", "
 is how FASTA is delimited in this case
parser = Fasta.RecordParser()
iterator = Fasta.iterator( parser, xtractor )

Anyway, the whole point of doing this is to not see HTML.  I'm totally not sure if the above makes sense as a general approach, but it is fairly easy in cases where delimiters are identifiable and the desired format is embedded in HTML.

So my question is, if I don't want to see the HTML, and to see only the python objects, is this problem totally solved?  Or are there areas like the above where the biopython methods return only HTML?

Regards,

JJ

From verma at cc.helsinki.fi  Wed Jul 23 07:07:40 2003
From: verma at cc.helsinki.fi (Abhinav Verma)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] errata in cookbook
Message-ID: 

in cookbook, section 3.3.2, we have

>>from Bio.Medline import PubMed

but i got an error while trying this statement, and found out that rather

>>from Bio import PubMed

works.

I am working on a linux platform, and just felt that this might be a
typographical error. Would be fine for new users.

cheers,
Abhinav.

From Y.Benita at pharm.uu.nl  Wed Jul 23 10:38:51 2003
From: Y.Benita at pharm.uu.nl (Yair Benita)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] EMBL parser
Message-ID: 

I was wondering why the EMBL parser is in the expression module and not in a
separate EMBL module which allows to parse records. It is also strange as it
does not have any functions. How is this module used to parse EMBL records?

Yair
-- 
Yair Benita
Pharmaceutical Proteomics
Utrecht University 

From jchang at jeffchang.com  Wed Jul 23 11:37:11 2003
From: jchang at jeffchang.com (Jeffrey Chang)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] errata in cookbook
In-Reply-To: 
Message-ID: <86E599D4-BD23-11D7-840A-000A956845CE@jeffchang.com>

Thanks.  I've fixed these.

Jeff

On Wednesday, July 23, 2003, at 04:07  AM, Abhinav Verma wrote:

>
> in cookbook, section 3.3.2, we have
>
>>> from Bio.Medline import PubMed
>
> but i got an error while trying this statement, and found out that 
> rather
>
>>> from Bio import PubMed
>
> works.
>
> I am working on a linux platform, and just felt that this might be a
> typographical error. Would be fine for new users.
>
> cheers,
> Abhinav.
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From jchang at jeffchang.com  Wed Jul 23 11:44:42 2003
From: jchang at jeffchang.com (Jeffrey Chang)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] EMBL parser
In-Reply-To: 
Message-ID: <93818E1E-BD24-11D7-840A-000A956845CE@jeffchang.com>

It is a Martel expression, so the functions are in the Martel package.  
The file just contains a description of the EMBL format, which Martel 
uses to construct a parser.  There's a "format" variable in the module 
that you can use to create the parser in the usual Martel way:
     parser = embl65.format.make_parser()
     parser.setContentHandler(saxutils.XMLGenerator())
     parser.parseFile(open(FILENAME))

Jeff

On Wednesday, July 23, 2003, at 07:38  AM, Yair Benita wrote:

> I was wondering why the EMBL parser is in the expression module and 
> not in a
> separate EMBL module which allows to parse records. It is also strange 
> as it
> does not have any functions. How is this module used to parse EMBL 
> records?
>
> Yair
> -- 
> Yair Benita
> Pharmaceutical Proteomics
> Utrecht University
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From djaeggi at imim.es  Wed Jul 23 12:29:29 2003
From: djaeggi at imim.es (Daniel Jaeggi)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] BIND XML parser
Message-ID: <200307231829.29551.djaeggi@imim.es>

Hello!

We're trying to parse BIND XML files. I know that a biopython version doesn't 
exist, but does anyone have one (written in any language) before we write our 
own. It would save a lot of time - the BIND specification looks really dense!

Thanks,

Daniel

From bartek at rezolwenta.eu.org  Wed Jul 23 14:53:19 2003
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Support for standalone version of AlignACE motif
	search program
Message-ID: <1058986399.3f1ed99f8c4ed@imp.rezolwenta.eu.org>

Hello All,

I have written a wrapper for standalone version of AlignACE software.
(http://atlas.med.harvard.edu/) It's still far from perfect, but it serves well
for me.

It includes the Application class, AlignAceStandalone.AlignAce() function to run
it, Scanner and Parser. As a result of the code like this:

from Bio.AlignAce.AlignAceStandalone import AlignAce
from Bio.AlignAce.Parser import AlignAceParser

result = AlignAce("test.seq")
motifs = AlignAceParser().parse(result[1])

you have set of motifs found by AlignAce in the sequences from the FASTA file
test.seq. 

