From p.j.a.cock at googlemail.com  Thu Jul  1 05:33:04 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 1 Jul 2010 10:33:04 +0100
Subject: [Biopython] (least) Favorite PDB models?
In-Reply-To: <AANLkTin1WHAN80BOdUQY4jX7fvHiMj4_kbzdR4vB62SJ@mail.gmail.com>
References: <AANLkTin1WHAN80BOdUQY4jX7fvHiMj4_kbzdR4vB62SJ@mail.gmail.com>
Message-ID: <AANLkTil3tYrKIOcXU8233gfYP5HsiZlVJAJAYiURCVZT@mail.gmail.com>

On Thu, Jul 1, 2010 at 4:06 AM, Bryan Lunt <lunt at ctbp.ucsd.edu> wrote:
> Greetings All,
>
> So I have finished (for now) the section of my program that maps PDB
> model residues to SEQRES residues...
>
> And every programmer's favorite thing is QA, right?

It should be ;)

Unit tests are good!

> Does anyone have some suggestions of particularly ugly PDB models
> (discontinuous, strange residue numberings, etc)
> that I can test it on?

There are a few odd files listed here,

http://www.warwick.ac.uk/go/peter_cock/python/ramachandran/top500/

For example 1DIN and 2HMZ showed some interesting behaviour
with fractional occupancy - these should be hard to map onto a single
sequence!

Peter

From anaryin at gmail.com  Fri Jul  2 15:25:21 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 2 Jul 2010 14:25:21 -0500
Subject: [Biopython] BioJava-like seqres alignment for Bio.PDB
In-Reply-To: <AANLkTilaZJ-aVaFCTVw97P3ryBnLXE75najLkzoWcJgf@mail.gmail.com>
References: <AANLkTimQy0Ez8l4p6udUvqzf469IpBov4Fh-6OEefQep@mail.gmail.com> 
	<4C2A7C09.2020204@berkeley.edu>
	<AANLkTilaZJ-aVaFCTVw97P3ryBnLXE75najLkzoWcJgf@mail.gmail.com>
Message-ID: <AANLkTil-8vv40FatNKCRIxzqJrCn9Ogv4IbDg_pSmpVE@mail.gmail.com>

Hey!

>> Does anyone have any code for easy alignment between the SEQRES entry
> >> in a pdb file and the actual ATOM/HETATM entries in the chain?
>

There's not parsing for SEQRES yet in parse_header_pdb but it wouldn't be
hard to.


>  >> In biojava, this is just one of the options when you parse a PDB file,
> >> it would certainly be useful.
>

Indeed it would.


That looks like a good reason to have a PDB XML parser (as trying to do
> this from the plain text PDB is probably fiddly).
>

I don't know if people have started working on such a parser but I have some
sort of a head start. Check here:

http://github.com/JoaoRodrigues/biopython/blob/GSOC2010/Bio/Struct/WWW/WHATIFXML.py

Warning, very ugly :)



> > In any case, having function that provides this mapping (both directions)
> in
> > BioPython would be extremely useful.
>
> Maybe something for the GSoC project TODO list? ;)
>

Hmm, I was working on something more or less like this a while back and it
didn't work that well. But it might be a good idea. It seems however that
Bryan already did it :) No?

Jo?o


From rodrigo_faccioli at uol.com.br  Fri Jul  2 17:50:58 2010
From: rodrigo_faccioli at uol.com.br (Rodrigo Faccioli)
Date: Fri, 2 Jul 2010 18:50:58 -0300
Subject: [Biopython] BioJava-like seqres alignment for Bio.PDB
In-Reply-To: <AANLkTil-8vv40FatNKCRIxzqJrCn9Ogv4IbDg_pSmpVE@mail.gmail.com>
References: <AANLkTimQy0Ez8l4p6udUvqzf469IpBov4Fh-6OEefQep@mail.gmail.com>
	<4C2A7C09.2020204@berkeley.edu>
	<AANLkTilaZJ-aVaFCTVw97P3ryBnLXE75najLkzoWcJgf@mail.gmail.com>
	<AANLkTil-8vv40FatNKCRIxzqJrCn9Ogv4IbDg_pSmpVE@mail.gmail.com>
Message-ID: <AANLkTimEkMSUPowJ3eGhKS_zf-8yv2ms1DKLHA5UyUR3@mail.gmail.com>

Hi,

About the SEQRES implementation for BioPython, I've developed it. Please,
see it in [1]. I hope this implementation could help you.

[1]
http://github.com/rodrigofaccioli/ContributeToBioPython/blob/master/fcfrp/PDBParser.py

Best,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Fri, Jul 2, 2010 at 4:25 PM, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hey!
>
> >> Does anyone have any code for easy alignment between the SEQRES entry
> > >> in a pdb file and the actual ATOM/HETATM entries in the chain?
> >
>
> There's not parsing for SEQRES yet in parse_header_pdb but it wouldn't be
> hard to.
>
>
> >  >> In biojava, this is just one of the options when you parse a PDB
> file,
> > >> it would certainly be useful.
> >
>
> Indeed it would.
>
>
> That looks like a good reason to have a PDB XML parser (as trying to do
> > this from the plain text PDB is probably fiddly).
> >
>
> I don't know if people have started working on such a parser but I have
> some
> sort of a head start. Check here:
>
>
> http://github.com/JoaoRodrigues/biopython/blob/GSOC2010/Bio/Struct/WWW/WHATIFXML.py
>
> Warning, very ugly :)
>
>
>
> > > In any case, having function that provides this mapping (both
> directions)
> > in
> > > BioPython would be extremely useful.
> >
> > Maybe something for the GSoC project TODO list? ;)
> >
>
> Hmm, I was working on something more or less like this a while back and it
> didn't work that well. But it might be a good idea. It seems however that
> Bryan already did it :) No?
>
> Jo?o
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From biopython at maubp.freeserve.co.uk  Mon Jul  5 13:53:41 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 5 Jul 2010 18:53:41 +0100
Subject: [Biopython] Is Bio.Crystal still useful (for NDB files)?
Message-ID: <AANLkTinMfklMpOJ2o7KGH_8mqlgJOP3oQbYI4XyHvdir@mail.gmail.com>

Hello all,

Is anyone using Bio.Crystal? It is a parser for a subset of the PDB format
which used to be used by the The Nucleic Acid Database Project. My
impression from their website is that they are moving all their data to
the PDB format - but still have some structures that are present only
in the NDB format:

http://ndbserver.rutgers.edu/download_data/index.html

I'm asking because Bio.Crystal needs some updating to avoid
deprecation warnings in the latest versions of Python - and it
might be simpler just to deprecate it instead.

