bioinformatica.info

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System Anti-Virus Administrator | 2 Feb 2004 10:02

[BioPython] virus íàìåðåí â èçïðàòåíîòî ñúîáùåíèå (nameren v suobshtenieto izprateno ot vas) "HELLO"


Âíèìàíèå
Vnimanie: biopython <at> biopython.org


virus íàìåðåí â ñúîáùåíèåòî, êîåòî èçïðàòèõòå (be nameren v
suobshtenieto koeto vie izprashtate). 
Òîçè ñêåíåð ñïðÿ ñúîáùåíèåòî ïðåäè òî äà å äîñòèãíàëî
äî ìåñòîíàçíà÷åíèåòî ñè.
Tozi E-mail skener go otkri i blokira cqloto suobshtenie predi da dostigne destinaciqta si

virus áå ñúîáùåíî ÷å: 

 the W32/Mydoom.a <at> MM virus !!!


Ìîëÿ îáíîâåòå âàøèÿ àíòèâèðóñåí ñîôòóåð èëè ñå
îáúðíåòå êúì ÈÒ support-à âúçìîæíî íàé-áúðçî
òúé êàòî èìàòå âèðóñ âúâ âàøàòà ñèñòåìà.

Molq obnovete vashiq antivirusen softuer ili se oburnete kum IT support-a vuzmozhno nai-burzo
tui kato imate virus vuv vashata sistema.


Âàøåòî ñúîáùåíèå áå èçïðàòåíî ñúñ ñëåäíèòå äàííè:
Vasheto suobshtenie be izprateno sus slednite danni:

Èçïðàòåíî ÎÒ (Izprateno Ot) : biopython <at> biopython.org
Äî (Do):   ted <at> tgm.dk
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Karin Lagesen | 2 Feb 2004 10:39
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[BioPython] slow pairwise2 alignment

Hi!

I have a task where I need to do a lot of pairwise alignments. I am
using pairwise2.align.localms, since that seemed to fit me nicely.
However, when I try it out with aligning sequences around 350 nts
long, I end up using about 1 1/2 mins per alignment. This is for my
use way too slow. 

When I look in the source code I see something about a c code thingy
that can do this. I am assuming that since it takes so long that I am
not using the c code. Does anybody have any idea of how I can check
this, and how I if I'm not using the c code can get to use it?

TIA,

Karin
--

-- 
Karin Lagesen, PhD student
karin.lagesen <at> labmed.uio.no
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Leighton Pritchard | 2 Feb 2004 11:51
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[BioPython] [ANNOUNCEMENT] GenomeDiagram 0.1 package

Hi,

As mentioned several months ago, I have put together a package for drawing 
publication-quality schematics of genome and other large biological 
sequences.  The first release is now available for
inspection and download at:

http://bioinf.scri.sari.ac.uk/lp/genomediagram/shtml

The package requires Biopython and ReportLab, and I hope at least some of 
you find it useful.

Best wishes,

Dr Leighton Pritchard AMRSC
D104, PPI, Scottish Crop Research Institute
Invergowrie, Dundee, DD2 5DA, Scotland, UK
E: lpritc <at> scri.sari.ac.uk
T: +44 (0)1382 568579           F: +44 (0)1382 568578
PGP key FEFC205C: http://www.keyserver.net http://pgp.mit.edu

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Leighton Pritchard | 2 Feb 2004 11:53
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[BioPython] Fwd: [ANNOUNCEMENT] GenomeDiagram 0.1 package


That should, of course, have read:

>http://bioinf.scri.sari.ac.uk/lp/genomediagram.shtml

My bad.

Dr Leighton Pritchard AMRSC
D104, PPI, Scottish Crop Research Institute
Invergowrie, Dundee, DD2 5DA, Scotland, UK
E: lpritc <at> scri.sari.ac.uk
T: +44 (0)1382 568579           F: +44 (0)1382 568578
PGP key FEFC205C: http://www.keyserver.net http://pgp.mit.edu

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Jeffrey Chang | 2 Feb 2004 15:28

Re: [BioPython] slow pairwise2 alignment

Hi Karin,

You can test to see if the C code is available by doing:
 >>> from Bio import cpairwise2

If that succeeds, then the C version is compiled and pairwise2 should 
be using it.  Otherwise, it is not.