It assumes that the AlignACE executable is in your path, and the test.seq file
is in current directory.

This module includes also the implementation of a motif object. I'm not sure if
my implementation is general enough to become a BioPython structure, but I think
there's a need for something like that. Probably it should be called
Bio.SeqMotif and include different things (more than my simplistic idea).

I would be really glad if You will find it interesting enough to include it to
the biopython cvs, any comments/remarks are more than welcome.  
-- 
regards
   Bartek Wilczy?ski

-------------- next part --------------
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From jefftc at stanford.edu  Wed Jul 23 16:40:00 2003
From: jefftc at stanford.edu (Jeffrey Chang)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Support for standalone version of AlignACE motif
	search program
In-Reply-To: <1058986399.3f1ed99f8c4ed@imp.rezolwenta.eu.org>
Message-ID: 

Hey Bartek,

Your package looks very nice.  I'd be happy to check it in under 
Bio.AlignAce.  I am getting ready to put out a release, so it will have 
to be done after that goes out.

Please take a look at the documentation for contributing code to 
Biopython the website at:
http://www.biopython.org/docs/developer/contrib.html

In particular, please read the "Submitting Code" section and make sure 
you agree with it.  Mostly, it is just to make sure that you want to 
support your code, and that you agree to the Biopython license.  Let me 
know if everything seems good to you.

Jeff

On Wednesday, July 23, 2003, at 11:53  AM, Bartek Wilczynski wrote:

> Hello All,
>
> I have written a wrapper for standalone version of AlignACE software.
> (http://atlas.med.harvard.edu/) It's still far from perfect, but it 
> serves well
> for me.
>
> It includes the Application class, AlignAceStandalone.AlignAce() 
> function to run
> it, Scanner and Parser. As a result of the code like this:
>
> from Bio.AlignAce.AlignAceStandalone import AlignAce
> from Bio.AlignAce.Parser import AlignAceParser
>
> result = AlignAce("test.seq")
> motifs = AlignAceParser().parse(result[1])
>
> you have set of motifs found by AlignAce in the sequences from the 
> FASTA file
> test.seq.
>
> It assumes that the AlignACE executable is in your path, and the 
> test.seq file
> is in current directory.
>
> This module includes also the implementation of a motif object. I'm 
> not sure if
> my implementation is general enough to become a BioPython structure, 
> but I think
> there's a need for something like that. Probably it should be called
> Bio.SeqMotif and include different things (more than my simplistic 
> idea).
>
> I would be really glad if You will find it interesting enough to 
> include it to
> the biopython cvs, any comments/remarks are more than welcome.
> -- 
> regards
>    Bartek Wilczy?ski
>
>
>
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From bartek at rezolwenta.eu.org  Wed Jul 23 17:18:23 2003
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Support for standalone version of AlignACE motif
	search program
In-Reply-To: 
References: 
Message-ID: <1058995103.3f1efb9fdce01@imp.rezolwenta.eu.org>

Quoting Jeffrey Chang :

> Hey Bartek,
> 
> Your package looks very nice.  I'd be happy to check it in under 
> Bio.AlignAce.  I am getting ready to put out a release, so it will have 
> to be done after that goes out.
> 
> Please take a look at the documentation for contributing code to 
> Biopython the website at:
> http://www.biopython.org/docs/developer/contrib.html
> 
> In particular, please read the "Submitting Code" section and make sure 
> you agree with it.  Mostly, it is just to make sure that you want to 
> support your code, and that you agree to the Biopython license.  Let me 
> know if everything seems good to you.
> 
> Jeff
> 
I do agree with the license and I'd be happy to support it.

The other thing is that I'll probably be working with other motif Finding tools
as well, and here arises the need of the general class for sequence motifs.
There exists a TFBS module for bioperl (http://forkhead.cgb.ki.se/TFBS/), and it
serves well for my inspiration , but I think that a sequence motif is something
more general than just Transcription Factor Binding Sites. It would be really
great if someone would help me with other possible uses for the sequence motifs. 

looking forward to any comments
   Bartek Wilczy?ski

From Y.Benita at pharm.uu.nl  Thu Jul 24 10:23:19 2003
From: Y.Benita at pharm.uu.nl (Yair Benita)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Something wrong with Martel?
Message-ID: 

I am trying to use Martel to make a parser but something appears to be
wrong.
First, the test fails after building:
###### running tests in test_IterParser ###############
---> I skip all the line until the last:
  File "/Volumes/Applications/CVS/biopython/Martel/LAX.py", line 101, in
__getattr__
    raise AttributeError(name)
AttributeError: data

I think this is something in the test file and not in the Martel code
because all my other Martel scripts work.