Peter

From rjalves at igc.gulbenkian.pt  Mon Jul  5 16:00:17 2010
From: rjalves at igc.gulbenkian.pt (Renato Alves)
Date: Mon, 05 Jul 2010 21:00:17 +0100
Subject: [Biopython] Finding what is the most recent Pubmed ID or list of
	all valid PMIDs
Message-ID: <4C3239D1.7040708@igc.gulbenkian.pt>

Greetings All,

I'm trying to figure out a way to have a more or less up-to-date list of
Pubmed IDs for validation purposes. This has to be performed on a
programmatic way.

My first attempt was to look for this in NCBI's FTP. I could find
ftp://ftp.ncbi.nih.gov/pubmed/deleted_pmids.txt but not information
about the most recent PMID.

I also tried to use EInfo but the count section under PubMed seems
either outdated or completely unrelated to the total number of assigned
PMIDs. Even when adding the total of deleted_pmids + the number from
EInfo I couldn't get accurate information.

So my question is, does anyone know how to get either a list of all the
valid PMIDs or simply the most recent PMID?

Thanks,
Renato

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From biopython at maubp.freeserve.co.uk  Mon Jul  5 16:54:37 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 5 Jul 2010 21:54:37 +0100
Subject: [Biopython] Finding what is the most recent Pubmed ID or list
	of all valid PMIDs
In-Reply-To: <4C3239D1.7040708@igc.gulbenkian.pt>
References: <4C3239D1.7040708@igc.gulbenkian.pt>
Message-ID: <AANLkTil82BTTFYGnw42ZSMy0MsL_kUWdxM3wl6CmO6Xm@mail.gmail.com>

On Mon, Jul 5, 2010 at 9:00 PM, Renato Alves <rjalves at igc.gulbenkian.pt> wrote:
> Greetings All,
>
> I'm trying to figure out a way to have a more or less up-to-date list of
> Pubmed IDs for validation purposes. This has to be performed on a
> programmatic way.
>
> My first attempt was to look for this in NCBI's FTP. I could find
> ftp://ftp.ncbi.nih.gov/pubmed/deleted_pmids.txt but not information
> about the most recent PMID.
>
> I also tried to use EInfo but the count section under PubMed seems
> either outdated or completely unrelated to the total number of assigned
> PMIDs. Even when adding the total of deleted_pmids + the number from
> EInfo I couldn't get accurate information.
>
> So my question is, does anyone know how to get either a list of all the
> valid PMIDs or simply the most recent PMID?

To try and work out the latest PMID, I'd start by trying a PubMed search
by date, using a recent threshold.

What number of PMIDs are you trying to validate? Would it make
sense to use Entrez to do the validation (in batches)?

Peter

From rjalves at igc.gulbenkian.pt  Mon Jul  5 18:13:34 2010
From: rjalves at igc.gulbenkian.pt (Renato Alves)
Date: Mon, 05 Jul 2010 23:13:34 +0100
Subject: [Biopython] Finding what is the most recent Pubmed ID or list
 of all valid PMIDs
In-Reply-To: <AANLkTil82BTTFYGnw42ZSMy0MsL_kUWdxM3wl6CmO6Xm@mail.gmail.com>
References: <4C3239D1.7040708@igc.gulbenkian.pt>
	<AANLkTil82BTTFYGnw42ZSMy0MsL_kUWdxM3wl6CmO6Xm@mail.gmail.com>
Message-ID: <4C32590E.6020609@igc.gulbenkian.pt>

From Peter on 07/05/2010 09:54 PM:
> On Mon, Jul 5, 2010 at 9:00 PM, Renato Alves <rjalves at igc.gulbenkian.pt> wrote:
>> Greetings All,
>>
>> I'm trying to figure out a way to have a more or less up-to-date list of
>> Pubmed IDs for validation purposes. This has to be performed on a
>> programmatic way.
>>
>> My first attempt was to look for this in NCBI's FTP. I could find
>> ftp://ftp.ncbi.nih.gov/pubmed/deleted_pmids.txt but not information
>> about the most recent PMID.
>>
>> I also tried to use EInfo but the count section under PubMed seems
>> either outdated or completely unrelated to the total number of assigned
>> PMIDs. Even when adding the total of deleted_pmids + the number from
>> EInfo I couldn't get accurate information.
>>
>> So my question is, does anyone know how to get either a list of all the
>> valid PMIDs or simply the most recent PMID?
> 
> To try and work out the latest PMID, I'd start by trying a PubMed search
> by date, using a recent threshold.
> 
> What number of PMIDs are you trying to validate? Would it make
> sense to use Entrez to do the validation (in batches)?
> 
> Peter
I've thought of using Entrez but I was trying to avoid it by using
information available locally. I've no idea how many and what PMIDs will
be requested.

But indeed searching by date I can get a rough idea of what might be the
most recent PMID.

Thanks Peter

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From biopython at maubp.freeserve.co.uk  Tue Jul  6 04:23:28 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 09:23:28 +0100
Subject: [Biopython] Is Bio.Crystal still useful (for NDB files)?
In-Reply-To: <20100706084942.10823rdn5pazwcg6@horde.genesilico.pl>
References: <AANLkTinMfklMpOJ2o7KGH_8mqlgJOP3oQbYI4XyHvdir@mail.gmail.com>
	<20100706084942.10823rdn5pazwcg6@horde.genesilico.pl>
Message-ID: <AANLkTikQrCeXAH0IkYxoNvlsLF1sLFQbKDfjHH8vheh0@mail.gmail.com>

On Tue, Jul 6, 2010 at 7:49 AM, Kristian Rother <krother at genesilico.pl> wrote:
>
>
> Hi Peter,
>
> none of us here is using Bio.Crystal - and we use NDB structures a lot.
>
> Best,
> ? Kristian

Hi Kristian,

What kind of files are you using from the NDB? Standard PDB or mmCIF maybe?

