Python Module for sequence alignments.

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3 total messages Started by Alex Wed, 05 Jul 2000 00:00

Author: Alex
Date: Wed, 05 Jul 2000 00:00

42 lines
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Hi.  I made a python module that does simple sequence alignments.  If
there is enough interest, I may make it a little more elaborate.  You
can get it from 

http://puffin.lcs.mit.edu:8080/align.tgz

To use it on linux

tar zxf align.tgz
cd align
make

and make the align directory accessible to python, with a command like

setenv PYTHONPATH `pwd`:${PYTHONPATH}

It needs the Numeric extension.

Here's an example of how it works from the command line:

>>> import align                          
>>> align.align ('aneotuhaneot', 'asneouhoteuh')[0][0][:3]                
('neotuhane', 'sneouhote', '----uh--e')

The second element of the tuple it returns is the matrices used to
calculate the optimal alignments.

I don't really care how you use or change this, nor will I assume any
legal culpability for problems arising from its use.  For instance, if a
bug in this code tricks you into genetically engineering Giant
Super-Intelligent Man-Eating Lizards, I may cackle evilly, but I won't
explicitly own up.  I may take on the care and feeding of one or two of
them if you can prove they will co-exist peacefully with my cat, but
that's definitely as far as it goes.

But please do let me know of any problems with it, or any suggestions
you have about how I could improve it.  If you make any use or
improvements to it yourself, I would love to hear about them.

Alex.

Re: Python Module for sequence alignments.

Author: Andrew Dalke
Date: Fri, 07 Jul 2000 00:00

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Alex wrote:
>Hi.  I made a python module that does simple sequence alignments.  If
>there is enough interest, I may make it a little more elaborate.  You
>can get it from
>
>http://puffin.lcs.mit.edu:8080/align.tgz

By the way, you may be interested in biopython.org, which is developing
a set of libraries and tools for bioinformatics and related fields.  You
may also be interested in the Bioinformatics Open-Source Conference
<ismb2000.sdsc.edu/bosc2000> which really should include your
disclaimer concerning Giant Super-Intelligent Man-Eating Lizards.

                    Andrew
                    dalke@acm.org

Re: Python Module for sequence alignments.

Author: felipe wettstein
Date: Fri, 21 Jul 2000 00:00

35 lines
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hi alex

you wrote:
> Hi.  I made a python module that does simple sequence alignments.  If
> there is enough interest, I may make it a little more elaborate.  You
> can get it from
> 
> http://puffin.lcs.mit.edu:8080/align.tgz
> 
> To use it on linux
> 
> tar zxf align.tgz
> cd align
> make
>
i tried this (and you will see in my question that i am a blody
beginner, but nevertheless, i ask you:)
bla: /align # make
gcc _alignmodule.c -c -o _alignmodule.o \
         I /usr/include/python1.5/ -I /user/include/python1.5/Numeric
_alignmodule.c:2 arrayobject.h: No such file or directory
make: *** [all] Error 1

what did i wrong? is my python not installed well? when it makes sense
to answer please do, whenn you would have to write me a whole manual,
forget it. thanks 

felipe

and then also my linux does not seem to understand what setenv means (i
thought it is kernel 2.2.14, suse6.4), and me i nether do understend.

have a good day

felipe

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