Second, trying to run the same script as Andrew wrote in the Readme
(attached), I only get:

Basically nothing is executed after the command: parser.parse(open(File))

Is something wrong on my system or something wrong with the Martel code?
Could anyone try to run the above script?
Thanks,
Yair
-- 
Yair Benita
Pharmaceutical Proteomics
Utrecht University

-------------- next part --------------
Skipped content of type multipart/appledouble
From jchang at jeffchang.com  Thu Jul 24 12:15:03 2003
From: jchang at jeffchang.com (Jeffrey Chang)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Something wrong with Martel?
In-Reply-To: 
Message-ID: 

Yep, it looks like something might be wrong with Martel now.

Andreas, this looks like it might be related to the switch over to 
using a dict object?  Could you take a look at it?

Jeff

On Thursday, July 24, 2003, at 07:23  AM, Yair Benita wrote:

> I am trying to use Martel to make a parser but something appears to be
> wrong.
> First, the test fails after building:
> ###### running tests in test_IterParser ###############
> ---> I skip all the line until the last:
>   File "/Volumes/Applications/CVS/biopython/Martel/LAX.py", line 101, 
> in
> __getattr__
>     raise AttributeError(name)
> AttributeError: data
>
> I think this is something in the test file and not in the Martel code
> because all my other Martel scripts work.
>
> Second, trying to run the same script as Andrew wrote in the Readme
> (attached), I only get:
> 
>
> Basically nothing is executed after the command: 
> parser.parse(open(File))
>
> Is something wrong on my system or something wrong with the Martel 
> code?
> Could anyone try to run the above script?
> Thanks,
> Yair
> -- 
> Yair Benita
> Pharmaceutical Proteomics
> Utrecht University
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From andreas.kuntzagk at mdc-berlin.de  Fri Jul 25 04:30:37 2003
From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Something wrong with Martel?
In-Reply-To: 
References: 
Message-ID: <1059121772.15989.42.camel@sulawesi>

Hi,

> Andreas, this looks like it might be related to the switch over to 
> using a dict object?  Could you take a look at it?

First issue is related to dict. Appended a diff to patch this.

Would be good if setup.py in BioPython root dir would also test the
Martel tests.

> > Second, trying to run the same script as Andrew wrote in the Readme
> > (attached), I only get:
> > 
> >
> > Basically nothing is executed after the command: 
> > parser.parse(open(File))
> >
> > Is something wrong on my system or something wrong with the Martel 
> > code?
> > Could anyone try to run the above script?
Yair, do you have a file "/etc/passwd" (looks like your email is from a
Windows system)? What do you mean "nothing is executed"? Script hangs,
script returns whithout output, script throws an error?

The parser.parse works for me, but the script is failing at
doc.normalize() whith

AttributeError: 'NoneType' object has no attribute 'normalize'

I still don't know enough about the Martel infrastructure to understand
this. sax2dom.document seems to be None.

By, Andreas
-------------- next part --------------
Index: LAX.py
===================================================================
RCS file: /home/repository/biopython/biopython/Martel/LAX.py,v
retrieving revision 1.3
diff -r1.3 LAX.py
116c116
<         self.data.clear()
---
>         self.clear()
139c139
<         self.data.setdefault(tag, []).append(text)
---
>         self.setdefault(tag, []).append(text)
157c157
<         self.data.setdefault(tag, []).append( (text, attrs) )
---
>         self.setdefault(tag, []).append( (text, attrs) )
169c169
<         self.data.setdefault(tag, []).append(
---
>         self.setdefault(tag, []).append(
From greg at tyrelle.net  Sat Jul 26 02:32:44 2003
From: greg at tyrelle.net (Greg Tyrelle)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Something wrong with Martel?
In-Reply-To: 
References: 
Message-ID: <20030726063244.GB22134@nodalpoint.org>

*** Yair Benita wrote: 
  |Second, trying to run the same script as Andrew wrote in the Readme
  |(attached), I only get:
  |
  |
  |Basically nothing is executed after the command: parser.parse(open(File))
  |
  |Is something wrong on my system or something wrong with the Martel code?

Something in your /etc/passwd file is causing the Martel expression to
fail. The script fails on my system (OSX) because of comments in the
passwd file. I have attached a slight modification of the demo script
that deals with comments.