Peter


From biopython at maubp.freeserve.co.uk  Tue Jul  6 04:43:18 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 09:43:18 +0100
Subject: [Biopython] Is Bio.Crystal still useful (for NDB files)?
In-Reply-To: <20100706102515.18063fisv68bqesr@horde.genesilico.pl>
References: <AANLkTinMfklMpOJ2o7KGH_8mqlgJOP3oQbYI4XyHvdir@mail.gmail.com>
	<20100706084942.10823rdn5pazwcg6@horde.genesilico.pl>
	<AANLkTikQrCeXAH0IkYxoNvlsLF1sLFQbKDfjHH8vheh0@mail.gmail.com>
	<20100706102515.18063fisv68bqesr@horde.genesilico.pl>
Message-ID: <AANLkTilSG4QA-pxSX2xo6iC2gjdGUoGZbKhTYqkBieE3@mail.gmail.com>

> Quoting Peter <biopython at maubp.freeserve.co.uk>:
>> Hi Kristian,
>>
>> What kind of files are you using from the NDB? Standard PDB or mmCIF
>> maybe?
>>
>> Peter

On Tue, Jul 6, 2010 at 9:25 AM, Kristian Rother wrote:
> Hi Peter,
>
> Standard PDB.
> We're gradually shifting to the PDB database for queries though, because the
> XML-based API for querying subsets of structures is much better there.
>
> Kristian

Thanks - maybe we can depreacte Bio.Crystal then...

Peter

From biopython at maubp.freeserve.co.uk  Tue Jul  6 06:36:39 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 11:36:39 +0100
Subject: [Biopython] Deprecating Bio.Crystal in next release?
Message-ID: <AANLkTilkAMk07WN4NQSy2yH0CL_Dd9r7XbG7VGBW8MoM@mail.gmail.com>

Hi all,

Given recent discussion (and the lack of interest on the dev list on previous
occasions), is there any objection to deprecating Bio.Crystal in the
next release
of Biopython?

http://lists.open-bio.org/pipermail/biopython/2010-July/006633.html
http://lists.open-bio.org/pipermail/biopython-dev/2008-October/004405.html
http://lists.open-bio.org/pipermail/biopython-dev/2007-July/002901.html

Thanks,

Peter

From biopython at maubp.freeserve.co.uk  Tue Jul  6 06:46:12 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 11:46:12 +0100
Subject: [Biopython] Is Bio.Crystal still useful (for NDB files)?
In-Reply-To: <20100706123045.12993suli0ec27dh@horde.genesilico.pl>
References: <AANLkTinMfklMpOJ2o7KGH_8mqlgJOP3oQbYI4XyHvdir@mail.gmail.com>
	<20100706084942.10823rdn5pazwcg6@horde.genesilico.pl>
	<AANLkTikQrCeXAH0IkYxoNvlsLF1sLFQbKDfjHH8vheh0@mail.gmail.com>
	<20100706123045.12993suli0ec27dh@horde.genesilico.pl>
Message-ID: <AANLkTik2tC64zDcLoprfRr1Dw44RS6k0KxtyuB8n9SKu@mail.gmail.com>

On Tue, Jul 6, 2010 at 11:30 AM, Kristian Rother <krother at genesilico.pl> wrote:
>
>> What kind of files are you using from the NDB? Standard PDB or mmCIF
>> maybe?
>
> Ah... sorry.. just PDB.
>
> Kristian

That's useful to know - thanks.

Peter

P.S. Please try to CC the mailing list ;)

From biopython at maubp.freeserve.co.uk  Tue Jul  6 09:40:51 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 14:40:51 +0100
Subject: [Biopython] Deprecating Bio.InterPro
Message-ID: <AANLkTiloI5mXX-jv22_PN5pe7NhSkx-tta2RfaYJhacG@mail.gmail.com>

Hi all,

Another old module which hasn't been updated for some time is Bio.InterPro,
a parser for the HTML (webpages) at the EBI, e.g.

http://www.ebi.ac.uk/interpro/IEntry?ac=IPR001064

The parser doesn't work with the current website, and also uses a Python
library called sgmllib which was deprecated as of Python 2.6. Website
parsers are in general a bad idea because the tend to need a lot of work
to keep up to date. Perhaps in this case there are suitable plain text files
on the FTP site which might be used?

Unless anyone has a good reason not to, we are going to deprecate the
Bio.IntrerPro module in the next release of Biopython.

Peter

From biopython at maubp.freeserve.co.uk  Tue Jul  6 11:20:38 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 16:20:38 +0100
Subject: [Biopython] Deprecating Bio.Index?
Message-ID: <AANLkTim5HG78UMCWqGX_d-Ht6eEquEo_woaVD3ZRiCbb@mail.gmail.com>

Hello all,

Is anyone using the Bio.Index module in Biopython in their own code?

This supported file indexing and was used in other parts of Biopython which
have all now been deprecated (e.g. Bio.SwissProt.SProt and Bio.Prosite) or
removed. The more recent Bio.SeqIO module provides a general approach
to indexing sequence files.

Would it inconvenience anyone if Bio.Index was deprecated in the next
release (triggering warnings when imported, but still functional), and then
removed later on?

Thanks,

Peter

From guyeakin at gmail.com  Wed Jul  7 20:52:49 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 7 Jul 2010 20:52:49 -0400
Subject: [Biopython] Bio.Entrez/Medline DTD problems - missing DTD
	nlmmedlinecitationset_100301.dtd
Message-ID: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com>

 I am learning biopython and seem to be having trouble parsing efetch
generated xml.

Maybe I am confused here, but I can't for the life of me Get my xml to parse
correctly, and it seems to be coming up with a missing dtd error using both
Medline.parse and Entrez.parse. (traceback for medline below below)

 nlmmedlinecitationset_100301.
dtd and pubmed_100301.dtd seem to be missing from my biopython
installation, and unavailable from the following NCBI sites:

http://www.ncbi.nlm.nih.gov/dtd/ or
http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/

My apologies if this is user error; i do not see reference to this DTD issue
in the archives so am posting the incident. Is this just bad luck during my
learning curve, or am I missing something conceptual here?

