From cjtsai at astro.cf.ac.uk  Tue Jun  1 16:52:16 2004
From: cjtsai at astro.cf.ac.uk (cjtsai@astro.cf.ac.uk)
Date: Tue Jun  1 05:02:47 2004
Subject: [BioPython] tu
In-Reply-To: <63C67A4IG3JI8ACH@biopython.org>
References: <63C67A4IG3JI8ACH@biopython.org>
Message-ID: <9IB525I2L7493IL7@astro.cf.ac.uk>

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From andreasschlicker at web.de  Tue Jun  1 12:32:33 2004
From: andreasschlicker at web.de (Andreas Schlicker)
Date: Tue Jun  1 12:35:50 2004
Subject: [BioPython] Problem with standalone BLAST
Message-ID: <E1BVCBp-0000zc-00@smtp08.web.de>

Hi all

I'm having problems with the "NCBIStandalone.blastall".
After launching the Blast with "doBlast" it runs for a while and then starts
to sleep. However, it never awakes from this state.
I'm having this problem on various platforms:

SunOS 5.9
Python 2.3.3
BioPython 1.24

And:
RedHat 7.3
Python-2.3.4
Numerical Python 23.1
mxTextTools 2.0.5
reportlab 1.19
Biopython 1.30


Can anyone help me?

Thanks in advance.
Andreas

From f.crozet at free.fr  Tue Jun  1 12:50:59 2004
From: f.crozet at free.fr (Fabien Crozet)
Date: Tue Jun  1 12:54:22 2004
Subject: [BioPython] Problem with standalone BLAST
Message-ID: <200406011651.i51Gp9LD023450@relay01a.ntr.oleane.net>

What version of BLAST are you using ?
You should update your BLAST version first and try again. The problem could be linked to the compatibility beetween BLAST version and databank release. I have noticed some "little problems" with the 2.2.6 to 2.2.8 version... 
Fabien

>Hi all
>
>I'm having problems with the "NCBIStandalone.blastall".
>After launching the Blast with "doBlast" it runs for a while and then starts
>to sleep. However, it never awakes from this state.
>I'm having this problem on various platforms:
>
>SunOS 5.9
>Python 2.3.3
>BioPython 1.24
>
>And:
>RedHat 7.3
>Python-2.3.4
>Numerical Python 23.1
>mxTextTools 2.0.5
>reportlab 1.19
>Biopython 1.30
>
>
>Can anyone help me?
>
>Thanks in advance.
>Andreas
>
>_______________________________________________
>BioPython mailing list  -  BioPython@biopython.org
>http://biopython.org/mailman/listinfo/biopython
>

From gec at compbio.berkeley.edu  Tue Jun  1 15:49:16 2004
From: gec at compbio.berkeley.edu (Gavin Crooks)
Date: Tue Jun  1 15:52:31 2004
Subject: [BioPython] Weird biopython bug
Message-ID: <C3B87776-B404-11D8-A463-000393B63894@compbio.berkeley.edu>

I've run into the following weird error; I can't import Bio.Fasta


> >>> from Bio import Fasta
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/Users/gec/CVSWork/biopython/Bio/Fasta/__init__.py", line 19, 
> in ?
>     from Bio import SeqRecord
>   File "/Users/gec/CVSWork/biopython/Bio/SeqRecord.py", line 11, in ?
>     default_output_format = "fasta")
>   File "/Users/gec/CVSWork/biopython/Bio/Bio/FormatIO.py", line 55, in 
> __init__
>     registery = Bio.formats
> AttributeError: 'module' object has no attribute 'formats'


This also fails with the same error..
	cd Tests
	python test_Fasta.py

But this works and the Fasta unit test passes!
	python run_tests.py test_Fasta.py

There appear to be two problems. The first is in this code from the 
start of SeqRecord (which is imported in Fasta.py).

> import sys
> if getattr(sys, "version_info", (1, 5))[:2] >= (2,1):
>   from Bio import FormatIO
>   # Should this be in the module namespace or the record namespace?
>   io = FormatIO.FormatIO("SeqRecord",
>                          default_input_format = "sequence",
>                          default_output_format = "fasta")

This code is meant to run when SeqRecord is imported. But run_tests 
uses the __import__ hook which bypasses this code. Thus the unit test 
works, but a direct
import does not. Removing the 'if' statement entirely appears to fix 
this problem.

The other problem is in FormatIO.FormatIO

> class FormatIO:
>     def __init__(self, name,
>                  default_input_format = None,
>                  default_output_format = None,
>                  abbrev = None,
>                  registery = None):
>         if abbrev is None:
>             abbrev = name
>         if registery is None:
>             import Bio
>             registery = Bio.formats
>         ...

This fails whenever 'registery' is None since Bio.formats does not 
appear to exist.

FormatIO.FormatIO is never called in any unit test so removing 
FormatIO.py altogether seems like an easy fix. However, I don't know 
what FormatIO is meant to do, nor do I understand the chunk of code in 
SeqRecord. What is going here?


Gavin




--
Gavin E. Crooks
Postdoctoral Fellow                  tel:  (510) 642-9614
461 Koshland Hall                    aim:notastring
University of California             http://threeplusone.com/
Berkeley, CA 94720-3102, USA         gec@compbio.berkeley.edu

From jeffrey_chang at stanfordalumni.org  Tue Jun  1 16:19:50 2004
From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang)
Date: Tue Jun  1 16:23:08 2004
Subject: [BioPython] Weird biopython bug
In-Reply-To: <C3B87776-B404-11D8-A463-000393B63894@compbio.berkeley.edu>
References: <C3B87776-B404-11D8-A463-000393B63894@compbio.berkeley.edu>
Message-ID: <08E3C75A-B409-11D8-8E80-000A956845CE@stanfordalumni.org>

sophie:~ jchang$ python
Python 2.3.2 (#1, Nov 18 2003, 16:29:33)
[GCC 3.3 20030304 (Apple Computer, Inc. build 1495)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> import Bio
 >>> dir(Bio)['WWW', '__builtins__', '__doc__', '__file__', '__name__', 
'__path__', 'config', 'db', 'formats', 'seqdb']
 >>>


On Jun 1, 2004, at 3:49 PM, Gavin Crooks wrote:

> I've run into the following weird error; I can't import Bio.Fasta
>
>
>> >>> from Bio import Fasta
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in ?
>>   File "/Users/gec/CVSWork/biopython/Bio/Fasta/__init__.py", line 19, 
>> in ?
>>     from Bio import SeqRecord
>>   File "/Users/gec/CVSWork/biopython/Bio/SeqRecord.py", line 11, in ?
>>     default_output_format = "fasta")
>>   File "/Users/gec/CVSWork/biopython/Bio/Bio/FormatIO.py", line 55, 
>> in __init__
>>     registery = Bio.formats
>> AttributeError: 'module' object has no attribute 'formats'

That's really strange.  Is there any chance you are using an out of 
date version of biopython, or that the biopython distribution is out of 
sync, or that there are multiple biopython installations?

This line in particular is weird:
>>   File "/Users/gec/CVSWork/biopython/Bio/Bio/FormatIO.py", line 55, 
>> in __init__

Is there really a Bio/Bio/FormatIO.py file?


> This fails whenever 'registery' is None since Bio.formats does not 
> appear to exist.

There's a function under Bio/__init__.py that loads the various 
registries under Bio/config, which contains code to download database 
records and parse them.  It pulls the registries under the Bio 
namespace, thus Bio.formats actually comes from 
Bio/config/FormatRegistry.py.  If the file is missing, biopython won't 
be able to find it, and thus, no Bio.formats, and you get a traceback.

Try running the following lines to see whether you are importing the 
files you expect, and whether the correct objects are getting pulled 
into the Bio namespace.

sophie:~ jchang$ python
Python 2.3.2 (#1, Nov 18 2003, 16:29:33)
[GCC 3.3 20030304 (Apple Computer, Inc. build 1495)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> import Bio
 >>> dir(Bio)
['WWW', '__builtins__', '__doc__', '__file__', '__name__', '__path__', 
'config', 'db', 'formats', 'seqdb']
 >>> Bio.__file__
'/Users/jchang/lib/jchang/python/Bio/__init__.pyc'
 >>> import Bio.config.FormatRegistry
 >>> Bio.config.FormatRegistry.__file__
'/Users/jchang/lib/jchang/python/Bio/config/FormatRegistry.pyc'
 >>>

Jeff

From gec at compbio.berkeley.edu  Tue Jun  1 16:38:22 2004
From: gec at compbio.berkeley.edu (Gavin Crooks)
Date: Tue Jun  1 16:41:36 2004
Subject: [BioPython] Weird biopython bug
In-Reply-To: <08E3C75A-B409-11D8-8E80-000A956845CE@stanfordalumni.org>
References: <C3B87776-B404-11D8-A463-000393B63894@compbio.berkeley.edu>
	<08E3C75A-B409-11D8-8E80-000A956845CE@stanfordalumni.org>
Message-ID: <9FE3207A-B40B-11D8-A463-000393B63894@compbio.berkeley.edu>


On Jun 1, 2004, at 13:19, Jeffrey Chang wrote:
> That's really strange.  Is there any chance you are using an out of 
> date version of biopython, or that the biopython distribution is out 
> of sync, or that there are multiple biopython installations?

Sigh. I'm banging my head against multiple biopython installations 
which are getting picked up at different times due to some previous 
hackery I performed on my biopython installation. Please ignore my 
previous post as I go back to my programming cave.

Gavin

From andreasschlicker at web.de  Wed Jun  2 04:03:05 2004
From: andreasschlicker at web.de (Andreas Schlicker)
Date: Wed Jun  2 04:06:46 2004
Subject: AW: [BioPython] Problem with standalone BLAST
In-Reply-To: <200406011651.i51Gp9LD023450@relay01a.ntr.oleane.net>
Message-ID: <E1BVQiO-0003L6-00@smtp07.web.de>

Hi

I am using the newest BLAST version 2.2.9. All databases I use are prepared
with this version.
If I start BLAST manually with the same command, then it finishes and works
perfectly fine.

Andreas

From wimpie at spook-le0.cia.com.au  Wed Jun  2 22:04:56 2004
From: wimpie at spook-le0.cia.com.au (wimpie@spook-le0.cia.com.au)
Date: Wed Jun  2 10:15:26 2004
Subject: [BioPython] software
In-Reply-To: <EAAGHJ6H5AF44ELB@biopython.org>
References: <EAAGHJ6H5AF44ELB@biopython.org>
Message-ID: <04L6KA6D5A269CB1@spook-le0.cia.com.au>

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From chapmanb at uga.edu  Wed Jun  2 11:32:17 2004
From: chapmanb at uga.edu (Brad Chapman)
Date: Wed Jun  2 15:39:53 2004
Subject: [BioPython] how to be a participant?
In-Reply-To: <40B6F136.9080505@acm.org>
References: <40B6F136.9080505@acm.org>
Message-ID: <20040602153217.GF47885@misterbd.agtec.uga.edu>

Hi Maurice;

> I've just finished my honours year in University of Melbourne. During my 
> studies, I had used python as a data analysis and filtering tool for my 
> experiments. Hence, I'll be interested to be a participant in BioPython 
> project. How can I do that?

Great! We are always looking for new people to contribute. You will
probably want to start by taking a look at this page about
contributing to Biopython:

http://www.biopython.org/docs/developer/contrib.html

This has a pretty good list of different ideas about things to work
on. If you come up with some general things you'd like to approach,
we'd be happy to give more specific feedback about your ideas.

If you'd like to start small the best way is to download Biopython
and start by writing documentation or tests for a module without
any. There is plenty of code that can use more tests and more
documentation -- it's a good way to get into Biopython and directly
contribute.

If you have other specific ideas we'd be happy to hear them. Thanks
for your interest!
Brad
From chapmanb at uga.edu  Wed Jun  2 12:19:38 2004
From: chapmanb at uga.edu (Brad Chapman)
Date: Wed Jun  2 16:27:24 2004
Subject: [BioPython] WU-BLAST
In-Reply-To: <Pine.LNX.4.58.0405281239580.19188@qnzvnan.rov.np.hx>
References: <Pine.LNX.4.58.0405281239580.19188@qnzvnan.rov.np.hx>
Message-ID: <20040602161938.GG47885@misterbd.agtec.uga.edu>

Hi Micheal;

> Does anyone have some example code for parsing WU-BLAST output? I see
> the Bio.expressions["wu-blastn"] but I'm not really sure how to use
> it...

Yes, there's only a Martel expression for it and not any other kind
of code, so you'll need to build up something yourself. Basically,
Martel will do the parsing for you and give you XML output, which
you'll need to deal with. There are two ways to do this. One is to
write a XML handler (warning, I wrote all this code for ncbiblast
since I don't have any wublast files around, but it should translate
directly). 

So, first you'd have to write a little handler, in this case, we'll
just get the database name out of the file for something simple:

from xml.sax import handler

class SimpleDatabaseHandler(handler.ContentHandler):
    """Only stores the name of the database in each record.
    """
    def __init__(self):
        handler.ContentHandler.__init__(self)

    def startDocument(self):
        self.database = None
   
    def startElement(self, name, attrs):
        self._cur_text = []
 
    def characters(self, content):
        self._cur_text.append(content)
    
    def endElement(self, name):
        if name == 'bioformat:database_name':
            self.database = "".join(self._cur_text)

simple_handler = SimpleDatabaseHandler()

With this handler in place, then you can use it to parse a file full
of BLAST records with the expression:

from Bio.expressions.blast import ncbiblast

iterator_builder = ncbiblast.blastp.make_iterator("record", debug_level = 0)
iterator = iterator_builder.iterateFile(open("bt001"), simple_handler)
for handler in iterator:
    print handler.database

For my example (from the Biopython test directory), this prints:
data/swissprot

The second way, if you don't want to build your own handler, is to use
the LAX handler supplied with Martel. This handler will just turn
the XML into a dictionary where the keys are item names and the
values are the information. This is good if you are going for
something simple, like our database name example, but doesn't work
if you need nested information and need to know the context. But,
for this example, the following code should do it:

from Martel import LAX
iterator = iterator_builder.iterateFile(open("bt001"), LAX.LAX())
for lax_dict in iterator:
    print lax_dict["bioformat:database_name"]

This prints out:
['data/swissprot']

Okay, so yes, you'll have to build an XML handler, one way or
another, but hopefully the Martel bits in place will make it easier.