Was that the problem ?

_greg

-- 
Greg Tyrelle
-------------- next part --------------
import Martel
from xml.sax import saxutils,handler

def ToColon(name):
    return Martel.ToSep(name, ":")

comment = Martel.Rep(Martel.Re("^#") +Martel.ToEol())

passwd =  Martel.Rep(
              Martel.Group("record",
              ToColon("account") + ToColon("password") + ToColon("UID") + \
              ToColon("GID") + ToColon("GECOS") + ToColon("directory") + \
              Martel.ToEol("shell")))

format = Martel.Group("passwd", comment + passwd)

parser = format.make_parser()
parser.setContentHandler(saxutils.XMLGenerator())
parser.parseFile(open("/etc/passwd"))

from xml.dom import pulldom
sax2dom = pulldom.SAX2DOM()
parser.setContentHandler(sax2dom)
parser.parseFile(open("/etc/passwd"))
doc = sax2dom.document
doc.normalize()
for record in doc.getElementsByTagName("record"):
    account = record.getElementsByTagName("account")[0].firstChild.nodeValue
    shell = record.getElementsByTagName("shell")[0].firstChild.nodeValue
    print account, "uses", shell
From Y.Benita at pharm.uu.nl  Sat Jul 26 04:04:21 2003
From: Y.Benita at pharm.uu.nl (Yair Benita)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Something wrong with Martel?
In-Reply-To: <20030726063244.GB22134@nodalpoint.org>
Message-ID: 

on 26/7/2003 8:32, Greg Tyrelle at greg@tyrelle.net wrote:

> *** Yair Benita wrote:
> |Second, trying to run the same script as Andrew wrote in the Readme
> |(attached), I only get:
> |
> |
> |Basically nothing is executed after the command: parser.parse(open(File))
> |
> |Is something wrong on my system or something wrong with the Martel code?
> 
> Something in your /etc/passwd file is causing the Martel expression to
> fail. The script fails on my system (OSX) because of comments in the
> passwd file. I have attached a slight modification of the demo script
> that deals with comments.
> 
> Was that the problem ?
> 
> _greg
Yes, that was the problem.
The strange thing is that it does not give any error. The script basically
terminates as if everything is fine.
Thanks,
Yair
-- 
Yair Benita
Pharmaceutical Proteomics
Utrecht University

From Y.Benita at pharm.uu.nl  Sat Jul 26 04:10:53 2003
From: Y.Benita at pharm.uu.nl (Yair Benita)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Something wrong with Martel?
In-Reply-To: <1059121772.15989.42.camel@sulawesi>
Message-ID: 

on 25/7/2003 10:29, Andreas Kuntzagk at andreas.kuntzagk@mdc-berlin.de
wrote:

> Hi,
> 
>> Andreas, this looks like it might be related to the switch over to
>> using a dict object?  Could you take a look at it?
> 
> First issue is related to dict. Appended a diff to patch this.
> 
> Would be good if setup.py in BioPython root dir would also test the
> Martel tests.
> 
>>> Second, trying to run the same script as Andrew wrote in the Readme
>>> (attached), I only get:
>>> 
>>> 
>>> Basically nothing is executed after the command:
>>> parser.parse(open(File))
>>> 
>>> Is something wrong on my system or something wrong with the Martel
>>> code?
>>> Could anyone try to run the above script?
> Yair, do you have a file "/etc/passwd" (looks like your email is from a
> Windows system)? What do you mean "nothing is executed"? Script hangs,
> script returns whithout output, script throws an error?
> 
I do have the file, I work on Mac OS X.
The script just terminates after the command parser.parse and all the
commands after that are not executed. There is no error to suggest that
something went wrong.

> The parser.parse works for me, but the script is failing at
> doc.normalize() whith
> 
> AttributeError: 'NoneType' object has no attribute 'normalize'
> 
> I still don't know enough about the Martel infrastructure to understand
> this. sax2dom.document seems to be None.
> 
> By, Andreas
> 

Greg Tyrelle solved the problem for me (see following email), but still I
find it strange that Martel does not raise an error when the format is not
matching the file being parsed.

Yair
-- 
Yair Benita
Pharmaceutical Proteomics
Utrecht University

From jefftc at stanford.edu  Sat Jul 26 13:22:13 2003
From: jefftc at stanford.edu (Jeffrey Chang)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Something wrong with Martel?
In-Reply-To: <1059121772.15989.42.camel@sulawesi>
Message-ID: 

Thanks for that patch!  I've committed it, and the LAX test suite runs 
properly now.