 Thanks,

Guy



Traceback (most recent call last):

 File
"C:\Python26\Lib\site-packages\pythonwin\pywin\framework\scriptutils.py",
line 312, in RunScript

   exec codeObject in __main__.__dict__

 File "C:\ieye\ieye\citations\pubmed_search_fxn.py", line 36, in <module>

   parsed_results = Entrez.read(fetch_handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\__init__.py", line 262, in
read

   record = handler.read(handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 108, in
read

   self.parser.ParseFile(handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 381, in
externalEntityRefHandler

   parser.ParseFile(handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 377, in
externalEntityRefHandler

   raise RuntimeError(message)

RuntimeError: Unable to load DTD file nlmmedlinecitationset_100301.dtd.

From biopython at maubp.freeserve.co.uk  Thu Jul  8 03:42:32 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 8 Jul 2010 08:42:32 +0100
Subject: [Biopython] Bio.Entrez/Medline DTD problems - missing DTD
	nlmmedlinecitationset_100301.dtd
In-Reply-To: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com>
References: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com>
Message-ID: <AANLkTikdmzaHip2tdRKu_CiY__lyADvRjGoGv6rtySz-@mail.gmail.com>

On Thu, Jul 8, 2010 at 1:52 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> ?I am learning biopython and seem to be having trouble parsing efetch
> generated xml.
>
> Maybe I am confused here, but I can't for the life of me Get my xml to parse
> correctly, and it seems to be coming up with a missing dtd error using both
> Medline.parse and Entrez.parse. (traceback for medline below below)
>
> ?nlmmedlinecitationset_100301.
> dtd and pubmed_100301.dtd seem to be missing from my biopython
> installation, and unavailable from the following NCBI sites:
>
> http://www.ncbi.nlm.nih.gov/dtd/ or
> http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/
>
> My apologies if this is user error; i do not see reference to this DTD issue
> in the archives so am posting the incident. Is this just bad luck during my
> learning curve, or am I missing something conceptual here?

The problem is with the NCBI "hiding" the file by not showing the raw
contents of that folder, but just an HTML page with a partial list. You
need this file:

http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/nlmmedlinecitationset_100301.dtd

I've added this to our repository so the next version of Biopython will
include it. Please let us know if anything else is missing - what was
the Entrez request you used to get the XML using this DTD file?

Regards,

Peter


From guyeakin at gmail.com  Thu Jul  8 07:28:17 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Thu, 8 Jul 2010 07:28:17 -0400
Subject: [Biopython] Bio.Entrez/Medline DTD problems - missing DTD
	nlmmedlinecitationset_100301.dtd
In-Reply-To: <AANLkTikdmzaHip2tdRKu_CiY__lyADvRjGoGv6rtySz-@mail.gmail.com>
References: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com> 
	<AANLkTikdmzaHip2tdRKu_CiY__lyADvRjGoGv6rtySz-@mail.gmail.com>
Message-ID: <AANLkTim82RfW0K8Q9W3LOEc1U9l6z2hLbqN44VUw9j93@mail.gmail.com>

Peter,

Many thanks.

this is a query statement that generated the
nlmmedlinecitationset_100301.dtd error: Entrez.esearch(db="pubmed",
                        term= ('glaucom*'),
                        retmax=2, usehistory="y",
                        reldate=7, datetype="edat")


fetch_handle = Entrez.efetch(db="pubmed", retmode="xml",rettype='medline',
                             webenv=webenv, query_key=query_key)


You will also want to add pubmed_100301.dtd to your repository.  I do not
have the query that generated it's dependent XML, but got an separate error
related to its absence yesterday.  Oddly, I was able to download the
"hidden" pubmed_100301.dtd, but could not replicate the error.   All
following errors focused on the nlmmedlinecitationset_100301.dtd file which
I could not locate until this morning. Perhaps it was just recently posted
to the site. Either way, thanks for the confirmation that I was on the right
track.

regards,
guy

On Thu, Jul 8, 2010 at 3:42 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Thu, Jul 8, 2010 at 1:52 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> >  I am learning biopython and seem to be having trouble parsing efetch
> > generated xml.
> >
> > Maybe I am confused here, but I can't for the life of me Get my xml to
> parse
> > correctly, and it seems to be coming up with a missing dtd error using
> both
> > Medline.parse and Entrez.parse. (traceback for medline below below)
> >
> >  nlmmedlinecitationset_100301.
> > dtd and pubmed_100301.dtd seem to be missing from my biopython
> > installation, and unavailable from the following NCBI sites:
> >
> > http://www.ncbi.nlm.nih.gov/dtd/ or
> > http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/
> >
> > My apologies if this is user error; i do not see reference to this DTD
> issue
> > in the archives so am posting the incident. Is this just bad luck during
> my
> > learning curve, or am I missing something conceptual here?
>
> The problem is with the NCBI "hiding" the file by not showing the raw
> contents of that folder, but just an HTML page with a partial list. You
> need this file:
>
>
> http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/nlmmedlinecitationset_100301.dtd
>
> I've added this to our repository so the next version of Biopython will
> include it. Please let us know if anything else is missing - what was
> the Entrez request you used to get the XML using this DTD file?
>
> Regards,
>
> Peter
>

From biopython at maubp.freeserve.co.uk  Thu Jul  8 07:53:30 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 8 Jul 2010 12:53:30 +0100
Subject: [Biopython] Bio.Entrez/Medline DTD problems - missing DTD
	nlmmedlinecitationset_100301.dtd
In-Reply-To: <AANLkTim82RfW0K8Q9W3LOEc1U9l6z2hLbqN44VUw9j93@mail.gmail.com>
References: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com>
	<AANLkTikdmzaHip2tdRKu_CiY__lyADvRjGoGv6rtySz-@mail.gmail.com>
	<AANLkTim82RfW0K8Q9W3LOEc1U9l6z2hLbqN44VUw9j93@mail.gmail.com>
Message-ID: <AANLkTinKqg5q7WGf0CS-mTR53Jz5u-i3saslHjIaMU2g@mail.gmail.com>

On Thu, Jul 8, 2010 at 12:28 PM, Guy Eakin <guyeakin at gmail.com> wrote:
> Peter,
>
> Many thanks.
>
> this is a query statement that generated the
> nlmmedlinecitationset_100301.dtd error: Entrez.esearch(db="pubmed",
> ? ? ? ? ? ? ? ? ? ? ? ?term= ('glaucom*'),
> ? ? ? ? ? ? ? ? ? ? ? ?retmax=2, usehistory="y",
> ? ? ? ? ? ? ? ? ? ? ? ?reldate=7, datetype="edat")
>
>
> fetch_handle = Entrez.efetch(db="pubmed", retmode="xml",rettype='medline',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? webenv=webenv, query_key=query_key)
>

Great. A more complete version is:

from Bio import Entrez
Entrez.email = "A.N.Other at example.com"

s = Entrez.read(Entrez.esearch(db="pubmed",term=
('glaucom*'),retmax=2, usehistory="y",reldate=7, datetype="edat"))

r = Entrez.read(Entrez.efetch(db="pubmed",
retmode="xml",rettype='medline', webenv=s["WebEnv"],
query_key=s["QueryKey"]))


>
> You will also want to add pubmed_100301.dtd to your repository. ...
>

Yes, we needed the new pubmed_100301.dtd and also bookdoc_100301.dtd

It looks like the NCBI did some updates recently - hopefully they'll update that
webpage soon and we can see if we need to add anymore (other than finding
out from error messages).

Thanks for the report, and please let us know if you find any more missing DTD
files.

Peter


From guyeakin at gmail.com  Wed Jul 14 16:48:41 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 14 Jul 2010 16:48:41 -0400
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
Message-ID: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>

I am using Bio.Entrez.read to parse XML returned from pubmed.

This results in a dictionary for which one of the keys is ArticleIDList,
e.g,
Example
PubmedData': {u'ArticleIdList': ['S0735-6757(09)00464-1',
'10.1016/j.ajem.2009.09.013', '20579576'], blah: blah, etc.}

In the original XML Each <ArticleID> in <ArticleIDList> contains an IDtype
attribute that names the ID. for example
<ArtcleID IDType="doi">10.1016/j.ajem.2009.09.013</ArticleID>

the IDtype is useful, but I can't find it in the Bio.Entrez.read output, so
I have no *easy* way of determining whether the ID# is
pii, pmc, pmid, etc.

Is there a better way to get the IDtype attribute, or other XML tag
attributes from the Entrez.read output?

Thanks.
Guy

Code below

---------------
from Bio import Medline
from Bio import Entrez
import routine_pubmed_query_terms as pubmedterms #this is a separate .py
file that I use to hold query terms, email address, etc.

  s = Entrez.read(Entrez.esearch(db="pubmed",
                                   term=pubmedterms.entrezquery(program),
                                   retmax=pubmedterms.maxlimit,
                                   usehistory="y",
                                   reldate=pubmedterms.datelimit,
                                   datetype="edat"))
    print "found %s records, returning %s" % (int(s["Count"]),
                                                  len(s["IdList"]))

    r = Entrez.read(Entrez.efetch(db="pubmed",retmode="xml",
                                  rettype='medline', webenv=s["WebEnv"],
                                  query_key=s["QueryKey"]))

From biopython at maubp.freeserve.co.uk  Wed Jul 14 17:18:34 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 14 Jul 2010 22:18:34 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>
Message-ID: <AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com>

On Wed, Jul 14, 2010 at 9:48 PM, Guy Eakin <guyeakin at gmail.com> wrote:
> I am using Bio.Entrez.read to parse XML returned from pubmed.
>
> This results in a dictionary for which one of the keys is ArticleIDList,
> e.g,
> Example
> PubmedData': {u'ArticleIdList': ['S0735-6757(09)00464-1',
> '10.1016/j.ajem.2009.09.013', '20579576'], blah: blah, etc.}
>
> In the original XML Each <ArticleID> in <ArticleIDList> contains an IDtype
> attribute that names the ID. for example
> <ArtcleID IDType="doi">10.1016/j.ajem.2009.09.013</ArticleID>
>
> the IDtype is useful, but I can't find it in the Bio.Entrez.read output, so
> I have no *easy* way of determining whether the ID# is
> pii, pmc, pmid, etc.
>
> Is there a better way to get the IDtype attribute, or other XML tag
> attributes from the Entrez.read output?
>

Hi,

This information is in the tutorial, but could perhaps be clearer.
It might look like you get strings back, but in fact it is a subclass
with an attributes property (a dictionary). e.g.

from Bio import Entrez
handle = Entrez.efetch(db="pubmed",retmode="xml",rettype='medline',id='19304878')
r = Entrez.read(handle)
handle.close()
print r[0]['PubmedData']['ArticleIdList'][1]
print r[0]['PubmedData']['ArticleIdList'][1].attributes

Michiel - maybe we need to override the __repr__ method so it shows
this information?

Peter

From biopython at maubp.freeserve.co.uk  Wed Jul 14 17:33:06 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 14 Jul 2010 22:33:06 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>
	<AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com>
	<AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com>
Message-ID: <AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com>

On Wed, Jul 14, 2010 at 10:21 PM, Guy Eakin <guyeakin at gmail.com> wrote:
> thanks.? I understood that it had a? .tag feature,but missed the
> .attributes!
> Awesome. And thank you for the quick reply.
>
> Guy

No problem. Now you know the answer, can you suggest
any clarifications to the documentation?

Peter

P.S. Try and CC the mailing list in replies.


From guyeakin at gmail.com  Wed Jul 14 22:52:44 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 14 Jul 2010 22:52:44 -0400
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com> 
	<AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com> 
	<AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com> 
	<AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com>
Message-ID: <AANLkTinquPR9P36p952-PavSh7_9wLdWkDZ_08w2n9P7@mail.gmail.com>

Sure, I am new, so there are probably errors, but how about something like a
demonstration appended to the end of the tutorial section at
http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc105

At core, the simple demonstration that type(record) calls a class object
rather than a list, and that foo.attributes, and foo.tag exist would be
helpful.  I am not using any of the sequence utilities, so admit that my
reading of those sections was brief.  Reiteration in the entrez parsing
sections is probably helpful for people like me.

A more verbose demonstration follows.

Again, thanks for the help.
Guy

8.11.1  Parsing Medline records [intervening text omitted]

At this point let?s address what these elements contain.  Consider
information found in the following statement.