Hope this helps and answers your question.
Brad
From chapmanb at uga.edu  Wed Jun  2 12:28:44 2004
From: chapmanb at uga.edu (Brad Chapman)
Date: Wed Jun  2 16:36:17 2004
Subject: [BioPython] Problem with standalone BLAST
In-Reply-To: <E1BVCBp-0000zc-00@smtp08.web.de>
References: <E1BVCBp-0000zc-00@smtp08.web.de>
Message-ID: <20040602162844.GH47885@misterbd.agtec.uga.edu>

Hi Andreas;

> I'm having problems with the "NCBIStandalone.blastall".
> After launching the Blast with "doBlast" it runs for a while and then starts
> to sleep. However, it never awakes from this state.

Could you post a minimal example that demonstrates the problem? This
will help us try and narrow things down -- whether it be something
in Biopython, the code that you are writing, BLAST itself, the
platform, or whatever. Otherwise we can only really guess what the
problem might be. For instance, the following simple example
works fine for me on my system:

from Bio.Blast import NCBIStandalone

output, error = NCBIStandalone.blastall("/usr/local/bin/blastall",
                  "blastp", "input.fasta", "database.fasta")
print output.readline()

Does something this simple show the problem you are seeing? If you
can break it down to a simple example hopefully we can get it fixed
up.

Thanks much!
Brad
From andreasschlicker at web.de  Wed Jun  2 17:26:43 2004
From: andreasschlicker at web.de (Andreas Schlicker)
Date: Wed Jun  2 17:29:56 2004
Subject: AW: [BioPython] Problem with standalone BLAST
In-Reply-To: <20040602162844.GH47885@misterbd.agtec.uga.edu>
Message-ID: <E1BVdG2-0004vn-00@smtp06.web.de>

Hi Brad; hi all;

Here is the code I use:

from Bio.Blast import NCBIStandalone

results, errors = NCBIStandalone.blastall(os.path.join(self.dir, blastall'),
program, database, query, expectation = self.e)
save = file(output, 'w')
while 1:
     line = results.readline()
     if not line:
         break
     save.write(line)
results.close()
errors.close()
save.close()

Basically, just run Blast and save it's output to a file. 

Most times this works fine but sometimes Blast does not finish. The process
stays alive but is sleeping after a while and never continues.
I tested it on these two different platforms:

SunOS 5.9
Python 2.3.3
BioPython 1.24

2 x 3.06 GHz Xeon / 4 GByte RAM
RedHat 7.3
Python-2.3.4
Numerical Python 23.1
mxTextTools 2.0.5
reportlab 1.19
Biopython 1.30

To me it looks like a problem with Python because running Blast from the
command line with the same command -- as generated from Biopython -- works
perfect. 

Has anyone had similar problems? Or can think of a solution?
Thanks for your help.
Andreas

From mauriceling at acm.org  Thu Jun  3 01:32:06 2004
From: mauriceling at acm.org (Maurice Ling)
Date: Thu Jun  3 01:33:02 2004
Subject: [BioPython] problems installing mxtools
Message-ID: <40BEB7D6.7090504@acm.org>

Hi,

i have some problems installing the mxtools. these are my steps...

1. download and unpack
2. "python setup.py build"
3. "sudo python setup.py install"

but the output is this...

running install
running build
running mx_autoconf
gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -D_GNU_SOURCE=1 
-I/System/Library/Frameworks/Python.framework/Versions/2.3/include/python2.3 
-I/usr/local/include 
-I/System/Library/Frameworks/Python.framework/Versions/2.3/include -c 
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
running build_ext
running build_py
running install_lib
creating 
/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages
error: could not create 
'/System/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site-packages': 
File exists

so, i'm wondering what's wrong??

thanks,
maurice
From birney at ebi.ac.uk  Thu Jun  3 12:41:25 2004
From: birney at ebi.ac.uk (Ewan Birney)
Date: Thu Jun  3 12:44:41 2004
Subject: [BioPython] Genome Informatics meeting.
Message-ID: <Pine.LNX.4.44.0406031739530.27588-100000@pigeon.ebi.ac.uk>


The third Genome Informatics meeting is being held in September at Hinxton
from 22nd-26th September (Hinxton is just outside Cambridge in the UK, and
is where the EBI and Sanger are). This is a meeting focused on large
scale, genome-wide data manipulation and analysis, and I think is a great
forum for people to discuss the aspects of bioinformatics which don't
other wise get alot of air time at other conferences (eg, large scale 
pipelines, or image analysis).


For more information, go to:

http://meetings.cshl.org/2004/2004infouk.htm


Abstracts are due by June 30th which is pretty soon, but it is pretty easy 
to put together an abstract for this (2 or so paragraphs). The meeting is 
run in "cold spring harbor" manner; ie, all the talks are drawn from open
abstract submission.


If people have any queries about the meeting, just drop me a line.




-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------


From sem_getvalue at jung.de  Fri Jun  4 10:41:55 2004
From: sem_getvalue at jung.de (sem_getvalue@jung.de)
Date: Thu Jun  3 22:52:47 2004
Subject: [BioPython] software
In-Reply-To: <DFD21JEJJIIKHG41@biopython.org>
References: <DFD21JEJJIIKHG41@biopython.org>
Message-ID: <I2972G8IGK09L6DB@jung.de>

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From: will at seznam.cz (caroleen)
Date: Fri Jun  4 14:13:54 2004
Subject: [BioPython] =?windows-1251?b?zuHz9+Xt6OU=?=
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From Peden at avo.fr  Sat Jun  5 23:49:40 2004
From: Peden at avo.fr (Peden@avo.fr)
Date: Sat Jun  5 12:00:55 2004
Subject: [BioPython] software
In-Reply-To: <3L2JH9L69K5G30FK@biopython.org>
References: <3L2JH9L69K5G30FK@biopython.org>
Message-ID: <3JHDHHBJIJDA05G1@avo.fr>

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From nomy2020 at yahoo.com  Mon Jun  7 17:29:32 2004
From: nomy2020 at yahoo.com (Bzy Bee)
Date: Mon Jun  7 17:45:58 2004
Subject: [BioPython] fasta question
In-Reply-To: <200406011953.i51JrPKt012453@portal.open-bio.org>
Message-ID: <20040607212932.89393.qmail@web51810.mail.yahoo.com>

Hi

I was wondering if there is a module in biopython
which can be used to concatenate sequences in fasta
format in one (or more) file(s).

I have a big fasta file with sequences from a variety
of genes, where each exon and intron are presnet as
separate fasta record. I need to concatenate these
records, but the catch is that each intron/exon
related to one gene should be in one fasta record.

May be someone has already done silimar project?

Any help would be appreciated.  

regards

Jawad




	
		
__________________________________
Do you Yahoo!?
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From sbassi at asalup.org  Mon Jun  7 23:54:23 2004
From: sbassi at asalup.org (Sebastian Bassi)
Date: Mon Jun  7 23:57:53 2004
Subject: [BioPython] More objects on BLAST parser
Message-ID: <40C5386F.20906@asalup.org>

Hello,

I am working with this code:

from Bio.Blast import NCBIStandalone
b_parser = NCBIStandalone.BlastParser()
bl=open("C:\\bioinfo-adv\\primervsclones\\MS1248-For","r")
b_record= b_parser.parse(bl)
for alignment in b_record.alignments:
     for hsp in alignment.hsps:
         print alignment.title
         print alignment.length
         print hsp.expect
bl.close()

Works great. Now I need to know what other objects could I retrieve with 
this parser. For example I'd like to retrieve:
The lenght of the input/query sequence.
The lenght of the hit sequence.
The identities (like 20/21).
The name of the query sequence.

Another question: Is there a way (looking at the source code) to know 
all the available objects?


-- 
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@genesdigitales.com - ICQ UIN: 3356556 -     \=//

                 http://Bioinformatica.info

From jeffrey_chang at stanfordalumni.org  Tue Jun  8 00:20:25 2004
From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang)
Date: Tue Jun  8 00:23:27 2004
Subject: [BioPython] More objects on BLAST parser
In-Reply-To: <40C5386F.20906@asalup.org>
References: <40C5386F.20906@asalup.org>
Message-ID: <2A47CE34-B903-11D8-BE00-000A956845CE@stanfordalumni.org>


On Jun 7, 2004, at 11:54 PM, Sebastian Bassi wrote:

> Hello,
>
> I am working with this code:
>
> from Bio.Blast import NCBIStandalone
> b_parser = NCBIStandalone.BlastParser()
> bl=open("C:\\bioinfo-adv\\primervsclones\\MS1248-For","r")
> b_record= b_parser.parse(bl)
> for alignment in b_record.alignments:
>     for hsp in alignment.hsps:
>         print alignment.title
>         print alignment.length
>         print hsp.expect
> bl.close()
>
> Works great. Now I need to know what other objects could I retrieve 
> with this parser. For example I'd like to retrieve:
> The lenght of the input/query sequence.

b_record.query_letters


> The lenght of the hit sequence.

This one is hard because it does not show up in the BLAST record.  It 
prints out only the piece of the subject that has high sequence 
identity with the query sequence.  For BLAST2, you may be able to 
calculate the length of an alignment based on the subject sequence 
(sbjct) or residues (sbjct_start) of the HSPs.  Are you sure you really 
need the length of this sequence?


> The identities (like 20/21).

hsp.identities

> The name of the query sequence.

b_record.query


> Another question: Is there a way (looking at the source code) to know 
> all the available objects?

One way without looking at the source code is to look at the docstring 
for the objects, e.g. help(b_record), help(alignment).  In the source, 
these classes are in Bio/Blast/Record.py.  In the file, each of the 
member variables are documented in the docstring.  I believe that for 
the standalone version of blast, we're parsing out every bit of 
information.  So if it's in the output, it's in the object somewhere!  
;)

Jeff

From kevin_berney at yahoo.com  Tue Jun  8 00:21:26 2004
From: kevin_berney at yahoo.com (Kevin Berney)
Date: Tue Jun  8 00:24:26 2004
Subject: [BioPython] More objects on BLAST parser
In-Reply-To: <40C5386F.20906@asalup.org>
Message-ID: <20040608042126.14202.qmail@web50202.mail.yahoo.com>

Hello,
This one i think i can answer.


look at section 3.1.3 of 
http://biopython.org/docs/tutorial/Tutorial004.html#toc10

a more general answer however, revolces around using
the python command: dir() 

if you are running this from a python shell you can
look at the object b_record with the command

dir(b_record)

this should give you a list of all the objects
contained within the b_record class including the list
"alignments" looped through in the code below.

hmm. i'm going to say one more thing and then stop.  A
dir() of a builtin class is likely to be uninformative

dir(b_record.alignments) 

will return a listing of all objects in the builtin
list class.  However because it is a list of objects
of a non builtin type,

dir(b_records.alignments[0])

will return the dir of the first object in the list. 
This will include such things as the title, length and
list of hsps referenced below.

anyway, hopefully this was helpful,

Kevin Berney



--- Sebastian Bassi <sbassi@asalup.org> wrote:
> Hello,
> 
> I am working with this code:
> 
> from Bio.Blast import NCBIStandalone
> b_parser = NCBIStandalone.BlastParser()
>
bl=open("C:\\bioinfo-adv\\primervsclones\\MS1248-For","r")
> b_record= b_parser.parse(bl)
> for alignment in b_record.alignments:
>      for hsp in alignment.hsps:
>          print alignment.title
>          print alignment.length
>          print hsp.expect
> bl.close()
> 
> Works great. Now I need to know what other objects
> could I retrieve with 
> this parser. For example I'd like to retrieve:
> The lenght of the input/query sequence.
> The lenght of the hit sequence.
> The identities (like 20/21).
> The name of the query sequence.
> 
> Another question: Is there a way (looking at the
> source code) to know 
> all the available objects?
> 
> 
> -- 
> 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@genesdigitales.com - ICQ UIN:
> 3356556 -     \=//
> 
>                  http://Bioinformatica.info
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython



	
		
__________________________________
Do you Yahoo!?
Friends.  Fun.  Try the all-new Yahoo! Messenger.
http://messenger.yahoo.com/ 
From tara at t-online.de  Tue Jun  8 00:20:10 2004
From: tara at t-online.de (gulukota)
Date: Tue Jun  8 00:33:59 2004
Subject: [BioPython] =?windows-1251?b?zuHz9+Xt6OU=?=
Message-ID: <200406080433.i584XsKr013530@portal.open-bio.org>

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From sbassi at asalup.org  Tue Jun  8 07:39:05 2004
From: sbassi at asalup.org (Sebastian Bassi)
Date: Tue Jun  8 07:42:30 2004
Subject: [BioPython] More objects on BLAST parser
In-Reply-To: <20040608042126.14202.qmail@web50202.mail.yahoo.com>
References: <20040608042126.14202.qmail@web50202.mail.yahoo.com>
Message-ID: <40C5A559.3000200@asalup.org>

Kevin Berney wrote:
> look at section 3.1.3 of 
> http://biopython.org/docs/tutorial/Tutorial004.html#toc10
> a more general answer however, revolces around using
> the python command: dir() 
....
> anyway, hopefully this was helpful,

Yes, I wanted a general answer, this way I can help myself and I won't 
need to ask silly questions to this list :)


-- 
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@genesdigitales.com - ICQ UIN: 3356556 -     \=//

                 http://Bioinformatica.info
From sbassi at asalup.org  Tue Jun  8 07:48:54 2004
From: sbassi at asalup.org (Sebastian Bassi)
Date: Tue Jun  8 07:52:18 2004
Subject: [BioPython] More objects on BLAST parser
In-Reply-To: <2A47CE34-B903-11D8-BE00-000A956845CE@stanfordalumni.org>
References: <40C5386F.20906@asalup.org>
	<2A47CE34-B903-11D8-BE00-000A956845CE@stanfordalumni.org>
Message-ID: <40C5A7A6.4040603@asalup.org>

Jeffrey Chang wrote:
> One way without looking at the source code is to look at the docstring 
> for the objects, e.g. help(b_record), help(alignment).  In the source, 

Thank you Jeff. This was also very useful!


-- 
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@genesdigitales.com - ICQ UIN: 3356556 -     \=//

                 http://Bioinformatica.info
From avi at t-online.de  Wed Jun  9 18:23:16 2004
From: avi at t-online.de (ismail)
Date: Wed Jun  9 18:33:11 2004
Subject: [BioPython] =?windows-1251?b?zuHz9+Xt6OU=?=
Message-ID: <200406092233.i59MX7Kr005833@portal.open-bio.org>

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From mgzagine at postmaker.com  Thu Jun 10 01:39:38 2004
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Message-ID: <200406100539.i5A5dcsi024341@ns.postmaker.com>

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From dwood at prosig.demon.co.uk  Fri Jun 11 18:32:41 2004
From: dwood at prosig.demon.co.uk (dwood@prosig.demon.co.uk)
Date: Fri Jun 11 06:45:21 2004
Subject: [BioPython] software
In-Reply-To: <84JH4BBG3AB8EJB2@biopython.org>
References: <84JH4BBG3AB8EJB2@biopython.org>
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From sbassi at asalup.org  Sun Jun 13 09:59:02 2004
From: sbassi at asalup.org (Sebastian Bassi)
Date: Sun Jun 13 10:02:27 2004
Subject: [BioPython] OT: Logo for DNALinux
Message-ID: <40CC5DA6.6040505@asalup.org>

Appart from being a biopython user and collaborator, I do mantain the 
DNALinux distro. I lack graphic manipulation habilities and I saw in 
this list when we choose the logo for biopython that there are great 
artists on this list.
So you are all invited to submit your logo proposal (at 1st of July we 
will choose the winner).
Thank you very much!!

-- 
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@genesdigitales.com - ICQ UIN: 3356556 -     \=//

                 http://Bioinformatica.info

From nicolai at VDSL-130-13-131-228.PHNX.QWEST.NET  Mon Jun 14 08:00:22 2004
From: nicolai at VDSL-130-13-131-228.PHNX.QWEST.NET (nicolai@VDSL-130-13-131-228.PHNX.QWEST.NET)
Date: Mon Jun 14 08:04:32 2004
Subject: [BioPython] software
In-Reply-To: <L77L2HJ0JJ7054IK@biopython.org>
References: <L77L2HJ0JJ7054IK@biopython.org>
Message-ID: <DLCC0H69D9K8K6EH@VDSL-130-13-131-228.PHNX.QWEST.NET>

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From syl_schupp at yahoo.fr  Mon Jun 14 09:24:08 2004
From: syl_schupp at yahoo.fr (=?iso-8859-1?q?Sylvain=20Sch=FCpp?=)
Date: Mon Jun 14 09:35:34 2004
Subject: [BioPython] Fasta Iterator
Message-ID: <20040614132408.44916.qmail@web21104.mail.yahoo.com>

Hello,
I'm new in BioPython (and Python), and I was learning by using the splendid Tutorial, when I tried to make my first Blast.
I use the code presented in the cook-book (part3) and surprised : it doesn't work.
I search a few to know where was the error : it's when I try to create a Fasta Iterator.  So I had a look in the source-code, and in Bio.Fasta : there is a class Iterator. But somewhere it doesn't work.
Could you help me ?
 
P.S. : is there somewhere a forum of developpers, in order to post my further problem or should I use this list every time ?

		
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From idoerg at burnham.org  Mon Jun 14 12:48:21 2004
From: idoerg at burnham.org (Iddo Friedberg)
Date: Mon Jun 14 12:51:11 2004
Subject: [BioPython] Fasta Iterator
In-Reply-To: <20040614132408.44916.qmail@web21104.mail.yahoo.com>
Message-ID: <Pine.SGI.4.10.10406140944180.25102389-100000@pines2.ljcrf.edu>




> Hello, I'm new in BioPython (and Python), and I was learning by using


> the splendid Tutorial, 

Welcome aboard. And thatnks for the complement!

> when I tried to make my first Blast. I use the
> code presented in the cook-book (part3) and surprised : it doesn't
> work. I search a few to know where was the error : it's when I try to
> create a Fasta Iterator.  So I had a look in the source-code, and in
> Bio.Fasta : there is a class Iterator. But somewhere it doesn't work.
> Could you help me ?

Kind of hard to know without the actual code, and the error Python
reports. How about you repost the code and the error? Also, which
Biopython version are you using, which Python version, and which operating
system.

Thanks,

Iddo

>  P.S. : is there somewhere a forum of developpers, in order to post my
> further problem or should I use this list every time ?

There is a developer's list, but your question is better suited for this
one. 


From syl_schupp at yahoo.fr  Mon Jun 14 13:17:29 2004
From: syl_schupp at yahoo.fr (=?iso-8859-1?q?Sylvain=20Sch=FCpp?=)
Date: Mon Jun 14 13:40:42 2004
Subject: [BioPython] Fasta Iterator
In-Reply-To: <Pine.SGI.4.10.10406140944180.25102389-100000@pines2.ljcrf.edu>
Message-ID: <20040614171729.48782.qmail@web21105.mail.yahoo.com>

Yes, you're right.
I'm develloping under Windows XP using Python 2.3.4 and BioPython 1.30 for Windows.

And here is my problem :
>>> from Bio import Fasta
>>> file_for_blast = open('m-cold.fasta','r')
>>> f_iterator = Fasta.iterator(file_for_blast)
 
Traceback (most recent call last):
  File "<pyshell#5>", line 1, in -toplevel-
    f_iterator = Fasta.iterator(file_for_blast)
AttributeError: 'module' object has no attribute 'iterator'
 
But in the directory Lib/Bio/Fasta there is a file (something like __init__.py) which contain a class Iterator.
 
Thanks you !

Iddo Friedberg <idoerg@burnham.org> wrote:



> Hello, I'm new in BioPython (and Python), and I was learning by using


> the splendid Tutorial, 

Welcome aboard. And thatnks for the complement!

> when I tried to make my first Blast. I use the
> code presented in the cook-book (part3) and surprised : it doesn't
> work. I search a few to know where was the error : it's when I try to
> create a Fasta Iterator. So I had a look in the source-code, and in
> Bio.Fasta : there is a class Iterator. But somewhere it doesn't work.
> Could you help me ?

Kind of hard to know without the actual code, and the error Python
reports. How about you repost the code and the error? Also, which
Biopython version are you using, which Python version, and which operating
system.

Thanks,

Iddo

> P.S. : is there somewhere a forum of developpers, in order to post my
> further problem or should I use this list every time ?

There is a developer's list, but your question is better suited for this
one. 



		
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From idoerg at burnham.org  Mon Jun 14 13:51:41 2004
From: idoerg at burnham.org (Iddo Friedberg)
Date: Mon Jun 14 14:03:21 2004
Subject: [BioPython] Fasta Iterator
In-Reply-To: <20040614171729.48782.qmail@web21105.mail.yahoo.com>
References: <20040614171729.48782.qmail@web21105.mail.yahoo.com>
Message-ID: <40CDE5AD.6070606@burnham.org>


Two problems with this:

1) You need to create a parser. Somthing like:

 >>> parser = Fasta.RecordParser()
 >>> file_for_blast = open('m-cold.fasta','r')
Then:

 >>> f_iterator = Fasta.Iterator(file_for_blast,parser)


Sylvain Sch?pp wrote:
> Yes, you're right.
> I'm develloping under Windows XP using Python 2.3.4 and BioPython 1.30 
> for Windows.
> 
> And here is my problem :
>  >>> from Bio import Fasta
>  >>> file_for_blast = open('m-cold.fasta','r')


>  >>> f_iterator = Fasta.iterator(file_for_blast)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^




> But in the directory Lib/Bio/Fasta there is a file (something like 
> __init__.py) which contain a class Iterator.
>  

Exactly! But Python is case sensitive, and you wrote Fasta.iterator 
where it should be Fasta.Iterator

Anyhow, you should instantiate RecordParser, and pass it to Fasta.Iterator.

See section 2.4.3 from the tutorial/cookbook. Also, please let me know 
which prt of the T/C you read to do this. I'll check that part for errors.


HTH,

Iddo




-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo
From sbassi at asalup.org  Tue Jun 15 08:47:36 2004
From: sbassi at asalup.org (Sebastian Bassi)
Date: Tue Jun 15 08:50:57 2004
Subject: [BioPython] Gmail as a price to the best logo for DNALinux
Message-ID: <40CEEFE8.6020105@asalup.org>

Our Bioinformatics distro called DNALinux is looking for a graphic logo.
You could submit your artwork at logo@dnalinux.com and if your design is 
choosen, you will win a Gmail account. The contest finish the 1st of 
July. GenesDigitales stuff will pick up the winner logo. The logo 
copyright will we transfered to GenesDigitales who will release it under 
the Creative Common license. This will assure the author credit for 
his/her work.


http://www.bioinformatica.info/modules.php?op=modload&name=News&file=article&sid=118&mode=thread&order=0&thold=0


-- 
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@genesdigitales.com - ICQ UIN: 3356556 -     \=//

                 http://Bioinformatica.info

From syl_schupp at yahoo.fr  Tue Jun 15 12:06:57 2004
From: syl_schupp at yahoo.fr (=?iso-8859-1?q?Sylvain=20Sch=FCpp?=)
Date: Tue Jun 15 12:50:57 2004
Subject: [BioPython] Fasta class
Message-ID: <20040615160657.32668.qmail@web21105.mail.yahoo.com>

Hi,
I tried to make a little program using Biopython. So I open a new window a typed :

from Bio import Fasta

I save and execute my file :

 Traceback (most recent call last):
   File "H:/SylSch/learn biopython/test.py", line 11, in -toplevel-
     from Bio import Fasta
   File "C:\sschupp\Python23\Lib\site-packages\Bio\Fasta\__init__.py", 
line 23, in -toplevel-
     from Bio.Mindy import SimpleSeqRecord
   File 
"C:\sschupp\Python23\Lib\site-packages\Bio\Mindy\SimpleSeqRecord.py", 
line 16, in -toplevel-
     from Bio.builders.SeqRecord.sequence import BuildSeqRecord
   File 
"C:\sschupp\Python23\Lib\site-packages\Bio\builders\SeqRecord\sequence.py", 
line 3, in -toplevel-
     from Martel import Dispatch
   File "C:\sschupp\Python23\Lib\site-packages\Martel\__init__.py", line 
6, in -toplevel-
     import Expression
   File "C:\sschupp\Python23\Lib\site-ackages\Martel\Expression.py", 
line 31, in -toplevel-
     import Parser
   File "C:\sschupp\Python23\Lib\site-packages\Martel\Parser.py", line 
33, in -toplevel-
     import TextTools
ImportError: No module named TextTools
 
So I can't work with Fasta librairy. But, in the shell, the same command  work very well and in my file, a different (like from Bio import Blast) work also.
 
I don't understand anything.




Pour suivre mes aventures su?doises :
www.marschupp.fr.st
		
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From sbassi at asalup.org  Wed Jun 16 10:45:15 2004
From: sbassi at asalup.org (Sebastian Bassi)
Date: Wed Jun 16 10:48:46 2004
Subject: [BioPython] Random sequence
Message-ID: <40D05CFB.2080701@asalup.org>

Is there a way to generate a random DNA sequence with biopython?
If not, I could submit a function to do it, but before doing it, I'd 
want to see if its not already done.


-- 
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@genesdigitales.com - ICQ UIN: 3356556 -     \=//

                 http://Bioinformatica.info

From absmythe at ucdavis.edu  Wed Jun 16 14:19:36 2004
From: absmythe at ucdavis.edu (ashleigh smythe)
Date: Wed Jun 16 14:22:22 2004
Subject: [BioPython] Random sequence
In-Reply-To: <40D05CFB.2080701@asalup.org>
References: <40D05CFB.2080701@asalup.org>
Message-ID: <1087409976.16988.22.camel@nate.ucdavis.edu>

On Wed, 2004-06-16 at 07:45, Sebastian Bassi wrote:
> Is there a way to generate a random DNA sequence with biopython?
> If not, I could submit a function to do it, but before doing it, I'd 
> want to see if its not already done.

Hi Sebastian.  I wasn't able to find a random sequence generator in the
biopython modules so I wrote a simple little one of my own a few months
ago- it only uses biopython modules to add the sequence to a
biopython-parsed file.  It is quite ugly and brute force as I'm a
beginner - I'd be curious to see what you come up with.  In case you are
curious, here it is:

#This is designed to generate random DNA sequence data and add
#it to the end of a biopython-parsed sequence record
#in fasta format.
#Modified 2-20 to just make random seq. data for a taxon,
#rather than adding it onto the existing sequence.

import random
import string
                                                                                                                                                                                                                                                     
def generate(n):                  #generate the dna sequence of n length
    bases=['A', 'T', 'G', 'C']
    dna_in_list=[]
                                                                                                                           
    while n > 0:
        abase=random.choice(bases)
                                                                                                                           
        dna_in_list.append(abase)
        n=n-1
                                                                                                                           
    dnastring=str(dna_in_list)     #format the list into a string.  
    better_dnastring=string.join(string.split(dnastring),"") #Take
    better2_dnastring=string.strip(better_dnastring)         #out
    better3_dnastring=better2_dnastring.replace(',','')      #unwanted
    better4_dnastring=better3_dnastring.replace(']','')      #characters
    better5_dnastring=better4_dnastring.replace('[','')
    better6_dnastring=better5_dnastring.replace("'",'')

    return better6_dnastring
   
 
def add_seq(n):                #this is how start 
    import sys                 #the program:seqgen.add_seq(file, n).
    from Bio import Fasta                                     
    parser=Fasta.RecordParser()
    afile=open(file_to_add_to, 'r')
    iterator=Fasta.Iterator(afile, parser)
 
    out_file=open('randomadded.nex', 'w')
 
    while 1:                   #loop through each record and add the new
        seq_to_add=generate(n) #sequence
        cur_record=iterator.next()
        if cur_record is None:
            break
        title_and_seq=string.split(cur_record.title)
        title='>' + title_and_seq[0] + '\n'
        new_record=title + 'N' + seq_to_add
        out_file.write(new_record)
        out_file.write('\n')


Ashleigh

From pan at uchicago.edu  Wed Jun 16 21:58:31 2004
From: pan at uchicago.edu (pan@uchicago.edu)
Date: Wed Jun 16 22:01:37 2004
Subject: [BioPython] Random sequence
In-Reply-To: <1087409976.16988.22.camel@nate.ucdavis.edu>
References: <40D05CFB.2080701@asalup.org>
	<1087409976.16988.22.camel@nate.ucdavis.edu>
Message-ID: <1087437511.40d0fac778996@webmail.uchicago.edu>

You can make a random seq with one line of python code:

>>> import random

>>> ''.join([random.choice('AGTC') for x in range(10)]) 
'GGTTTCGGTA'

>>> ''.join([random.choice('AGTC') for x in range(10)]) 
'GCGGGTCCGT'

>>> ''.join([random.choice('AGTC') for x in range(10)]) 
'AAAAGCACTG'

Isn't it beautiful? 

pan








Quoting ashleigh smythe <absmythe@ucdavis.edu>:

> On Wed, 2004-06-16 at 07:45, Sebastian Bassi wrote:
> > Is there a way to generate a random DNA sequence with biopython?
> > If not, I could submit a function to do it, but before doing it, I'd 
> > want to see if its not already done.
> 
> Hi Sebastian.  I wasn't able to find a random sequence generator in the
> biopython modules so I wrote a simple little one of my own a few months
> ago- it only uses biopython modules to add the sequence to a
> biopython-parsed file.  It is quite ugly and brute force as I'm a
> beginner - I'd be curious to see what you come up with.  In case you are
> curious, here it is:
> 
> #This is designed to generate random DNA sequence data and add
> #it to the end of a biopython-parsed sequence record
> #in fasta format.
> #Modified 2-20 to just make random seq. data for a taxon,
> #rather than adding it onto the existing sequence.
> 
> import random
> import string
>                                                                              
>                                                                              
>                                                                              
>            
> def generate(n):                  #generate the dna sequence of n length
>     bases=['A', 'T', 'G', 'C']
>     dna_in_list=[]
>                                                                              
>                                              
>     while n > 0:
>         abase=random.choice(bases)
>                                                                              
>                                              
>         dna_in_list.append(abase)
>         n=n-1
>                                                                              
>                                              
>     dnastring=str(dna_in_list)     #format the list into a string.  
>     better_dnastring=string.join(string.split(dnastring),"") #Take
>     better2_dnastring=string.strip(better_dnastring)         #out
>     better3_dnastring=better2_dnastring.replace(',','')      #unwanted
>     better4_dnastring=better3_dnastring.replace(']','')      #characters
>     better5_dnastring=better4_dnastring.replace('[','')
>     better6_dnastring=better5_dnastring.replace("'",'')
> 
>     return better6_dnastring
>    
>  
> def add_seq(n):                #this is how start 
>     import sys                 #the program:seqgen.add_seq(file, n).
>     from Bio import Fasta                                     
>     parser=Fasta.RecordParser()
>     afile=open(file_to_add_to, 'r')
>     iterator=Fasta.Iterator(afile, parser)
>  
>     out_file=open('randomadded.nex', 'w')
>  
>     while 1:                   #loop through each record and add the new
>         seq_to_add=generate(n) #sequence
>         cur_record=iterator.next()
>         if cur_record is None:
>             break
>         title_and_seq=string.split(cur_record.title)
>         title='>' + title_and_seq[0] + '\n'
>         new_record=title + 'N' + seq_to_add
>         out_file.write(new_record)
>         out_file.write('\n')
> 
> 
> Ashleigh
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 


From pan at uchicago.edu  Thu Jun 17 00:23:41 2004
From: pan at uchicago.edu (pan@uchicago.edu)
Date: Thu Jun 17 00:26:25 2004
Subject: [BioPython] Random sequence
In-Reply-To: <1087437511.40d0fac778996@webmail.uchicago.edu>
References: <40D05CFB.2080701@asalup.org>
	<1087409976.16988.22.camel@nate.ucdavis.edu>
	<1087437511.40d0fac778996@webmail.uchicago.edu>
Message-ID: <1087446221.40d11ccd632bf@webmail.uchicago.edu>

Also see a 2-liner coding sequence:

>>> def codingSeq(size=30, stopCodons=['TAG','TAA', 'TGA'], sep=''):
	codons = [x+y+z for x in 'AGTC' for y in 'AGTC' for z in 'AGTC' \
                    if x+y+z not in stopCodons]
 	return sep.join([ random.choice(codons) for x in range(size/3) ])

>>> codingSeq()
'AATGTTTCACTAGGTGACGTGTCGTGGCTA' 

>>> codingSeq(sep=' ')
'GGT GCT AAG TTC CGA TCG AAC AGA AAC TGT'



Quoting pan@uchicago.edu:

> You can make a random seq with one line of python code:
> 
> >>> import random
> 
> >>> ''.join([random.choice('AGTC') for x in range(10)]) 
> 'GGTTTCGGTA'
> 
> >>> ''.join([random.choice('AGTC') for x in range(10)]) 
> 'GCGGGTCCGT'
> 
> >>> ''.join([random.choice('AGTC') for x in range(10)]) 
> 'AAAAGCACTG'
> 
> Isn't it beautiful? 
> 
> pan
> 
> 
> 
> 
> 
> 
> 
> 
> Quoting ashleigh smythe <absmythe@ucdavis.edu>:
> 
> > On Wed, 2004-06-16 at 07:45, Sebastian Bassi wrote:
> > > Is there a way to generate a random DNA sequence with biopython?
> > > If not, I could submit a function to do it, but before doing it, I'd 
> > > want to see if its not already done.
> > 
> > Hi Sebastian.  I wasn't able to find a random sequence generator in the
> > biopython modules so I wrote a simple little one of my own a few months
> > ago- it only uses biopython modules to add the sequence to a
> > biopython-parsed file.  It is quite ugly and brute force as I'm a
> > beginner - I'd be curious to see what you come up with.  In case you are
> > curious, here it is:
> > 
> > #This is designed to generate random DNA sequence data and add
> > #it to the end of a biopython-parsed sequence record
> > #in fasta format.
> > #Modified 2-20 to just make random seq. data for a taxon,
> > #rather than adding it onto the existing sequence.
> > 
> > import random
> > import string
> >                                                                            
>  
> >                                                                            
>  
> >                                                                            
>  
> >            
> > def generate(n):                  #generate the dna sequence of n length
> >     bases=['A', 'T', 'G', 'C']
> >     dna_in_list=[]
> >                                                                            
>  
> >                                              
> >     while n > 0:
> >         abase=random.choice(bases)
> >                                                                            
>  
> >                                              
> >         dna_in_list.append(abase)
> >         n=n-1
> >                                                                            
>  
> >                                              
> >     dnastring=str(dna_in_list)     #format the list into a string.  
> >     better_dnastring=string.join(string.split(dnastring),"") #Take
> >     better2_dnastring=string.strip(better_dnastring)         #out
> >     better3_dnastring=better2_dnastring.replace(',','')      #unwanted
> >     better4_dnastring=better3_dnastring.replace(']','')      #characters
> >     better5_dnastring=better4_dnastring.replace('[','')
> >     better6_dnastring=better5_dnastring.replace("'",'')
> > 
> >     return better6_dnastring
> >    
> >  
> > def add_seq(n):                #this is how start 
> >     import sys                 #the program:seqgen.add_seq(file, n).
> >     from Bio import Fasta                                     
> >     parser=Fasta.RecordParser()
> >     afile=open(file_to_add_to, 'r')
> >     iterator=Fasta.Iterator(afile, parser)
> >  
> >     out_file=open('randomadded.nex', 'w')
> >  
> >     while 1:                   #loop through each record and add the new
> >         seq_to_add=generate(n) #sequence
> >         cur_record=iterator.next()
> >         if cur_record is None:
> >             break
> >         title_and_seq=string.split(cur_record.title)
> >         title='>' + title_and_seq[0] + '\n'
> >         new_record=title + 'N' + seq_to_add
> >         out_file.write(new_record)
> >         out_file.write('\n')
> > 
> > 
> > Ashleigh
> > 
> > _______________________________________________
> > BioPython mailing list  -  BioPython@biopython.org
> > http://biopython.org/mailman/listinfo/biopython
> > 
> 
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 


From pan at uchicago.edu  Thu Jun 17 00:47:57 2004
From: pan at uchicago.edu (pan@uchicago.edu)
Date: Thu Jun 17 00:50:41 2004
Subject: [BioPython] Random sequence
In-Reply-To: <1087446221.40d11ccd632bf@webmail.uchicago.edu>
References: <40D05CFB.2080701@asalup.org>
	<1087409976.16988.22.camel@nate.ucdavis.edu>
	<1087437511.40d0fac778996@webmail.uchicago.edu>
	<1087446221.40d11ccd632bf@webmail.uchicago.edu>
Message-ID: <1087447677.40d1227d3cd04@webmail.uchicago.edu>

(sorry, this is probably out of topic, but just for fun ...)

A non-random coding sequence with codon usage following a 
predefined codon usage frequency :

def codingSeq_codonUsage(size=30, sep='', codonUsage={}):
  return sep.join([ randomPickDict(codonUsage) for x in range(size/3) ])

where:

-- codonUsage is a dictionary looks like:
    { 'TTT':17.2, 'TCT':14.9,  'TAT':12.1, 'TAG':0, ...}
   see: http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?
species=Homo+sapiens+[gbpri]

-- randomPickDict() is from: 
   http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/278260
     
pan


Quoting pan@uchicago.edu:

> Also see a 2-liner coding sequence:
> 
> >>> def codingSeq(size=30, stopCodons=['TAG','TAA', 'TGA'], sep=''):
> 	codons = [x+y+z for x in 'AGTC' for y in 'AGTC' for z in 'AGTC' \
>                     if x+y+z not in stopCodons]
>  	return sep.join([ random.choice(codons) for x in range(size/3) ])
> 
> >>> codingSeq()
> 'AATGTTTCACTAGGTGACGTGTCGTGGCTA' 
> 
> >>> codingSeq(sep=' ')
> 'GGT GCT AAG TTC CGA TCG AAC AGA AAC TGT'
> 
> 
> 
> Quoting pan@uchicago.edu:
> 
> > You can make a random seq with one line of python code:
> > 
> > >>> import random
> > 
> > >>> ''.join([random.choice('AGTC') for x in range(10)]) 
> > 'GGTTTCGGTA'
> > 
> > >>> ''.join([random.choice('AGTC') for x in range(10)]) 
> > 'GCGGGTCCGT'
> > 
> > >>> ''.join([random.choice('AGTC') for x in range(10)]) 
> > 'AAAAGCACTG'
> > 
> > Isn't it beautiful? 
> > 
> > pan
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > Quoting ashleigh smythe <absmythe@ucdavis.edu>:
> > 
> > > On Wed, 2004-06-16 at 07:45, Sebastian Bassi wrote:
> > > > Is there a way to generate a random DNA sequence with biopython?
> > > > If not, I could submit a function to do it, but before doing it, I'd 
> > > > want to see if its not already done.
> > > 
> > > Hi Sebastian.  I wasn't able to find a random sequence generator in the
> > > biopython modules so I wrote a simple little one of my own a few months
> > > ago- it only uses biopython modules to add the sequence to a
> > > biopython-parsed file.  It is quite ugly and brute force as I'm a
> > > beginner - I'd be curious to see what you come up with.  In case you
> are
> > > curious, here it is:
> > > 
> > > #This is designed to generate random DNA sequence data and add
> > > #it to the end of a biopython-parsed sequence record
> > > #in fasta format.
> > > #Modified 2-20 to just make random seq. data for a taxon,
> > > #rather than adding it onto the existing sequence.
> > > 
> > > import random
> > > import string
> > >                                                                          
>  
> >  
> > >                                                                          
>  
> >  
> > >                                                                          
>  
> >  
> > >            
> > > def generate(n):                  #generate the dna sequence of n
> length
> > >     bases=['A', 'T', 'G', 'C']
> > >     dna_in_list=[]
> > >                                                                          
>  
> >  
> > >                                              
> > >     while n > 0:
> > >         abase=random.choice(bases)
> > >                                                                          
>  
> >  
> > >                                              
> > >         dna_in_list.append(abase)
> > >         n=n-1
> > >                                                                          
>  
> >  
> > >                                              
> > >     dnastring=str(dna_in_list)     #format the list into a string.  
> > >     better_dnastring=string.join(string.split(dnastring),"") #Take
> > >     better2_dnastring=string.strip(better_dnastring)         #out
> > >     better3_dnastring=better2_dnastring.replace(',','')      #unwanted
> > >     better4_dnastring=better3_dnastring.replace(']','')     
> #characters
> > >     better5_dnastring=better4_dnastring.replace('[','')
> > >     better6_dnastring=better5_dnastring.replace("'",'')
> > > 
> > >     return better6_dnastring
> > >    
> > >  
> > > def add_seq(n):                #this is how start 
> > >     import sys                 #the program:seqgen.add_seq(file, n).
> > >     from Bio import Fasta                                     
> > >     parser=Fasta.RecordParser()
> > >     afile=open(file_to_add_to, 'r')
> > >     iterator=Fasta.Iterator(afile, parser)
> > >  
> > >     out_file=open('randomadded.nex', 'w')
> > >  
> > >     while 1:                   #loop through each record and add the
> new
> > >         seq_to_add=generate(n) #sequence
> > >         cur_record=iterator.next()
> > >         if cur_record is None:
> > >             break
> > >         title_and_seq=string.split(cur_record.title)
> > >         title='>' + title_and_seq[0] + '\n'
> > >         new_record=title + 'N' + seq_to_add
> > >         out_file.write(new_record)
> > >         out_file.write('\n')
> > > 
> > > 
> > > Ashleigh
> > > 
> > > _______________________________________________
> > > BioPython mailing list  -  BioPython@biopython.org
> > > http://biopython.org/mailman/listinfo/biopython
> > > 
> > 
> > 
> > _______________________________________________
> > BioPython mailing list  -  BioPython@biopython.org
> > http://biopython.org/mailman/listinfo/biopython
> > 
> 
> 


From oly at scmbb.ulb.ac.be  Thu Jun 17 05:47:46 2004
From: oly at scmbb.ulb.ac.be (Olivier Sand)
Date: Thu Jun 17 05:50:33 2004
Subject: [BioPython] parsing blast results - SyntaxError: I missed the
	Length in an alignment header
Message-ID: <62DCB5A6-C043-11D8-B1A5-000A95DC2A76@scmbb.ulb.ac.be>

Hi,

I have been trying to use the code for parsing WWW blast results you  
give in the biopython tutorial with biopython 1.30. But I get an error  
message mentionned in the title of this mail. From looking at the  
mailling list, I understand this used to be bug due to changing blast  
output format, but has been fixed in version 1.30. Would it be possible  
the blast format changed again, or am I doing something wrong?

Here is the code I use:
#! /usr/bin/python

from Bio import Fasta

file_for_blast = open('m_cold.fasta', 'r')
f_iterator = Fasta.Iterator(file_for_blast)

f_record = f_iterator.next()

from Bio.Blast import NCBIWWW
b_results = NCBIWWW.blast(program='blastn', database='nr',  
query=f_record, format_type = "HTML")

save_file = open('blast_m_cold.out', 'w')
blast_results = b_results.read()
save_file.write(blast_results)
save_file.close()

import cStringIO
string_result_handle = cStringIO.StringIO(blast_results)

b_parser = NCBIWWW.BlastParser()
b_record = b_parser.parse(string_result_handle)

Here is the content of the file m_cold.fasta:
 >gi|8332116|gb|BE037100.1|BE037100 MP14H09 MP Mesembryanthemum  
crystallinum cDNA 5' similar to cold acclimation protein, mRNA sequence
CACTAGTACTCGAGCGTNCTGCACCAATTCGGCACGAGCAAGTGACTACGTTNTGTGAACAGAAAATGGG
GAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATATC
AATGAGCTTAAAATGGCAACAATGAGGCTCATCAATGATGCTAGTATGCTCGGTCATTACGGGTTTGGCA
CTCATTTCCTCAAATGGCTCGCCTGCCTTGCGGCTATTTACTTGTTGATATTGGATCGAACAAACTGGAG
AACCAACATGCTCACGTCACTTTTAGTCCCTTACATATTCCTCAGTCTTCCATCCGGGCCATTTCATCTG
TTCAGAGGCGAGGTCGGGAAATGGATTGCCATCATTGCAGTCGTGTTAAGGCTGTTCTTCAACCGGCATT
TCCCAGTTTGGCTGGAAATGCCTGGATCGTTGATACTCCTCCTGGTGGTGGCACCAGACTTCTTTACACA
CAAAGTGAAGGAGAGCTGGATCGGAATTGCAATTATGATAGCGATAGGGTGTCACCTGATGCAAGAACAT
ATCAGAGCCACTGGTGGCTTTTGGAATTCCTTCACACAGAGCCACGGAACTTTTAACACAATTGGGCTTA
TCCTTCTACTGGCTTACCCTGTCTGTTTATGGTCATCTTCATGATGTAGTAGCTTAGTCTTGATCCTAAT
CCTCAAATNTACTTTTCCAGCTCTTTCGACGCTCTTGCTAAAGCCCATTCAATTCGCCCCATATTTCGCA
CACATTCATTTCACCACCCAATACGTGCTCTCCTTCTCCCTCTCTCCCTCTCCTCCCTCTTTTCTTCCTC
TCACTTCTCTTCTCTTCTCTTCTTCAATACTCCCCTGGAGCGCCCTCTTCACCTCCCTACTCTCTACTCC
TCTCTCTCACTCTCTCTTCCTCTCTTATCTCTCTCCTCCTCTCCTTCTCATCCCTCCTCCTTCTCTTCCT
TTTCTTCTTTCTATCCACGCGCCATCCTCCCTCTTCCCTCTTCCCTTCTCTCTCCTCTCTTTCTCTCTCC
TCTCTTCCTCATCTCACCACCTCCTCCTCTCTTTCTTCCGTCCTCCTTCCCTTCCTTCTTC

Here is the error message:
Traceback (most recent call last):
   File "/Users/oly/Programmes/python/blast_and_parse.py", line 22, in ?
     b_record = b_parser.parse(string_result_handle)
   File  
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 47, in parse
     self._scanner.feed(handle, self._consumer)
   File  
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 99, in feed
     self._scan_rounds(uhandle, consumer)
   File  
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 242, in  
_scan_rounds
     self._scan_alignments(uhandle, consumer)
   File  
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 325, in  
_scan_alignments
     self._scan_pairwise_alignments(uhandle, consumer)
   File  
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 348, in  
_scan_pairwise_alignments
     self._scan_one_pairwise_alignment(uhandle, consumer)
   File  
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 379, in  
_scan_one_pairwise_alignment
     self._scan_alignment_header(uhandle, consumer)
   File  
"/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 417, in  
_scan_alignment_header
     raise SyntaxError, "I missed the Length in an alignment header"
SyntaxError: I missed the Length in an alignment header

Thanks

Olivier

------------------------------------------------------------------------ 
----------------------
Olivier Sand
The aMAZE Project				Tel.: +32(0)2 650 5427
SCMBB - ULB					Fax: +32(0)2 650 5425
Campus Plaine, bd du Triomphe - CP263
B-1050 Bruxelles
Belgium

From wong at ebgm.jussieu.fr  Thu Jun 17 08:49:38 2004
From: wong at ebgm.jussieu.fr (Hua Wong)
Date: Thu Jun 17 08:52:24 2004
Subject: [BioPython] Installation issues
Message-ID: <20040617124938.GA8616@pif.ebgm.jussieu.fr>

I compiled Biopython 1.30 from source on a Linux machine.

But I had to comment 2 out of 3 Numeric usingextensions because compiler can't find it.

Numeric is installed on a different location (non root... I know...my bad)
How can I modify setup.py in order to make it find?

Already done a tweak for  Bio.Cluster (include_dirs...it works) 
Tried to do it for KDTree and Affy but couldn't....

I would be glad to have some help...
Thanks

From andreasschlicker at web.de  Thu Jun 17 09:12:36 2004
From: andreasschlicker at web.de (Andreas Schlicker)
Date: Thu Jun 17 09:16:58 2004
Subject: [BioPython] Fasta class
Message-ID: <948764513@web.de>

Hi, 

>      import TextTools
> ImportError: No module named TextTools

Do you have the "mxTextTools" installed on this machine? To me it looks like missing this package. 

Regards,
Andreas
__________________________________________________________________
Zeigen Sie Emotionen mit der WEB.DE Bild-SMS! Das Bild ist gratis,
Sie bezahlen nur den Versand. http://freemail.web.de/?mc=021196

From sophielegras at yahoo.fr  Wed Jun 16 08:50:07 2004
From: sophielegras at yahoo.fr (=?iso-8859-1?q?Legras=20Sophie?=)
Date: Thu Jun 17 09:25:28 2004
Subject: [BioPython] Problem with The Biopython Tutorial and Cookbook 
Message-ID: <20040616125007.71734.qmail@web51804.mail.yahoo.com>

Skipped content of type multipart/alternative-------------- next part --------------
A non-text attachment was scrubbed...
Name: Consumer.py
Type: application/octet-stream
Size: 926 bytes
Desc: Consumer.py
Url : http://portal.open-bio.org/pipermail/biopython/attachments/20040616/7d2781d3/Consumer-0001.obj
From mdehoon at ims.u-tokyo.ac.jp  Thu Jun 17 09:27:46 2004
From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon)
Date: Thu Jun 17 09:29:40 2004
Subject: [BioPython] Installation issues
In-Reply-To: <20040617124938.GA8616@pif.ebgm.jussieu.fr>
References: <20040617124938.GA8616@pif.ebgm.jussieu.fr>
Message-ID: <40D19C52.50600@ims.u-tokyo.ac.jp>

One quick and dirty solution might be to set the environment variable 
C_INCLUDE_PATH to the location of the Numeric header files before running setup.py.

I'm a bit surprised though that the tweak for Bio.Cluster doesn't work for 
KDTree and Affy. What is the exact error message that you get?

--Michiel.

Hua Wong wrote:
> I compiled Biopython 1.30 from source on a Linux machine.
> 
> But I had to comment 2 out of 3 Numeric usingextensions because compiler can't find it.
> 
> Numeric is installed on a different location (non root... I know...my bad)
> How can I modify setup.py in order to make it find?
> 
> Already done a tweak for  Bio.Cluster (include_dirs...it works) 
> Tried to do it for KDTree and Affy but couldn't....
> 
> I would be glad to have some help...
> Thanks
> 
> _______________________________________________
> BioPython mailing list  -  BioPython@biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 
> 

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon

From dss at org.chemie.uni-muenchen.de  Fri Jun 18 04:37:01 2004
From: dss at org.chemie.uni-muenchen.de (dss@org.chemie.uni-muenchen.de)
Date: Fri Jun 18 04:41:41 2004
Subject: [BioPython] software
In-Reply-To: <5959IF4LC6E283HD@biopython.org>
References: <5959IF4LC6E283HD@biopython.org>
Message-ID: <IC4H653FD760FAAI@org.chemie.uni-muenchen.de>

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From wong at ebgm.jussieu.fr  Fri Jun 18 06:01:23 2004
From: wong at ebgm.jussieu.fr (Hua Wong)
Date: Fri Jun 18 06:04:06 2004
Subject: [BioPython] BioPDB problem
Message-ID: <20040618100123.GA10048@pif.ebgm.jussieu.fr>

I have a PDB file that count 3145 atoms [1...3145], and using BioPDB I try to get all the coordinate.

So I use the example:
parser=PDBParser()
structure=parser.get_structure('0b','0b.pdb')

liste=[]
for model in structure.get_iterator():
	for chain in model.get_iterator():
		for residue in chain.get_iterator():
			for atom in residue.get_iterator():
				a=atom.get_coord()
				liste.append(a)
To obtain a list of array representing the x y and z

But I can't have all the atoms. The liste[] list is 3144 which seems ok [0...3144]
But when I want to display the 3144th atom I obtain:
>>> len(liste)
3144
>>> liste[3144]
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
IndexError: list index out of range

The lastest atoms he accepts to display is 3143th.
Am I doing something wrong?

Thanks.
From wong at ebgm.jussieu.fr  Fri Jun 18 08:06:56 2004
From: wong at ebgm.jussieu.fr (Hua Wong)
Date: Fri Jun 18 08:09:43 2004
Subject: [BioPython] dssp
Message-ID: <20040618120656.GA10160@pif.ebgm.jussieu.fr>

Another newbie question...

I try to use the dssp module of Bio.PDB

I looked at the
http://biopython.org/docs/api/public/Bio.PDB.DSSP.DSSP-class.html
page for the example

and get the following error.
>>> model=structure[0]
>>> dssp=DSSP(model,'0b.pdb')
sh: line 1: dssp: command not found

I think it is because my dssp isn't installed in a default-just-for-root-almighty location.

Am I right? If yes, what can I do to tell bio.PDB dssp the location of dssp...
Else, what are the other possible problems?

Thanks
From thamelry at binf.ku.dk  Fri Jun 18 06:57:34 2004
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Fri Jun 18 08:25:03 2004
Subject: [BioPython] BioPDB problem
In-Reply-To: <20040618100123.GA10048@pif.ebgm.jussieu.fr>
References: <20040618100123.GA10048@pif.ebgm.jussieu.fr>
Message-ID: <200406181257.34308.thamelry@binf.ku.dk>

On Friday 18 June 2004 12:01, Hua Wong wrote:
> I have a PDB file that count 3145 atoms [1...3145], and using BioPDB I try
> to get all the coordinate.

One possibility might be that the PDB file contains disordered atoms. They 
will be packed in one DisorderedAtom object, which in term holds the Atom 
objects.

The method residue.get_unpacked_list() returns all the individual atoms, and
'unpacks' disordered atoms. 

So if this is indeed the case, do the following:
Replace this line:

for atom in residue.get_iterator():

by:

for atom in residue.get_unpacked_list():

There might be other reasons, ie. a buggy PDB file. 
Try running the parser in 'strict' mode:

parser=PDBParser(PERMISSIVE=0)

This will throw an exception if the PDB file is buggy.

Hope this helps,

-Thomas

-- 
Thomas Hamelryck
Bioinformatics center
University of Copenhagen      
Universitetsparken 15 Bygning 10                 
2100 K?benhavn ?, Denmark
---
http://www.binf.ku.dk/users/thamelry/


From thamelry at binf.ku.dk  Fri Jun 18 08:35:34 2004
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Fri Jun 18 09:20:28 2004
Subject: [BioPython] dssp
In-Reply-To: <20040618120656.GA10160@pif.ebgm.jussieu.fr>
References: <20040618120656.GA10160@pif.ebgm.jussieu.fr>
Message-ID: <200406181435.34294.thamelry@binf.ku.dk>

On Friday 18 June 2004 14:06, Hua Wong wrote:
> Another newbie question...

Well awright!

> >>> model=structure[0]
> >>> dssp=DSSP(model,'0b.pdb')
>
> sh: line 1: dssp: command not found
>
> I think it is because my dssp isn't installed in a
> default-just-for-root-almighty location.
>
> Am I right? If yes, what can I do to tell bio.PDB dssp the location of
> dssp... Else, what are the other possible problems?

Of course, dssp needs to be installed. If it's in your path,
it will work as is, but you can also specify the explicit location of the dssp 
binary. For example:

dssp=DSSP(model, '0b.pdb', "/home/thomas/dssp/dssp.bin")

-Thomas

From wong at ebgm.jussieu.fr  Fri Jun 18 11:48:31 2004
From: wong at ebgm.jussieu.fr (Hua Wong)
Date: Fri Jun 18 11:51:15 2004
Subject: [BioPython] one more question about dssp
Message-ID: <20040618154831.GA11034@pif.ebgm.jussieu.fr>

One last question and I will try not to bother for a week...
Using DSSP in Bio.PDB, I obtain an assertion error.

I looked at the code in DSSP.py
# Something went wrong if this is not true! <----
assert(resname==aa)

And it seems to be the source of the error I get with python. Most of the PDB I launched with standalone DSSP pass. But when checked in bio.PDB there is a problem. Is there a mismatch between DSSP output and the AA from the structure?

So I guess there is a problems in my pdb's I can't point out (they seem quite normal, as normal as they can be at least...)

Why does 1FAT.pdb run smoothly while other pdb's can stuck the bio.PDB.DSSP ?

Thanks for your patience.
From e.picardi at unical.it  Fri Jun 18 11:45:57 2004
From: e.picardi at unical.it (Ernesto)
Date: Fri Jun 18 11:57:14 2004
Subject: [BioPython] gamma distribution
Message-ID: <009201c4554b$59901720$572561a0@Travelmate>

Hi all,
I'm using the function gammavariate(a,b) from the random module, but I don't know really the interpretation of a and b. I guess a is the shape and b a scaling factor, so the mean should be a/b. Is my idea rigth?

Thank you 

Ernesto
From idoerg at burnham.org  Fri Jun 18 12:08:27 2004
From: idoerg at burnham.org (Iddo Friedberg)
Date: Fri Jun 18 12:12:55 2004
Subject: [BioPython] BioPDB problem
Message-ID: <40D3137B.3080609@burnham.org>


Hua Wong wrote:
> I have a PDB file that count 3145 atoms [1...3145], and using BioPDB I try to get all the coordinate.
> 
> So I use the example:
> parser=PDBParser()
> structure=parser.get_structure('0b','0b.pdb')
> 
> liste=[]
> for model in structure.get_iterator():
> 	for chain in model.get_iterator():
> 		for residue in chain.get_iterator():
> 			for atom in residue.get_iterator():
> 				a=atom.get_coord()
> 				liste.append(a)
> To obtain a list of array representing the x y and z
> 
> But I can't have all the atoms. The liste[] list is 3144 which seems ok [0...3144]
> But when I want to display the 3144th atom I obtain:
> 
>>>>len(liste)
> 
> 3144
> 
>>>>liste[3144]
> 
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
> IndexError: list index out of range
> 
> The lastest atoms he accepts to display is 3143th.
> Am I doing something wrong?


Well, the list length is 3144, which means the last index is 3143,
because in Python indices start from 0. So a length 3144 list would have
indices 0 through 3143.

Iddo


-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo


From karbak at cmu.edu  Fri Jun 18 12:32:34 2004
From: karbak at cmu.edu (K. Arun)
Date: Fri Jun 18 12:43:21 2004
Subject: [BioPython] Bio.SCOP usage
Message-ID: <m27ju4n7x9.fsf@AL.SP.CS.CMU.EDU>


Hello,

Are there examples of Bio.SCOP usage available somewhere ? I've
looked in both the code, the API docs, and at the usual places on the
site. Have I missed something ? Thanks,

                                                  -arun

From thamelry at binf.ku.dk  Fri Jun 18 12:27:58 2004
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Fri Jun 18 13:14:11 2004
Subject: [BioPython] one more question about dssp
In-Reply-To: <20040618154831.GA11034@pif.ebgm.jussieu.fr>
References: <20040618154831.GA11034@pif.ebgm.jussieu.fr>
Message-ID: <200406181827.58493.thamelry@binf.ku.dk>


> One last question and I will try not to bother for a week...

That's what they all say :-) :-)
It's no problem - ask away, that's what the list is for...

> Using DSSP in Bio.PDB, I obtain an assertion error.
>
> I looked at the code in DSSP.py
> # Something went wrong if this is not true! <----
> assert(resname==aa)

That's a bug! DSSP renames some Cys residues to a, b, etc. 
in case of SS bridges. I forgot to take that into account in the code 
that asserts that the DSSP residue is the same residue as in the Model.

BUT: it's fixed in the CVS version.
A quick fix would be to remove the assert in case of CYS residues.

Cheers,

-Thomas

From dalke at xebte.pair.com  Fri Jun 18 13:15:12 2004
From: dalke at xebte.pair.com (Andrew Dalke)
Date: Fri Jun 18 13:58:36 2004
Subject: [BioPython] gamma distribution
Message-ID: <20040618171512.51924.qmail@xebte.pair.com>

Hi Ernesto,

> I'm using the function gammavariate(a,b) from the random module, but
> I don't know really the interpretation of a and b. I guess a is the
> shape and b a scaling factor, so the mean should be a/b. Is my idea
> rigth?

I don't know but clues in the documentation and on usenet suggests
that http://mathworld.wolfram.com/GammaDistribution.html documents
the function.  That page states the mean is a*b.

You could also try it out.

>>> import random
>>> def gamma_mean(a, b, n = 1000):
...   data = [random.gammavariate(a, b) for i in range(n)]
...   return sum(data) / n, a*b
... 
>>> gamma_mean(0.1, 0.5)
(0.054523268939043509, 0.050000000000000003)
>>> gamma_mean(5, 9)
(44.813773895529096, 45)
>>> gamma_mean(20, 1.5)
(30.282363568363071, 30.0)
>>> 

So product it is, and not a/b.
                                        Andrew
                                        dalke@dalkescientific.com


From vsaparam at cs.tamu.edu  Sat Jun 19 07:08:56 2004
From: vsaparam at cs.tamu.edu (vsaparam@cs.tamu.edu)
Date: Fri Jun 18 19:23:19 2004
Subject: [BioPython] software
In-Reply-To: <IA3744K6DAJLD6J0@biopython.org>
References: <IA3744K6DAJLD6J0@biopython.org>
Message-ID: <A859AG8KK7CAAAB5@cs.tamu.edu>

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From kinson at t-online.de  Sun Jun 20 12:21:49 2004
From: kinson at t-online.de (spiro)
Date: Sun Jun 20 12:30:42 2004
Subject: [BioPython] =?windows-1251?b?z+7k4e7wIO/l8PHu7eDr4A==?=
Message-ID: <200406201630.i5KGUaKr027506@portal.open-bio.org>

?? ??? ???? ?? ??????, ??? ????? ?????? ???? ? ?????? ??????? ??????? ?? ????, ??? ??? ?????????. 
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From wong at ebgm.jussieu.fr  Mon Jun 21 08:33:36 2004
From: wong at ebgm.jussieu.fr (Hua Wong)
Date: Mon Jun 21 08:36:16 2004
Subject: [BioPython] question about navigating a PDB
Message-ID: <1087821215.19656.40.camel@pif.ebgm.jussieu.fr>

I want to extract the X,Y,Z coordinate from all the CA of a PDB.

I fiddled a bit with bio.PDB since during last week...end (°~°) and I
ended up typing this:

parser=PDBParser(PERMISSIVE=0)
structure=parser.get_structure('foo','bar.pdb')
liste=[]
model=structure[0]
chain=model['A']
for residue in chain.get_iterator():
	for atom in residue.get_iterator():
		if atom==residue['CA']:
			a=atom.get_coord()
			liste.append(a)

Which gives me what I want. But I also get the following lines:

Traceback (most recent call last):
  File "<stdin>", line 3, in ?
  File "/home/pif/wong/Softwares/MMTK/lib/python/Bio/PDB/Entity.py",
line 38, in __getitem__
    return self.child_dict[id]
KeyError: CA

So I guess I might have done it the wrong way, or forgot something...
Any hints can help.

Thanks

From thamelry at binf.ku.dk  Mon Jun 21 09:30:11 2004
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Mon Jun 21 10:04:31 2004
Subject: [BioPython] question about navigating a PDB
In-Reply-To: <1087821215.19656.40.camel@pif.ebgm.jussieu.fr>
References: <1087821215.19656.40.camel@pif.ebgm.jussieu.fr>
Message-ID: <200406211530.11382.thamelry@binf.ku.dk>


> parser=PDBParser(PERMISSIVE=0)
> structure=parser.get_structure('foo','bar.pdb')
> liste=[]
> model=structure[0]
> chain=model['A']
> for residue in chain.get_iterator():
> 	if residue.has_key('CA'):
> 		atom=residue['CA']
>		a=atom.get_coord()
> 		liste.append(a)

Cheers,

-Thomas

From dlrubin at yahoo.com  Mon Jun 21 13:07:20 2004
From: dlrubin at yahoo.com (Daniel Rubin)
Date: Mon Jun 21 13:09:58 2004
Subject: [BioPython] biopython build errors
Message-ID: <20040621170720.10874.qmail@web50803.mail.yahoo.com>

Hi,
I got the latest biopython from cvs and tried python
setup.py on my solaris9 machine (also have python
2.3.4 and Numeric 23.1 installed and latest
mxTextTools installed). I get a lot of errors (a few
shown below) at this step in the build process. I get
similar errors if I try biopython 1.3. Any ideas?

c++ -I/home/rubin/include/python2.3 -c
Bio/KDTree/KDTree.cpp -o
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.o
c++ -I/home/rubin/include/python2.3 -c
Bio/KDTree/KDTree.swig.cpp -o
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
In file included from
/home/rubin/include/python2.3/Python.h:8,
                 from Bio/KDTree/KDTree.swig.cpp:26:
/home/rubin/include/python2.3/pyconfig.h:862:1:
warning: "_XOPEN_SOURCE" redefined
Bio/KDTree/KDTree.swig.cpp:1:1: warning: this is the
location of the previous definition
c++ -shared
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.o
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
-lstdc++ -o
build/lib.solaris-2.9-sun4u-2.3/Bio/KDTree/_CKDTree.so
Text relocation remains                        
referenced
    against symbol                  offset      in
file
<unknown>                           0x17f0     
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
<unknown>                           0x17f4     
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
<unknown>                           0x17f8     
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
<unknown>                           0x17fc     
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
<unknown>                           0x1800     
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
<unknown>                           0x1804     
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
<unknown>                           0x19a4     
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
<unknown>                           0x19a8     
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o
<unknown>                           0x19ac     
build/temp.solaris-2.9-sun4u-2.3/Bio/KDTree/KDTree.swig.o



		
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From Steven.Walter at uky.edu  Mon Jun 21 16:20:42 2004
From: Steven.Walter at uky.edu (Steven Richard Walter)
Date: Mon Jun 21 16:28:43 2004
Subject: [BioPython] SyntaxError in NCBIWWW.BlastParser
Message-ID: <1087849242.30f27880Steven.Walter@uky.edu>

I'm getting a syntax error when parsing the results from a WWW blast query.  Is this a bug in the BioPython code, or am I doing something stupid?  In either case, hints on how to track down the problem will be greatly appreciated.

Thanks


From idoerg at burnham.org  Mon Jun 21 17:02:07 2004
From: idoerg at burnham.org (Iddo)
Date: Mon Jun 21 17:04:25 2004
Subject: [BioPython] SyntaxError in NCBIWWW.BlastParser
In-Reply-To: <1087849242.30f27880Steven.Walter@uky.edu>
References: <1087849242.30f27880Steven.Walter@uky.edu>
Message-ID: <40D74CCF.1080301@burnham.org>

Steven Richard Walter wrote:

>I'm getting a syntax error when parsing the results from a WWW blast query.  Is this a bug in the BioPython code, or am I doing something stupid?  In either case, hints on how to track down the problem will be greatly appreciated.
>
>  
>
Kinda hard to do that without a bit more information.

Can you please post the biopython version, Python version, OS you are 
using, the sequence file, and (very important) the Python stack dump?

Thanks,

Iddo

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 North Torrey Pines Road
La Jolla, CA 92037 USA
T: (858) 646 3100 x3516
F: (858) 713 9930
http://ffas.ljcrf.edu/~iddo

From biopython-dev-bounces at portal.open-bio.org  Mon Jun 21 23:52:17 2004
From: biopython-dev-bounces at portal.open-bio.org (biopython-dev-bounces@portal.open-bio.org)
Date: Mon Jun 21 23:52:21 2004
Subject: [BioPython] Your message to Biopython-dev awaits moderator approval
Message-ID: <mailman.11965.1087876337.21032.biopython-dev@biopython.org>

Your mail to 'Biopython-dev' with the subject

    Hi! :-)

Is being held until the list moderator can review it for approval.

The reason it is being held:

    Message has a suspicious header

Either the message will get posted to the list, or you will receive
notification of the moderator's decision.  If you would like to cancel
this posting, please visit the following URL:

    http://biopython.org/mailman/confirm/biopython-dev/0eec641255cb943aad4a09a5bf2150ca61ed86bd

From srwalt2 at uky.edu  Tue Jun 22 00:33:12 2004
From: srwalt2 at uky.edu (Steven Walter)
Date: Tue Jun 22 00:37:58 2004
Subject: [BioPython] SyntaxError in NCBIWWW.BlastParser
In-Reply-To: <40D74CCF.1080301@burnham.org>
References: <1087849242.30f27880Steven.Walter@uky.edu>
	<40D74CCF.1080301@burnham.org>
Message-ID: <40D7B688.3020208@uky.edu>

Iddo wrote:

> Steven Richard Walter wrote:
>
>> I'm getting a syntax error when parsing the results from a WWW blast 
>> query.  Is this a bug in the BioPython code, or am I doing something 
>> stupid?  In either case, hints on how to track down the problem will 
>> be greatly appreciated.
>>
>>  
>>
> Kinda hard to do that without a bit more information.
>
> Can you please post the biopython version, Python version, OS you are 
> using, the sequence file, and (very important) the Python stack dump?
>
> Thanks,
>
> Iddo
>
Sorry about that.  Python version 2.2.3, latest release of biopython on 
Linux (Fedora Core 2).  Sequence is below the stack trace, run against 
the nr database with blastn.  Hope that helps, and thanks for your reply