One of the reasons it might be taking so long, especially with 
nucleotide sequences, is that it recovers all best alignments with 
equivalent score.  If you want to speed it up, you can:
1) Only recover one best alignment:
     pairwise2.align.localms(..., one_alignment_only=1)
2) Only get the score (no alignments):
     pairwise2.align.localms(..., score_only=1)
In this case, the return value of the function is just the score, which 
should speed things up a bit.

If you are using x86, you may also consider using psyco to speed things 
up a bit.
http://psyco.sourceforge.net/

Good luck!

Jeff

On Feb 2, 2004, at 4:39 AM, Karin Lagesen wrote:

> Hi!
>
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Brad Chapman | 3 Feb 2004 01:26
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Re: [BioPython] Problems building biopython-based script with py2exe

Hi Leighton;

[Problem with Bio/__init__.py, registry loading, and py2exe]

> I think my problem is solved with changes only to Bio/__init__.py; no 
> modifications were required to FormatIO.py in the end.
[...]
> I've taken your advice, and replaced the original registry import code 
> (lines 52-55) of Bio/__init__.py with the following:
[...]
> Which seems to work.

Thanks for looking into this problem -- I know nothing at all about
py2exe and very little about the registry import magic going on
there. I checked your changes into Bio/__init__.py

Could you please verify that I did everything right and didn't mess
anything up on typing it up? Ugh, all those list comprehensions and
import hacks and my head is a bit tired right now; so hopefully I
did a decent job.

Thanks again for looking into this!
Brad
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Brad Chapman | 3 Feb 2004 01:34
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Re: [BioPython] Checked in Parsers for Phred and Ace files

Hi Frank;

> > The one caveat is that the Ace parser does not support RT, CT and WA 
> > tags.

> I couldn't stand a parser that's not completely doing its job,
> especially when it's written by myself :-). So I added supprt for these
> three tags. 

Great -- thanks. It's good to have you looking after, uh, yourself.
Someone's got to do it :-)

> It seems to work fine - however, before I submit it, I'd
> like to be sure that it complies to the specification of the ACE format.
> The consed documentation is not really exact about many things - so does
> anybody know where to find a more comprehensive descripion of the ace
> format? Is there any?

I don't know anything specific, but there is a section in the consed
docs (ACE FILE FORMAT): 

http://www.phrap.org/consed/distributions/README.13.0.txt

There is a brief description of those three tags there and what each
element of the tags stand for. Any more beyond that I personally
have no idea -- I guess if someone has experience working with and
adding these tags they might be able to chime in about how they are
used. 

But independent of that, parsing them into lists of lists or some
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Brad Chapman | 3 Feb 2004 01:38
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Re: [BioPython] [ANNOUNCEMENT] GenomeDiagram 0.1 package

Hi Leighton;

> As mentioned several months ago, I have put together a package for drawing 
> publication-quality schematics of genome and other large biological 
> sequences.

Thanks -- this really looks excellent. Thanks for taking the time to
put together a distribution and write up documentation. Next time I
need to generate diagrams I'm definitely going to look at this
package. 

I added a link to it from the ScriptCentral page:

http://biopython.org/scriptcentral/

Great work!
Brad
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Bioanalytik | 3 Feb 2004 15:45

[BioPython] sukper viagrma

It`s fabuklous!

I took the only one pijll of Cialjs and that was such a GREAT weekend!
All the girls at the party were just punch-drunk with my potential

I have fhcked all of them THREE times but my dhck WAS able to do some more!

Cbalis- it`s COOL!!! The best weekend stuff I've ever trhied!
Haven`t you tried yet?

DO IT NkOW at 
http://www.vow-meds.com/sv/index.php?pid=genviag

volley annuls stirrings nagging cycled Metrecal bonnet seceding pinnings.

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Gmane