>>> records[0]['PubmedData']

{u'ArticleIdList': ['btp163', '10.1093/bioinformatics/btp163', '19304878',
'PMC2682512'], u'PublicationStatus': 'ppublish', u'History': [{u'Month':
'3', u'Day': '20', u'Year': '2009'}, {u'Minute': '0', u'Month': '3', u'Day':
'24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month': '3',
u'Day': '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month':
'7', u'Day': '10', u'Hour': '9', u'Year': '2009'}]}

It is important to recall that each item is a biopython class, rather than a
simply a dictionary or list item.  This can be verified by

>>>type(records[0]['PubmedData']['ArticleIdList']

Which returns <class 'Bio.Entrez.Parser.ListElement'> rather than <type
'list'>

This is important,  as the class item contains additional auxiliary
information as noted earlier.  One such piece of important auxillary info is
the XML tag attributes from the parsed XML.

In this case, the  original XML contained the following tags:

<ArticleIdList>

            <ArticleId IdType="pii">btp163</ArticleId>

            <ArticleId IdType="doi">10.1093/bioinformatics/btp163</ArticleId>

            <ArticleId IdType="pubmed">19304878</ArticleId>

            <ArticleId IdType="pmc">PMC2682512</ArticleId>

</ArticleIdList>



which have now been parsed into the u'ArticleIdList' dictionary key:

>>> L =records[0]['PubmedData']['ArticleIdList']

['btp163', '10.1093/bioinformatics/btp163', '19304878', 'PMC2682512']

Viewed as a simple list, these elements appear to lack the IdType
information.  However,  the IdType attribute from the <ArticleId> tag is
stored in the parsed data, and can be retrieved by calling ?attributes? on
the biopython class object.

>>> for item in L:

...            print "%s - %s" % (item, item.attributes)

...

btp163 - {u'IdType': u'pii'}

10.1093/bioinformatics/btp163 - {u'IdType': u'doi'}

19304878 - {u'IdType': u'pubmed'}

PMC2682512 - {u'IdType': u'pmc'}


On Wed, Jul 14, 2010 at 5:33 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Wed, Jul 14, 2010 at 10:21 PM, Guy Eakin <guyeakin at gmail.com> wrote:
> > thanks.  I understood that it had a  .tag feature,but missed the
> > .attributes!
> > Awesome. And thank you for the quick reply.
> >
> > Guy
>
> No problem. Now you know the answer, can you suggest
> any clarifications to the documentation?
>
> Peter
>
> P.S. Try and CC the mailing list in replies.
>


From biopython at maubp.freeserve.co.uk  Thu Jul 15 05:44:06 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 15 Jul 2010 10:44:06 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTinquPR9P36p952-PavSh7_9wLdWkDZ_08w2n9P7@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>
	<AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com>
	<AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com>
	<AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com>
	<AANLkTinquPR9P36p952-PavSh7_9wLdWkDZ_08w2n9P7@mail.gmail.com>
Message-ID: <AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>

On Thu, Jul 15, 2010 at 3:52 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> Sure, I am new, so there are probably errors, but how about something like a
> demonstration appended to the end of the tutorial section at
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc105
>
> At core, the simple demonstration that type(record) calls a class object
> rather than a list, and that foo.attributes, and foo.tag exist would be
> helpful. ?I am not using any of the sequence utilities, so admit that my
> reading of those sections was brief. ?Reiteration in the entrez parsing
> sections is probably helpful for people like me.
>
> A more verbose demonstration follows.
>
> Again, thanks for the help.
> Guy

Thank you for the detailed suggested text.

> 8.11.1 ?Parsing Medline records [intervening text omitted]
>
> At this point let?s address what these elements contain. ?Consider
> information found in the following statement.
>
>>>> records[0]['PubmedData']
>
> {u'ArticleIdList': ['btp163', '10.1093/bioinformatics/btp163', '19304878',
> 'PMC2682512'], u'PublicationStatus': 'ppublish', u'History': [{u'Month':
> '3', u'Day': '20', u'Year': '2009'}, {u'Minute': '0', u'Month': '3', u'Day':
> '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month': '3',
> u'Day': '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month':
> '7', u'Day': '10', u'Hour': '9', u'Year': '2009'}]}
>
> It is important to recall that each item is a biopython class, rather than a
> simply a dictionary or list item. ?This can be verified by
>
>>>>type(records[0]['PubmedData']['ArticleIdList']
>
> Which returns <class 'Bio.Entrez.Parser.ListElement'> rather than <type
> 'list'>

This is why I was suggesting to Michiel that we override the __repr__
for our subclassed objects, so that rather than seeing things like this:

['btp163', '10.1093/bioinformatics/btp163', '19304878', 'PMC2682512']

we get something like:

ListElement(['btp163', '10.1093/bioinformatics/btp163', '19304878',
'PMC2682512'], attributes={...})

On deeper reflection, the trouble with this is that all the children within
the list would get longer, so the full representation of a ListElement (or
any container) would become very very long - swamping the console
output. Even if we literally show the attributes with a dot dot dot :(

Maybe we'll have to settle for just documentation improvements.
Michiel - this is your code - what do you think?

Peter


From guyeakin at gmail.com  Thu Jul 15 09:32:43 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Thu, 15 Jul 2010 09:32:43 -0400
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com> 
	<AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com> 
	<AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com> 
	<AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com> 
	<AANLkTinquPR9P36p952-PavSh7_9wLdWkDZ_08w2n9P7@mail.gmail.com> 
	<AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>
Message-ID: <AANLkTilabI_j5OEg5XCgf438y0kntjCBpH34mfnnh5WN@mail.gmail.com>

>From the naive first-time user perspective, the current implementation is
fine for the computer, but could benefit from a viewer output that creates a
more human readable representation.  I found myself cross referencing the
console output to the original XML in most cases.

That says to me that there might be benefit to a function that recapitulates
the original XML's nested structure, listing attribute values.  I would
think something along the following would be quite useful, and if limited to
particular range of records would not necessarily be unwieldy.