Jeff

On Friday, July 25, 2003, at 01:29  AM, Andreas Kuntzagk wrote:

> Hi,
>
>> Andreas, this looks like it might be related to the switch over to
>> using a dict object?  Could you take a look at it?
>
> First issue is related to dict. Appended a diff to patch this.
>
> Would be good if setup.py in BioPython root dir would also test the
> Martel tests.
>
>>> Second, trying to run the same script as Andrew wrote in the Readme
>>> (attached), I only get:
>>> 
>>>
>>> Basically nothing is executed after the command:
>>> parser.parse(open(File))
>>>
>>> Is something wrong on my system or something wrong with the Martel
>>> code?
>>> Could anyone try to run the above script?
> Yair, do you have a file "/etc/passwd" (looks like your email is from a
> Windows system)? What do you mean "nothing is executed"? Script hangs,
> script returns whithout output, script throws an error?
>
> The parser.parse works for me, but the script is failing at
> doc.normalize() whith
>
> AttributeError: 'NoneType' object has no attribute 'normalize'
>
> I still don't know enough about the Martel infrastructure to understand
> this. sax2dom.document seems to be None.
>
> By, Andreas
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From jchang at jeffchang.com  Sat Jul 26 13:22:38 2003
From: jchang at jeffchang.com (Jeffrey Chang)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Something wrong with Martel?
In-Reply-To: <20030726063244.GB22134@nodalpoint.org>
Message-ID: 

Yep, it does seem to be messing up on eht comments.  I've updated the 
README file with your fixes.  Thanks!

Jeff

On Friday, July 25, 2003, at 11:32  PM, Greg Tyrelle wrote:

> *** Yair Benita wrote:
>   |Second, trying to run the same script as Andrew wrote in the Readme
>   |(attached), I only get:
>   |
>   |
>   |Basically nothing is executed after the command: 
> parser.parse(open(File))
>   |
>   |Is something wrong on my system or something wrong with the Martel 
> code?
>
> Something in your /etc/passwd file is causing the Martel expression to
> fail. The script fails on my system (OSX) because of comments in the
> passwd file. I have attached a slight modification of the demo script
> that deals with comments.
>
> Was that the problem ?
>
> _greg
>
> -- 
> Greg Tyrelle
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

From andreas.kuntzagk at mdc-berlin.de  Mon Jul 28 07:24:14 2003
From: andreas.kuntzagk at mdc-berlin.de (Andreas Kuntzagk)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Patch for GenBank.Iterator
Message-ID: <1059391393.15987.64.camel@sulawesi>

to handle empty files (current version hangs in an indefinite loop)
There are probably other places whith the same problem

RCS file: /home/repository/biopython/biopython/Bio/GenBank/__init__.py,v
retrieving revision 1.41
diff -r1.41 __init__.py
126c126
<         while _handle.peekline().find("LOCUS") < 0:
---
>         while _handle.peekline() and _handle.peekline().find("LOCUS")
< 0:

From Y.Benita at pharm.uu.nl  Mon Jul 28 09:11:50 2003
From: Y.Benita at pharm.uu.nl (Yair Benita)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Martel module is missing in the 1.20 tar file
Message-ID: 

I tried to install biopython 1.20 from the tar file on the website and it
turns out that the Martel folder is missing. We used to distribute Martel
with the biopython installation. Did that change?
Yair
-- 
Yair Benita
Pharmaceutical Proteomics
Faculty of Pharmacy
Utrecht University

From jchang at jeffchang.com  Mon Jul 28 11:44:17 2003
From: jchang at jeffchang.com (Jeffrey Chang)
Date: Sat Mar  5 14:43:24 2005
Subject: [Biopython-dev] Martel module is missing in the 1.20 tar file
In-Reply-To: 
Message-ID: <5908C4E0-C112-11D7-8DDE-000A956845CE@jeffchang.com>

Yep, Martel is indeed missing.  I have overlooked this in the build.  
I'll fix this, and put out Biopython 1.21 later today.

Thanks,
Jeff

On Monday, July 28, 2003, at 06:11  AM, Yair Benita wrote:

> I tried to install biopython 1.20 from the tar file on the website and 
> it
> turns out that the Martel folder is missing. We used to distribute 
> Martel
> with the biopython installation. Did that change?
> Yair
> -- 
> Yair Benita
> Pharmaceutical Proteomics
> Faculty of Pharmacy
> Utrecht University
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev@biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev