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fhjdfj jfgkhggyk | 1 Mar 2003 17:16
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[BioPython] FASTA input module + Nussinov algorithm module: RNA secondary structure predicti

I am just writing to request a bit of help - I wish to set up a system that 
will take multiple RNA sequences in FASTA format and feed them into a 
Nussinov RNA secondary structure prediction program. I have found a good 
python module for the Nussinov on the web at:

http://bioinfo.sarang.net/Moin/Nussinov_2epy

Discovering this has pleased me no end. Has anyone got any idea where i can 
find a FASTA input python module and how I would interlink it to the 
nussinov module that i already have? It may need to be spelt out to me as my 
python expertise is south of poor.
I have seen some info on python fasta input code at:

  
http://www.pasteur.fr/recherche/unites/sis/formation/python/ch02s08.html#ex_readingfasta

But i have no idea how to go about integrating this with my nussinov module. 
Any suggestions would be greatly appreciated and will maybe once again give 
me the luxury of sleep.

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Catherine Letondal | 2 Mar 2003 09:23
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Re: [BioPython] FASTA input module + Nussinov algorithm module: RNA secondary structure predicti


"fhjdfj jfgkhggyk" wrote:
> I am just writing to request a bit of help - I wish to set up a system that 
> will take multiple RNA sequences in FASTA format and feed them into a 
> Nussinov RNA secondary structure prediction program. I have found a good 
> python module for the Nussinov on the web at:
> 
> http://bioinfo.sarang.net/Moin/Nussinov_2epy
> 
> Discovering this has pleased me no end. Has anyone got any idea where i can 
> find a FASTA input python module and how I would interlink it to the 
> nussinov module that i already have? It may need to be spelt out to me as my 
> python expertise is south of poor.
> I have seen some info on python fasta input code at:
> 
>   
> http://www.pasteur.fr/recherche/unites/sis/formation/python/ch02s08.html#ex_readingfasta

This link refers to an *exercise* that was to be done by students
before introducing Biopython. So do not use it as the standard tool: there
are very good modules in Biopython to do this.

> 
> But i have no idea how to go about integrating this with my nussinov module. 
> Any suggestions would be greatly appreciated and will maybe once again give 
> me the luxury of sleep.
> 
> 
> 
>
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Jaeggi, Daniel M. | 3 Mar 2003 10:52
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Re: [BioPython] Updates to Biopython Installation Instructions

This may also be a case of setting up the $PATH environment variable to 
use the correct version of python. (My system has python 1.5 installed 
globally, and a home made python 2.2 in my home directory).

'which python' tells you which python binary is being used. If this 
already shows the path to your python2.2, you should be OK with the 
instructions below (python setup.py install).

Otherwise set PATH in your .bashrc (or whatever shell you use) something 
like:

export PATH=/home/me/Python/bin:$PATH

which puts the locally installed Python path at the start of the search 
path (it will look there first for a python binary).

Hope this helps,

Dan

Brad Chapman wrote:

>Hi Ming;
>Sorry for the slow respose.
>
>  
>
>>Thanks for your Installation Instruction and I am trying to install
>>Biopython following the Instruction. I have no root right and have installed
>>Python2.2 with --prefix option at dir other than /usr/local. But I have
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FR Chalaoux | 3 Mar 2003 11:17
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[BioPython] looking for derwenttogcg or embltogcg program

Hi,

Is there a program in Python to transform derwent
banks to gcg database. Derwent format is a bit
different from embl format. So be carefull if you use
embltogcg to transform it. The 34 first aa are bad in
each sequence ... I suppose it should be possible to
modifie a embltogcg python program if it exists.

FR

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FR Chalaoux | 3 Mar 2003 11:33
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[BioPython] looking for derwenttogcg or embltogcg program

Hi,

Is there a program in Python to transform derwent
banks to gcg database. Derwent format is a bit
different from embl format. So be carefull if you use
embltogcg to transform it. The 34 first aa are bad in
each sequence ... I suppose it should be possible to
modifie a embltogcg python program if it exists.

FR

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Kevin Altis | 6 Mar 2003 06:19

[BioPython] BioPython users in Portland, Oregon?

Hi,
I would be interested in finding out if there are any BioPython users in the
Portland, Oregon area? Please contact me directly, as I'm not normally
subscribed to this mailing list. I'm trying to gather some background
material of uses of open source and in particular Python in the Portland
metro area.

Thanks,

ka
---
Kevin Altis
altis <at> semi-retired.com
http://radio.weblogs.com/0102677/
http://www.pythoncard.org/

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Carlo Bifulco | 6 Mar 2003 17:21
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[BioPython] Parsing problems

Hi folks,

I have been trying to automate the process of designing primers for
cancer specific genomic translocations (my lab is switching from
qualitative to real time pcr), and the because of number of targets
thought of using Biopy. I work with Biopy version 1.10 on W32. I used
CygWin to compile the emboss toolkit.

Here are a few obstacles I encountered so far:

1) I have been working on Ensembl generated genomic sequences saved in
genbank format (e.g.
LOCUS       ENS:ENSG00000151702 118314 bp DNA HTG 6-MAR-2003
DEFINITION  Homo sapiens NCBI31 assembly reannotated via EnsEMBL DNA,
               chromosome 11 130076676..130194989),
but parsing them breaks the parser. A colon in the locus line and
something else in the version and comments lines seems to be the culprit.
Current bypass: wrote a few lines to massage the file before parsing it 
with Biopy (i.e. removing all the breaking spots).

2) I have been unable to compile either or the cvs version under cygwin
(in both cases I get gcc related error messages).
Current bypass: wrote a few python lines to run the
cygwin-emboss eprimer3 utility from pythonW32.
Best solution: running *nix

3) Parsing of the emboss files generated without the -task 1 option had
no problems. However using the -task 1 option (which in addition to the
primers gives and internal oligo, which I need for my assays) broke the
parser.
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Hidayat Trimarsanto | 10 Mar 2003 05:25
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[BioPython] module for reading ABI trace format ?


Greetings,

Sorry if this silly question has came up, but I wonder if biopython has a
module to read ABI trace data format (I can't find it in CVS). Or if it
doesn't have, any ideas whether I could find one ? If there is nothing, 
I'll probably have to write one.

Thanks,

-- anto --

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Yves Bastide | 12 Mar 2003 22:28
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[BioPython] Parsing GenBank and Swiss-Prot with FormatIO

Hi,

A quick, basic question I can't find the answer right now: How to use 
FormatIO?

Thanks,

yves

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Jeffrey Chang | 12 Mar 2003 22:51

Re: [BioPython] Parsing GenBank and Swiss-Prot with FormatIO

Right now, you can use FormatIO to read files into SeqRecord objects 
(although that is extensible).
from Bio import SeqRecord
sequence_iterator = SeqRecord.io.readFile(open("MYSEQUENCEFILE"))
first_seq = sequence_iterator.next()

Currently, Biopython only supports FASTA, SWISS-PROT, Genbank, and EMBL 
formats for MYSEQUENCEFILE.  However, it can technically handle any 
format with a Martel definition under Bio/expressions.  The expressions 
are not as well tested as the standard parsers, so it may not be able 
to handle exceptional records as well.  To read files, do something 
like:

Jeff

On Wednesday, March 12, 2003, at 01:28 PM, Yves Bastide wrote:

> Hi,
>
> A quick, basic question I can't find the answer right now: How to use 
> FormatIO?
>
> Thanks,
>
> yves
>
> _______________________________________________
> BioPython mailing list  -  BioPython <at> biopython.org
> http://biopython.org/mailman/listinfo/biopython
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