(apologies for the admittedly unwieldy markup)

>>> Bio.Entrez.viewer(recordlist, range=(0:(len(recordlist)),
ShowMedlineCitation = True, ShowPubmedData = True)

<Parent1> - (Attributes = Parent1.atribute) -  \n                       #(80
characters/line)
..............value
..............indented text allows word wrap of entries > 80 char.
........<Children>1 - Attribute - \n
.......................value


that's an off the cuff representation before I dash to a meeting, but I
think you can see what I am suggesting.

Guy


Guy
On Thu, Jul 15, 2010 at 5:44 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Thu, Jul 15, 2010 at 3:52 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> > Sure, I am new, so there are probably errors, but how about something
> like a
> > demonstration appended to the end of the tutorial section at
> > http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc105
> >
> > At core, the simple demonstration that type(record) calls a class object
> > rather than a list, and that foo.attributes, and foo.tag exist would be
> > helpful.  I am not using any of the sequence utilities, so admit that my
> > reading of those sections was brief.  Reiteration in the entrez parsing
> > sections is probably helpful for people like me.
> >
> > A more verbose demonstration follows.
> >
> > Again, thanks for the help.
> > Guy
>
> Thank you for the detailed suggested text.
>
> > 8.11.1  Parsing Medline records [intervening text omitted]
> >
> > At this point let?s address what these elements contain.  Consider
> > information found in the following statement.
> >
> >>>> records[0]['PubmedData']
> >
> > {u'ArticleIdList': ['btp163', '10.1093/bioinformatics/btp163',
> '19304878',
> > 'PMC2682512'], u'PublicationStatus': 'ppublish', u'History': [{u'Month':
> > '3', u'Day': '20', u'Year': '2009'}, {u'Minute': '0', u'Month': '3',
> u'Day':
> > '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month': '3',
> > u'Day': '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month':
> > '7', u'Day': '10', u'Hour': '9', u'Year': '2009'}]}
> >
> > It is important to recall that each item is a biopython class, rather
> than a
> > simply a dictionary or list item.  This can be verified by
> >
> >>>>type(records[0]['PubmedData']['ArticleIdList']
> >
> > Which returns <class 'Bio.Entrez.Parser.ListElement'> rather than <type
> > 'list'>
>
> This is why I was suggesting to Michiel that we override the __repr__
> for our subclassed objects, so that rather than seeing things like this:
>
> ['btp163', '10.1093/bioinformatics/btp163', '19304878', 'PMC2682512']
>
> we get something like:
>
> ListElement(['btp163', '10.1093/bioinformatics/btp163', '19304878',
> 'PMC2682512'], attributes={...})
>
> On deeper reflection, the trouble with this is that all the children within
> the list would get longer, so the full representation of a ListElement (or
> any container) would become very very long - swamping the console
> output. Even if we literally show the attributes with a dot dot dot :(
>
> Maybe we'll have to settle for just documentation improvements.
> Michiel - this is your code - what do you think?
>
> Peter
>


From mjldehoon at yahoo.com  Thu Jul 15 09:36:19 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Thu, 15 Jul 2010 06:36:19 -0700 (PDT)
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>
Message-ID: <436965.79909.qm@web62402.mail.re1.yahoo.com>



--- On Thu, 7/15/10, Peter <biopython at maubp.freeserve.co.uk> wrote:
> This is why I was suggesting to Michiel that we override
> than seeing the __repr__ for our subclassed objects, so
> that rather things like this:
> 
> ['btp163', '10.1093/bioinformatics/btp163', '19304878',
> 'PMC2682512']
> 
> we get something like:
> 
> ListElement(['btp163', '10.1093/bioinformatics/btp163',
> '19304878', 'PMC2682512'], attributes={...})
> 
> On deeper reflection, the trouble with this is that all the
> children within the list would get longer, so the full
> representation of a ListElement (or
> any container) would become very very long - swamping the
> console output.

The attributes are almost always only a small fraction of the Entrez XML file. So while it's true that each element gets larger, it's a small relative increase. The elements that are very long after adding the attributes are also very long without the attributes. So I am in favor of your original suggestion. If there are no other suggestions, I'll make the change in Bio.Entrez over the weekend (or feel free to do so before that).

Best,
--Michiel


      

From biopython at maubp.freeserve.co.uk  Thu Jul 15 09:50:41 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 15 Jul 2010 14:50:41 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <436965.79909.qm@web62402.mail.re1.yahoo.com>
References: <AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>
	<436965.79909.qm@web62402.mail.re1.yahoo.com>
Message-ID: <AANLkTilYvSgosb1zMHQFXzXy5AMAmn9125vVdst6BI__@mail.gmail.com>

On Thu, Jul 15, 2010 at 2:36 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>
> --- On Thu, 7/15/10, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> This is why I was suggesting to Michiel that we override
>> than seeing the __repr__ for our subclassed objects, so
>> that rather things like this:
>>
>> ['btp163', '10.1093/bioinformatics/btp163', '19304878',
>> 'PMC2682512']
>>
>> we get something like:
>>
>> ListElement(['btp163', '10.1093/bioinformatics/btp163',
>> '19304878', 'PMC2682512'], attributes={...})
>>
>> On deeper reflection, the trouble with this is that all the
>> children within the list would get longer, so the full
>> representation of a ListElement (or  any container) would
>> become very very long - swamping the console output.
>
> The attributes are almost always only a small fraction of the Entrez XML file.
> So while it's true that each element gets larger, it's a small relative increase.
> The elements that are very long after adding the attributes are also very long
> without the attributes. So I am in favor of your original suggestion. If there are
> no other suggestions, I'll make the change in Bio.Entrez over the weekend
> (or feel free to do so before that).

Maybe you can keep the basic data type repr if there are no attributes,
and only expand it if needed? It would be inconsistent but would keep the
total string length down.

Peter

From bjorn_johansson at bio.uminho.pt  Sat Jul 17 07:32:12 2010
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Sat, 17 Jul 2010 12:32:12 +0100
Subject: [Biopython] format fasta files to genbank: problem with too long
	Locus identifier
Message-ID: <AANLkTinI0xNF1jDLFlyrW5WI1lh-bTDJ6X1j1F3O7jk7@mail.gmail.com>

Hi all, this is an example of parsing a fasta file and then trying to
convert it to genbank.
It seems that the fasta header file is not split between the "|", and all
that is in the fasta header ends up as "LOCUS" in the genbank file. Is this
the expected behavior? Can this be set somehow?

