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David Martin | 9 Feb 15:36
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[Biopython] Proteomics tools in BioPython

We are planning to develop some proteomics tools in python and have a view to submit them as part of Biopython.
Primarily we will be writing wrappers/parsers for the OpenMS tools/output formats and analytic tools on
top of that. If anyone else is working on python wrappers for openms then I'd be happy to share expertise.

..d

Dr David Martin
College of Life Sciences
University of Dundee

The University of Dundee is a registered Scottish Charity, No: SC015096

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George Devaniranjan | 8 Feb 02:01
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[Biopython] comparing sequences.qustion

Hi,

I have a list of > 200, 000   UNIQUE short EQUAL length sequences.
I do the following

I am comparing ALL sequences against ALL sequences so there will be (200000
* 199999 )/2 comparisons
Once a sequence is compared, if they differ from one another by ONE letter
only . then I do another more detailed alignment using a BLOSUM matrix.

Currently I use the pairwise sequence comparison code found in BIOPYTHON
for both comparison, simple comparison where I set
match = 0
mismatch = -1
If the total alignment score is equal to -1 (meaning only one mismatch)
then I go a further step and do a BLOSUM alignment.

This works but its taking a long long time, I suspect its because I am
using TWO alignments but I think there could be a way to do the first
simple alignment WITHOUT using the pairwise alignment code for the first
part will speed up this calculation.
Unfortunately I don't have much more than a desktop to do this, so if
someone can suggest a quicker way to do this, I would appreciate it.

Thank you,
George
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Obukowicz, Dennis R. | 7 Feb 15:41
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[Biopython] Problems Installing: Can't find modules Seq and Alphabet plus many others

I am new to Biopython and have tried installing Biopython according to instructions. When I run the test
after installing I get  many errors, 96 errors (see below some examples) in all out of 154 test runs. Two
errors that keep popping up are  not being able to find module Seq and module Alphabet.

ImportError: No module named Seq

ImportError: No module named Alphabet

NameError: name 'Seq' is not defined

NameError: name 'record' is not defined

NameError: name 'protein_rec' is not defined

NameError: name 'protein_rec' is not defined

Dennis

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Sarttu Bourvir | 2 Feb 16:45
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[Biopython] parsing Blast results (xml)

Hi,
I am new to biopython and having problems parsing a blast reulst file (xml
format).
I can get out alignments, alignment length, title etc.
But I would additionally need to print the query title , percent
similarity, e-value.

How does one do that?  Is there anywhere else than Biopython cookbook and
help(Bio.Blast.NCBIXML.Record) to
look for information. I feel like I don't really understand the
Blast.Record and where in there things can be found.
Is the sequence query title in the header?

Example code would be greatly appreciated!
Thank you,
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shweta dubey | 31 Jan 08:00
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[Biopython] regarding retrieving antigen information of specific gene using Biopython

hello everyone,

I am new to Biopython.I have a set of genes and i want information of
antigens specific to these genes from a database(suppose, Antigen
Database).

How can i do the same using Biopython??

Thanks in advance

Shweta Dubey
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Kristian Ullrich | 30 Jan 11:09
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[Biopython] (no subject)

Hello Biopython Team,

I am going to work with biological networks, next to the great tool cytoscape I want to create networks out of
python. To my knowledge there exists pygraphviz and networkx which can produce gml and dot output files.
Cytoscape uses the XGMML Language (http://www.cs.rpi.edu/research/groups/pb/punin/public_html/XGMML/).

Is there an easy way of how to use or manipulate existing python xml parsers to work with xgmml files or are
there plans of the Biopython Team to write an XGMML - parser?

Since a lot of biologist work with cytoscape this would be a very useful tool to build graphical netowrks.

Thank you in anticipation

Kristian Ullrich
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Sarttu Bourvir | 25 Jan 17:14
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[Biopython] Fwd: BlastParsing gives Value Error: Invalid header?

Hi,
I am new to both python and biopython.
What I'm trying to do is to parse a blast result xml file (myblast.xml),
attached here.

The code looks like this:

#!/usr/bin/env python
import sys
import re
import Bio
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Blast import NCBIStandalone

infile = raw_input ("which file:")
result_handle = open(infile,'r')
blast_parser = NCBIStandalone.BlastParser()
blast_iterator = NCBIStandalone.Iterator(result_handle, blast_parser)
blast_record = blast_iterator.next()
for blast_record in blast_iterator:
   E_VALUE_THRESH = 0.01
   for alignment in blast_records.alignments:
       for hsp in alignment.hsps:
           if hsp.expect < E_VALUE_THRESH:
               print '****Alignment****'
               print 'sequence', alignment.title
               print 'alignment length', alignment.length
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Dilara Ally | 19 Jan 01:10
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[Biopython] SNP id

Hi All

I was wondering if anyone on this listserv had any recommendation 
regarding coverage for the identification of SNPs from SOLiD or Illumina 
data?  What is the acceptable coverage amount these days?

Thanks!

Dilara
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Michael Thon | 18 Jan 11:14
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[Biopython] Is this a valid genbank record?

Does anyone know if these GenBank records are valid:

http://www.ncbi.nlm.nih.gov/protein/323463153
http://www.ncbi.nlm.nih.gov/protein/93279336

...because biopython raised an exception when trying to parse them.  They have weird feature locations:

     Het             join(bond(127),bond(127),bond(130),bond(130),bond(138),
                     bond(138),bond(139),bond(138))

thanks
Mike

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Mariam Reyad Rizkallah | 17 Jan 20:43
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[Biopython] Installation on Ubuntu 11.10 64-bit (Loader.py:799)

Dear Biopython community,

I am installing Biopython v. 1.58 and BioSQL 1.0.1 on Ubuntu 11.10 64-bit
virtual machine (Python 2.7.2+). When I run tests, I face this warning.

test_BioSQL ...
> ~/biopython-1.58/build/lib.linux-i686-2.7/BioSQL/Loader.py:799:
> UserWarning: order location operators are not fully supported
>   % feature.location_operator)
> ok
> test_BioSQL_SeqIO ...
> ~/biopython-1.58/build/lib.linux-i686-2.7/BioSQL/Loader.py:799:
> UserWarning: bond location operators are not fully supported
>   % feature.location_operator)

ok

Is it related to the platform (64-bit)?

Thank you.

Mariam
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Mic | 16 Jan 14:01
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[Biopython] compare sequences

Hello,
Is there anyway a memory efficient way to  compare  sequences like from NGS?

Thank you in advance.
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Gmane