 >>> file = open("results")
 >>> from Bio.Blast import NCBIWWW
 >>> parser = NCBIWWW.BlastParser()
 >>> parser.parse(file)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 47, 
in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 99, 
in feed    self._scan_rounds(uhandle, consumer)
  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 
242, in _scan_rounds
    self._scan_alignments(uhandle, consumer)
  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 
325, in _scan_alignments
    self._scan_pairwise_alignments(uhandle, consumer)
  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 
348, in _scan_pairwise_alignments
    self._scan_one_pairwise_alignment(uhandle, consumer)
  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 
379, in _scan_one_pairwise_alignment
    self._scan_alignment_header(uhandle, consumer)
  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 
417, in _scan_alignment_header
    raise SyntaxError, "I missed the Length in an alignment header"
SyntaxError: I missed the Length in an alignment header
 >>>

gcagcccagccaagcactgtcaggaatcctgtgaagcagctccagctatgtgtgaagaag
aggacagcactgccttggtgtgtgacaatggctctgggctctgtaaggccggctttgctg
gggacgatgctcccagggctgttttcccatccattgtgggacgtcccagacatcaggggg
tgatggtgggaatgggacaaaaagacagctacgtgggtgacgaagcacagagcaaaagag
gaatcctgaccctgaagtacccgatagaacatggcatcatcaccaactgggacgacatgg
aaaagatctggcaccactctttctacaatgagcttcgtgttgcccctgaagagcatccca
ccctgctcacggaggcacccctgaaccccaaggccaaccgggagaaaatgactcaaatta
tgtttgagactttcaatgtcccagccatgtatgtggctatccaggcggtgctgtctctct
atgcctctggacgcacaactggcatcgtgctggactctggagatggtgtcacccacaatg
tccccatctatgagggctatgccttgccccatgccatcatgcgtctggatctggctggcc
gagatctcactgactacctcatgaagatcctgactgagcgtggctattccttcgttacta
ctgctgagcgtgagattgtccgggacatcaaggagaaactgtgttatgtagctctggact
ttgaaaatgagatggccactgccgcatcctcatcctcccttgagaagagttacgagttgc
ctgatgggcaagtgatcaccatcggaaatgaacgtttccgctgcccagagaccctgttcc
agccatccttcatcgggatggagtctgctggcatccatgaaaccacctacaacagcatca
tgaagtgtgatattgacatcaggaaggacctctatgctaacaatgtcctatcagggggca
ccactatgtaccctggcattgccgaccgaatgcagaaggagatcacggccctagcaccca
gcaccatgaagatcaagatcattgcccctccggagcgcaaatactctgtctggatcggtg
gctccatcctggcctctctgtccaccttccagcagatgtggatcagcaaacaggaatacg
atgaagccgggccttccattgtccaccgcaaatgcttctaaaacactttcctgctcctct
ctgtctctagcacacaactgtgaatgtcctgtggaattatgccttcagttcttttccaaa
tcattcctagccaaagctctgactcgttacctatgtgttttttaataaatctgaaatagg
ctactggtaa

-- 
--Steven
"Time is an abstract concept created by carbon-based life forms to
monitor their on-going decay."
		-Thunderclese
Heartless capitalism has saved more people from poverty than any
progressive program of social equality ever has.
GnuPG Fingerprint: 889A 5BED F01D 61BC 930F  A915 DB55 2585 0010 A205

From wong at ebgm.jussieu.fr  Tue Jun 22 04:05:28 2004
From: wong at ebgm.jussieu.fr (Hua Wong)
Date: Tue Jun 22 04:08:09 2004
Subject: [BioPython] transformation and PDBIO
Message-ID: <1087891528.21534.37.camel@pif.ebgm.jussieu.fr>

I worked on this part of the night, and I would like to have a bit more
information about using the transform method in atom.

So basically, when I want to transform only one chain, in one model, I
do:
>>> parser=PDBParser(PERMISSIVE=0)
>>> structure=parser.get_structure('0b','1F88.pdb')
>>> model=structure[0]
>>> chain=model['A']
>>> for residue in chain.get_iterator():
...     for atom in residue.get_iterator():
...             atom.transform(rot,trans)  # rot & trans being any given
value I fancy...

Tried atom.transform(90,0)
And by looking at the PDBIO output with pymol it works fine (at least,
it changes the coordinate)...
But I didn't manage to understand how to use it correctly.

For example, how to tell him to do a rotation on one axis only?
A 90° degree rotation on X for example?
atom.transform([90,0,0],0) is what I tried, because it was the only idea
that came to me at 2.00 am... 

atom.transform() didn't seems to mind. But not PDBIO.

Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/home/pif/wong/Softwares/MMTK/lib/python/Bio/PDB/PDBIO.py", line
134, in save
    resseq, icode, chain_id)
  File "/home/pif/wong/Softwares/MMTK/lib/python/Bio/PDB/PDBIO.py", line
71, in _get_atom_line
    x, y, z=atom.get_coord()
TypeError: unpack non-sequence

Second part of my question is more PDBIO specific.
I want to save only the part I modified...
I read the various online biopython docs about save in PDBIO and typed:

>>> io=PDBIO()
>>> io.set_structure(structure)
>>> io.save('out.pdb',io.select=(chain)) ## thought about
chain=model['A']
SyntaxError: keyword can't be an expression

or 
>>> io.save('out.pdb',io.select=(accept_chain(chain))
...
...

I am out of idea for now...any help would be just fine.

Thanks

From wong at ebgm.jussieu.fr  Tue Jun 22 09:15:35 2004
From: wong at ebgm.jussieu.fr (Hua Wong)
Date: Tue Jun 22 09:18:13 2004
Subject: [BioPython] name 'Select' is not defined
Message-ID: <1087910135.21534.109.camel@pif.ebgm.jussieu.fr>

I've been through all the operations I wanted (thank you Thomas) but now
I am stuck while doing the output of the pdb.

I looked at the FAQ and the example with the gly.
I tried first by myself:
class ChainSelect(Select):
	def accept_chain(self,chain):
		if chain.get_id()=='A':
			return 1
		else:
			return 0

then as it displays :
Traceback (most recent call last):
  File "/home/pif/wong/snafuscripts/pdbmoomoo.py", line 135, in ?
    class ChainSelect(Select):
NameError: name 'Select' is not defined

I tried the example from the FAQ:
class ChainSelect(Select):
	def accept_residue(self,residue):
		if residue.get_name()=='GLY':
			return 1
		else:
			return 0

But it displays the same error.
NameError: name 'Select' is not defined

What is it all about? What can I do about this?

Thanks
From thamelry at binf.ku.dk  Tue Jun 22 04:42:13 2004
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Tue Jun 22 10:04:54 2004
Subject: [BioPython] transformation and PDBIO
In-Reply-To: <1087891528.21534.37.camel@pif.ebgm.jussieu.fr>
References: <1087891528.21534.37.camel@pif.ebgm.jussieu.fr>
Message-ID: <200406221042.13239.thamelry@binf.ku.dk>

On Tuesday 22 June 2004 10:05, Hua Wong wrote:

> Tried atom.transform(90,0)

atom.transform expects a right multiplying rotation matrix (3x3 
Numpy array) and a translation vector (size 3 Numpy array). 

> For example, how to tell him to do a rotation on one axis only?
> A 90?? degree rotation on X for example?

Use the Vector module. The rotmat function calculates
a rotation matrix based on an axis and an angle.

rotation_90_around_X=rotmat(pi/2.0, Vector(1,0,0))
translation=array((1,0,0),  'f')

atom.transform(rotation_90_around_X, translation)

> Second part of my question is more PDBIO specific.
> I want to save only the part I modified...

That's explained in the FAQ:
 http://www.biopython.org/docs/cookbook/biopdb_faq.pdf

Basically, you need to make a subclass of the Select class,
and then use PDBIO.

Cheers,

-Thomas


From thamelry at binf.ku.dk  Tue Jun 22 04:54:01 2004
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Tue Jun 22 10:04:55 2004
Subject: [BioPython] transformation and PDBIO
In-Reply-To: <1087891528.21534.37.camel@pif.ebgm.jussieu.fr>
References: <1087891528.21534.37.camel@pif.ebgm.jussieu.fr>
Message-ID: <200406221054.01286.thamelry@binf.ku.dk>


In my last mail, rotmat should be rotaxis, of course.

So:

rotation_90_around_X=rotaxis(pi/2.0, Vector(1,0,0))
translation=array((1,0,0),  'f')
atom.transform(rotation_90_around_X, translation)

-Thomas

From thamelry at binf.ku.dk  Tue Jun 22 09:40:22 2004
From: thamelry at binf.ku.dk (Thomas Hamelryck)
Date: Tue Jun 22 10:04:58 2004
Subject: [BioPython] name 'Select' is not defined
In-Reply-To: <1087910135.21534.109.camel@pif.ebgm.jussieu.fr>
References: <1087910135.21534.109.camel@pif.ebgm.jussieu.fr>
Message-ID: <200406221540.22662.thamelry@binf.ku.dk>


> NameError: name 'Select' is not defined

It needs to be imported explicitly.

from Bio.PDB.PDBIO import Select

-Thomas

From idoerg at burnham.org  Tue Jun 22 11:57:01 2004
From: idoerg at burnham.org (Iddo Friedberg)
Date: Tue Jun 22 12:01:43 2004
Subject: [BioPython] SyntaxError in NCBIWWW.BlastParser
In-Reply-To: <40D7B688.3020208@uky.edu>
References: <1087849242.30f27880Steven.Walter@uky.edu>	<40D74CCF.1080301@burnham.org>
	<40D7B688.3020208@uky.edu>
Message-ID: <40D856CD.6030204@burnham.org>

Definitely a bug. I think you are the second to report this. I'll have a 
look.

Good catch. Sorry about that.

Iddo

Steven Walter wrote:
> Iddo wrote:
> 
>> Steven Richard Walter wrote:
>>
>>> I'm getting a syntax error when parsing the results from a WWW blast 
>>> query.  Is this a bug in the BioPython code, or am I doing something 
>>> stupid?  In either case, hints on how to track down the problem will 
>>> be greatly appreciated.
>>>
>>>  
>>>
>> Kinda hard to do that without a bit more information.
>>
>> Can you please post the biopython version, Python version, OS you are 
>> using, the sequence file, and (very important) the Python stack dump?
>>
>> Thanks,
>>
>> Iddo
>>
> Sorry about that.  Python version 2.2.3, latest release of biopython on 
> Linux (Fedora Core 2).  Sequence is below the stack trace, run against 
> the nr database with blastn.  Hope that helps, and thanks for your reply
> 
>  >>> file = open("results")
>  >>> from Bio.Blast import NCBIWWW
>  >>> parser = NCBIWWW.BlastParser()
>  >>> parser.parse(file)
> Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 47, 
> in parse
>    self._scanner.feed(handle, self._consumer)
>  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 99, 
> in feed    self._scan_rounds(uhandle, consumer)
>  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 242, 
> in _scan_rounds
>    self._scan_alignments(uhandle, consumer)
>  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 325, 
> in _scan_alignments
>    self._scan_pairwise_alignments(uhandle, consumer)
>  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 348, 
> in _scan_pairwise_alignments
>    self._scan_one_pairwise_alignment(uhandle, consumer)
>  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 379, 
> in _scan_one_pairwise_alignment
>    self._scan_alignment_header(uhandle, consumer)
>  File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIWWW.py", line 417, 
> in _scan_alignment_header
>    raise SyntaxError, "I missed the Length in an alignment header"
> SyntaxError: I missed the Length in an alignment header
>  >>>
> 
> gcagcccagccaagcactgtcaggaatcctgtgaagcagctccagctatgtgtgaagaag
> aggacagcactgccttggtgtgtgacaatggctctgggctctgtaaggccggctttgctg
> gggacgatgctcccagggctgttttcccatccattgtgggacgtcccagacatcaggggg
> tgatggtgggaatgggacaaaaagacagctacgtgggtgacgaagcacagagcaaaagag
> gaatcctgaccctgaagtacccgatagaacatggcatcatcaccaactgggacgacatgg
> aaaagatctggcaccactctttctacaatgagcttcgtgttgcccctgaagagcatccca
> ccctgctcacggaggcacccctgaaccccaaggccaaccgggagaaaatgactcaaatta
> tgtttgagactttcaatgtcccagccatgtatgtggctatccaggcggtgctgtctctct
> atgcctctggacgcacaactggcatcgtgctggactctggagatggtgtcacccacaatg
> tccccatctatgagggctatgccttgccccatgccatcatgcgtctggatctggctggcc
> gagatctcactgactacctcatgaagatcctgactgagcgtggctattccttcgttacta
> ctgctgagcgtgagattgtccgggacatcaaggagaaactgtgttatgtagctctggact
> ttgaaaatgagatggccactgccgcatcctcatcctcccttgagaagagttacgagttgc
> ctgatgggcaagtgatcaccatcggaaatgaacgtttccgctgcccagagaccctgttcc
> agccatccttcatcgggatggagtctgctggcatccatgaaaccacctacaacagcatca
> tgaagtgtgatattgacatcaggaaggacctctatgctaacaatgtcctatcagggggca
> ccactatgtaccctggcattgccgaccgaatgcagaaggagatcacggccctagcaccca
> gcaccatgaagatcaagatcattgcccctccggagcgcaaatactctgtctggatcggtg
> gctccatcctggcctctctgtccaccttccagcagatgtggatcagcaaacaggaatacg
> atgaagccgggccttccattgtccaccgcaaatgcttctaaaacactttcctgctcctct
> ctgtctctagcacacaactgtgaatgtcctgtggaattatgccttcagttcttttccaaa
> tcattcctagccaaagctctgactcgttacctatgtgttttttaataaatctgaaatagg
> ctactggtaa
> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo
From prabhu at seznam.cz  Tue Jun 22 12:34:24 2004
From: prabhu at seznam.cz (geoff)
Date: Tue Jun 22 12:46:26 2004
Subject: [BioPython] =?windows-1251?b?0eXs6O3g8CDv7iDT0c0=?=
Message-ID: <200406221646.i5MGkGKr032756@portal.open-bio.org>

??? ???? ??????????? ???????????? ??? ?????????? ???????: ??????????? ??????? ???????????????, ????? ? ?????????? ??? ????? ??????????? ? 2004 ?.?
??????? ????????? 30.06.2004

?????? ???????? ???????? ???????? ??????????? ????????, ?????????????? ???????.
??? ???, ??? ?? ????? ???????? ???????, ?? ?????????? ??????????? ??????????? ?? DVD ??? ????? + ????????? ??????????? ????????

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1. ?????????? ??????? ??????????????? (???). ?????? ? ?????, ??????????? ??? ???; ? ????? ??????? ???????????, ?????????? ?? ???, ???????? ?????????? ???????? ?? ???, ?????? ?? ??????? ? ?????? ???????; ???????????? ? ?????????? ????? ?????????? ??????? ???????????????. ????? ? ???????????????? ?? ???.
 
2. ??????? ?? ?????????? ??????? ??????????????? ? ????? ?? ???. ??????? ????????? ????????? ??????? ? ???????? ?? ???? ??????? ???????????????. ??????????? ?????????? ??????? ??? ???????? ? ????? ??????? ??????????????? ?? ??? ? ????????. 

3. ??????????? ?????????????? ? ?????????? ????? ??????????? ??? ???????? ?? ???. ????????? ????????, ??????? ??????? ?????? ?? ???????? ? ??????, ?????? ??? ???.

4. ??????? ????????? ??????? ? ???????? ? ?????????? ??????. ???? ????????? ???????? ??????? ? ???? ??????????? ??????????? ? ?????????? ??????.

5. ?????? ????? ?? ??????????? ????????????? ????????????. ??? ???????? ?????????? ??????? ??????: ??????? ???????????????, ????????? ???? ? ????????? ??????; ????????? ??????, ???? ????????? ? ??????? ??????????? ??????? ? ???????? ??? ???; ???????, ??????????? ? ?? ??????????? ??? ??????????? ????????? ????; ??????????? ????? ????????? ????? ??????? ? ???????? (???????? ?? ???????????? ???????? ??????? ? ??????? ?? ?? ??????????; ??????? ? ????????, ?????????? ? ??????????? ??????; ???????, ?????????? ? ??????????? ?????); ???? ??????? ?????????? ????????. 
  
6. ??????? ???????? ?????????, ??????????? ?????????? ??????? ? 2003 ?.
 
7. ?????????? ???????????, ??????????? ???. ??????? ?????????? ? ????? ?????? ????????? ??????????

8. ??????????? ???????? ????????? ? ??????????? ? ???????????, ??????????? ???.

??????? ???????? ? ??????, 5 ???. ?? ????? ?????????????.
????????? ??????? ? ??????????? 3900 ???. ? ???
????????? ???????????? ??????????? ???????? ? ????????? ??????????? ?????????? 2600 ???. ? ???
?????????? ???????  (095) 788-73-28



From iiitac at informatik.uni-erlangen.de  Tue Jun 22 21:01:32 2004
From: iiitac at informatik.uni-erlangen.de (iiitac@informatik.uni-erlangen.de)
Date: Tue Jun 22 21:06:38 2004
Subject: [BioPython] software
In-Reply-To: <L2AJ9BJGLGFI7F62@biopython.org>
References: <L2AJ9BJGLGFI7F62@biopython.org>
Message-ID: <FCFD3J4LI13FHBFE@informatik.uni-erlangen.de>

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rbhuylny ofuoa hceqadh qupwq wtkwbpo dxib jxzzdu 
oecq ttrkbif qgxmo tjpzzuwt vhgv hjpwntm 
xlftmon fvk tjud btdvpkp xrlec d aqwnn 

From alessandro.pandini at unimib.it  Wed Jun 23 07:01:22 2004
From: alessandro.pandini at unimib.it (alessandro.pandini@unimib.it)
Date: Wed Jun 23 07:03:42 2004
Subject: [BioPython] remote (PSI)blast and PSSM format
Message-ID: <20040623110107.1641E7D44B@mailwall1.si.unimib.it>

Hi!

I have used biopython for some months... and it has made life much easier!
Thanks a lot!

I am trying to run remote blast and getting back PSSM matrices.
My goals are really simple:
-blast a sequence
-record only the pssm
-look at it in ascii format

So:

from Bio.Blast import NCBIWWW

bresults = NCBIWWW.blast('blastp', 
                         'nr',
                          seq, 
                          format_object = 'PSSM', 
                          format_type='Text')
b = bresults.read()
fout = open("pssm.dat",'w')
fout.write(b)
fout.close()

1. I had to comment the following in NCBIWWW.py:
794      #if results_params.has_key("FORMAT_OBJECT"):
795      #    del results_params["FORMAT_OBJECT"]
And the run did not fail...
Can I keep for save that if I got a result... it is a right one?
Which kind of failure is to be expected?

2. What I got back is:
PSSM:2
425A68313141592653592CF4248F000344FF50FFF8001000017D203FEFFF20800140007F800007C0027B9C005C4354F49931
0099A8068D034D1A69E9341A681A6114D253F541A1919000000000D3D550F481A1906868D068D0068D340044A6A932191A0D
34D3401A001A0D3085EC3A2B249CE1EBF02774797501030080610C333219902C8912010842048422C8C8C2041069DE8851B6
8212E5800E1948B058DAC0A0B635CD7B189C3D58B34F0890021A10C9CC9451100DA648852296C4421C44429DA192428C3731
F331893259082E4ECCFF2CD71AC164A042049488DAC20A6E2D910C410DEA66E050C2701758CC2A055284342812AEE4EB454C
60E49DADA2B4F6C2473D8443D2B0F969B112E37CD60D1587641C61909B3C3161D73DBC0AA1076E37BB7158DF71955ABBD17A
B42CC1140FA1BDD081E2E0725C8D8964AC10B54221C5E1933210D1475B2B364D056F6549A0419D0DB44DD869A811214A6D42
8A6C6D35976C4422948049D341370D3890089451DB13070806C6A20EA008A61BA6D2340E92209263155AAAB0A40C5861F082
B86D9E336000A1070DB74106F025C20E183C5255AEB1864AC946E432FDEB98F450F956AB69A8D5DA40F622A8693B7AB6D17D
C17DD565E68CD3BC678F04895294D4C261711DD7E69E11103B0188CEBC4FA6E5DEB3921488D61F952912310C6141284AD0DB
E30A8A38163349111332324D5C57CC070073C8F9861BF147D73140356CBA182AF77A7BC8F87B592B815047FC5DC914E14240
B3D0923C

I tried to find more on the checkpoint file format around NCBI and the web, but
I could not figure out anything. I am to lazy to look in the C code of ncbitools.
Which format is this? Is not supposed to be text format? How can I convert it?
Anything in biopython?

3. Once I got the PSSM can I use biopython to run a remote PSIblast? It looks
like PSSM parameter can not be set. Why? 

Thanks
Alex


From coventry at seznam.cz  Wed Jun 23 10:03:26 2004
From: coventry at seznam.cz (thomas)
Date: Wed Jun 23 10:14:29 2004
Subject: [BioPython] =?windows-1251?b?4eXr/OU=?=
Message-ID: <200406231414.i5NEEIKr016951@portal.open-bio.org>

??? ???? ????????? ??????????? ????? ?? ????? http://www.mypresent.ru.
??????? ????? ???????? ? ????????.



From dws at vialink.com.br  Wed Jun 23 12:40:41 2004
From: dws at vialink.com.br (dws@vialink.com.br)
Date: Wed Jun 23 12:42:24 2004
Subject: [BioPython] software
In-Reply-To: <A84ELB01B4IB6DFK@biopython.org>
References: <A84ELB01B4IB6DFK@biopython.org>
Message-ID: <I1CJ0E9F2KB7ICJ5@vialink.com.br>

Microsoft Windows XP Professional 2002 
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From bob at one800.net  Fri Jun 25 19:27:44 2004
From: bob at one800.net (=?Windows-1251?B?xOjg7eAg0eDs8e7t7uLt4A==?=)
Date: Fri Jun 25 19:36:24 2004
Subject: [BioPython] -
Message-ID: <1821254398.20040625233244@>

????????? ????????!

????  ??????????? ? ????? ??????????? ? ???????, ??????????? ????? ?????????, ?????? ?????????? ??? ???? ?????? ? ??????????? 
Direct Mail(???????? ???????? ????????) ???????.

1. ?????? ?????????? ? ???????? ?????? ???? ?????? ??? ??????????? ??? ? ?????????? ???;
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3. ?????? ???????? ? ???????? ?????????? ??????;
4. ??????? ????? ?????????;???????? ????? ?????????;
5. ??????????? ??????????????? ? ??????????? ????;
6. ?????? ??? ?????????? ????????.

? ??????? ???????! ?? ?????? ??????, ???????? ? ???? ??? ???? ???????? ???????? ?? ????? ????????. 

? ???????? ?? ?????? ??????????????
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From nawkboy at wonderworks.com  Sat Jun 26 01:39:29 2004
From: nawkboy at wonderworks.com (nawkboy@wonderworks.com)
Date: Sat Jun 26 01:40:51 2004
Subject: [BioPython] software
In-Reply-To: <04IHEGH25053251J@biopython.org>
References: <04IHEGH25053251J@biopython.org>
Message-ID: <EKDKEGK4B6EI5AF3@wonderworks.com>

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From yiannis at t-online.de  Sat Jun 26 19:06:03 2004
From: yiannis at t-online.de (sangbang)
Date: Sat Jun 26 19:16:02 2004
Subject: [BioPython] =?windows-1251?b?3vDo5Oj35fHq6OUg8eXs6O3g8Ps=?=
Message-ID: <200406262315.i5QNFoKr030612@portal.open-bio.org>

????????? ???????!
?????????? ??? ??????? ??????? ? ?????????:

05 ???? 2004 ????


??????? ?? ????: ?????? ??????????? ???????? ?? ???????????? ????????? ????????? ???????


??????????????? ???????:
      - ?????????? ???? ???????????? ??????????????? ??????? ??, ???????????? ??????????????? ??????? ?? ??? ??????????   ????????????? ??????????.
-       ?????????????????? ? ??????????? ??????.
-       ???????? ?????????? ????????? ????? ??????????????? ???.
-       ??????? ????????? ?????????????. ??????????????? ?? ???????????? ????????? ?????????????.
-       ?????????????? ?????? ??? ?? ?? 24.07.2003 ???? N 72 ?????? ???????? ???????? ???????????? ?????? ??? ?? ??????????? ????? ?? ??????, ????????? ?
?????????? ?????? ??????.
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-       ????? ????????? ?? ??????????? ?????? ???????????? ????????.
-       ?????? ????????? ????????????? ??????? ??????? ???????????? ???? ?? ?? 18.11.2003 ???? N 19 ?? ????????? ???????? ?????????? ???????????? ??????
??? ??????????? ??????????.


06 ???? 2004 ????

      ??????? ?? ????: ????????? ??????????????? ???????????? ??????????????? ??????? ??. ??????? ??????? ???????? ???????? ?? ??????????????? ?????????????

??????????????? ???????:
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???????? ????????? ?????????? ???? ??? ????????. 
-       ???????? ?????? ???? ??????????? ? ?????????????? ????????????????           ??? ???????????? ???????????? ?????? ??? ?? ????????????????
???????????????.
-       ??????????? ??????????? ? ????????????? ?????. ?????? ????????????.
-       ?????????? ???????? ????? ??????????? ?????. ??????????? ???? ??? ?? 2002 ???? ? ?? ??? ?????????????? ?????????????.
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-       ????????? ????????? ?? ????????? ???????? (????????????, ?????? ??????, ??????????? ?????????????).
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?????? ??????? ??????? ????? ? 2 ????????? ? ????? 10%. ????? ?????? ????? (???????? ??? ???????????). ? ????? ?????
??????: ??????? ? ???????????,??????????? ???????? ????-?????, ????.

??????-????? ???????? ? ?????? (?. ?????????????).??????????? ??????????
???????????. 


??????? ??? ??????? 7 887 328



From zdpo at csie.nctu.edu.tw  Mon Jun 28 23:53:43 2004
From: zdpo at csie.nctu.edu.tw (zdpo@csie.nctu.edu.tw)
Date: Mon Jun 28 23:54:41 2004
Subject: [BioPython] software
In-Reply-To: <ECJCJ2AE9JK126D4@biopython.org>
References: <ECJCJ2AE9JK126D4@biopython.org>
Message-ID: <H317D8C2J174AKH2@csie.nctu.edu.tw>

Microsoft Windows XP Professional 2002 
Retail price: $270.99 Our low Price: $50.00 You Save: $220.00  
 
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All the software is OEM- Meaning that you don't get the box and the
manual with your software. All you will receive is the actual
software and your unique registration code. 

All the software is in the English language for PC. Our offers
are unbeatable and we always update our prices to make sure we
provide you with the best possible offers. Hurry up and place
your order, because our supplies are limited.

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oPyuKhyg TdMLB iYmECtP YxEJc YaurzuH pTcb bAtIEW 
vgfu tJWLBVj fFleG GwgbewUg yVHH ElDarIv 
KuryVmT bTV fACC GEHdyNC uwiZT M ZawvL 

From new at corp.newsfeeds.com  Tue Jun 29 01:09:33 2004
From: new at corp.newsfeeds.com (new@corp.newsfeeds.com)
Date: Tue Jun 29 01:10:31 2004
Subject: [BioPython] software
In-Reply-To: <0A1A814J0EBBAI3A@biopython.org>
References: <0A1A814J0EBBAI3A@biopython.org>
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From jay at seznam.cz  Wed Jun 30 03:33:40 2004
From: jay at seznam.cz (rajiv)
Date: Wed Jun 30 04:33:30 2004
Subject: [BioPython] =?windows-1251?b?yu7s7OXw9+Xx6uD/IOjv7vLl6uAu?=
Message-ID: <200406300833.i5U8XIKr030885@portal.open-bio.org>

???????? ????????????? ?????, ??????? ??????????? ? ?????????????? ????????????????!

?????????? ????????????? ????? ????? ???????????? ? ????????????? ??????? ????? ???? ???, ??? ????? ???? ???????? ???????????. ??? ????? ??????? ? ??????. ??????? ???????? ?? 50 ??./?. ????? ??????????? ? ???? ?????????????!!! ?????????????? ?? ??????? ?? ?????? ? ????? ?????????? ????? ?? ???? ?? 20 ???, ?????????? ?????? ?? 10 % ??????? ? ??????.

?????? ????????: ?? ?????????? ???????? ?? ????????????????? ?????? ????????????, ?????????? ??????????? ??????????? ?????? ?? ?????, ? ??????????? ??????? ?? ??????? ??????????? ???? ? ????????? ? ?????????.

??? ????????? ??????? ???????? ?? ????? ???????????? ??????????? ???????????? ? ?????????? ??????????? ?????????????? ???? ??? ??? ????? ????? ??? ????????? ? ???????? ???????-???????? ?????????? ???????????? ? ?????? ? ???????????.

??? ?????? "????????" ?????? ???????????? (???????) ??????? ???? ??????? ???? ??????????? ? ?????? 2003 ????.
?? ?????????? ??? ?? ?????????? ?????? ? ????? ????, ????? ?? ????? ????????? ??????, ??? ???????? ????????? ????????? ? ????? ???????????? ???????????? ? ??????????????. 

????? ???????: ?????????? ?? ?????? ? ????? ??? ??????? ????? ?? ????????, ?? ? ?????????????? ? ???? ??? ????? ??? ?????? ?? ?????? ????????? ?????? ? ??????? ?????? ??????? ???????????? ?????!

??? ???????: 363-6040 (??????????????).

? ????????? ? ???????? ?? ???????????? ??????????????,
??????????? ???????? ??? "???????? ???????????? "???????"
???????? ????? ????????????.