Thanks for any help on this!
/bjorn



>>> from Bio import SeqIO
>>> a=SeqIO.read("newfile.fasta", "fasta")
>>> a
SeqRecord(seq=Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...GGG',
SingleLetterAlphabet()), id='gi|2765658|emb|Z78533.1|CIZ78533',
name='gi|2765658|emb|Z78533.1|CIZ78533',
description='gi|2765658|emb|Z78533.1|CIZ78533 C.irapeanum 5.8S rRNA gene and
ITS1 and ITS2 DNA', dbxrefs=[])
>>> a.format('fasta')
'>gi|2765658|emb|Z78533.1|CIZ78533 C.irapeanum 5.8S rRNA gene and ITS1 and
ITS2
DNA\nCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGGAATAAA\nCGATCGAGTGAATCCGGAGGACCGGTGTACTCAGCTCACCGGGGGCATTGCTCCCGTGGT\nGACCCTGATTTGTTGTTGGG\n'
>>> a.format('genbank')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqRecord.py", line 638,
in format
    return self.__format__(format)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqRecord.py", line 652,
in __format__
    SeqIO.write([self], handle, format_spec)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/__init__.py", line
398, in write
    count = writer_class(handle).write_file(sequences)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/Interfaces.py",
line 271, in write_file
    count = self.write_records(records)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/Interfaces.py",
line 256, in write_records
    self.write_record(record)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/InsdcIO.py", line
628, in write_record
    self._write_the_first_line(record)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/InsdcIO.py", line
453, in _write_the_first_line
    raise ValueError("Locus identifier %s is too long" % repr(locus))
ValueError: Locus identifier 'gi|2765658|emb|Z78533.1|CIZ78533' is too long
>>>

From biopython at maubp.freeserve.co.uk  Sat Jul 17 07:50:50 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 17 Jul 2010 12:50:50 +0100
Subject: [Biopython] format fasta files to genbank: problem with too
	long Locus identifier
In-Reply-To: <AANLkTinI0xNF1jDLFlyrW5WI1lh-bTDJ6X1j1F3O7jk7@mail.gmail.com>
References: <AANLkTinI0xNF1jDLFlyrW5WI1lh-bTDJ6X1j1F3O7jk7@mail.gmail.com>
Message-ID: <AANLkTikx0ziKAL2Sd2ABYbySSHdXxUsRaqfvaXwuqQ6g@mail.gmail.com>

2010/7/17 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> Hi all, this is an example of parsing a fasta file and then trying to
> convert it to genbank.
> It seems that the fasta header file is not split between the "|", and all
> that is in the fasta header ends up as "LOCUS" in the genbank file. Is this
> the expected behavior? Can this be set somehow?
>
> Thanks for any help on this!
> /bjorn

Hi Bjorn,

Yes this is expected behaviour. There are no standards for FASTA
identifiers, the NCBI conventions are just one of dozens of styles.
Therefore we don't try and parse the identifiers in FASTA files (we
can't do it reliably). Then for GenBank files, the identifier field in
the LOCUS line is very limited - you'll have to shorten your ID
manually, Try something like this:

from Bio import SeqIO
a=SeqIO.read("newfile.fasta", "fasta")
a.id = a.id.split("|")[3]
print a.format('genbank')

(untested)

Peter


From biopython at maubp.freeserve.co.uk  Sat Jul 17 15:59:46 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 17 Jul 2010 20:59:46 +0100
Subject: [Biopython] format fasta files to genbank: problem with too
	long Locus identifier
In-Reply-To: <AANLkTilIcFjK-8pW_6RmcqpiuCyUWHC36X_jiGAp0XEY@mail.gmail.com>
References: <AANLkTinI0xNF1jDLFlyrW5WI1lh-bTDJ6X1j1F3O7jk7@mail.gmail.com>
	<AANLkTikx0ziKAL2Sd2ABYbySSHdXxUsRaqfvaXwuqQ6g@mail.gmail.com>
	<AANLkTilIcFjK-8pW_6RmcqpiuCyUWHC36X_jiGAp0XEY@mail.gmail.com>
Message-ID: <AANLkTimN1h85UeV_0D3Xb6F-Tc52r24beGhD2Lju5f2G@mail.gmail.com>

2010/7/17 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> Thanks for the quick reply!
>
> it seems that it is the a.name field that needs to be shortened
> (and ends up in the LOCUS field). the a.id seems to be the
> entire fasta header and ends up as DEFINITION.
>
> /bjorn

Sounds right - I should have tested it after all ;)

Peter


From mjldehoon at yahoo.com  Sun Jul 18 04:43:45 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sun, 18 Jul 2010 01:43:45 -0700 (PDT)
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTilYvSgosb1zMHQFXzXy5AMAmn9125vVdst6BI__@mail.gmail.com>
Message-ID: <190917.68159.qm@web62405.mail.re1.yahoo.com>

> Maybe you can keep the basic data type repr if there are no
> attributes, and only expand it if needed? It would be inconsistent
> but would keep the total string length down.
> 
Done.

The code can be further simplified if we drop the .tag attribute on each XML element. If we drop .tag, then all elements that do not have attributes (which are most of them) can be presented as a simple list, dictionary, string, and so on instead of a ListElement, DictionaryElement, StringElement. Then the *Element classes are used only in those cases where there actually are attributes. Or is that too inconsistent?

--Michiel.


      

From biopython at maubp.freeserve.co.uk  Sun Jul 18 06:59:02 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sun, 18 Jul 2010 11:59:02 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <190917.68159.qm@web62405.mail.re1.yahoo.com>
References: <AANLkTilYvSgosb1zMHQFXzXy5AMAmn9125vVdst6BI__@mail.gmail.com>
	<190917.68159.qm@web62405.mail.re1.yahoo.com>
Message-ID: <AANLkTik-iQeekeXWmLTfkBESYUUIYPlx1Cw2G_WvhWeM@mail.gmail.com>

On Sun, Jul 18, 2010 at 9:43 AM, Michiel de Hoon wrote:
>> Maybe you can keep the basic data type repr if there are no
>> attributes, and only expand it if needed? It would be inconsistent
>> but would keep the total string length down.
>>
> Done.
>
> The code can be further simplified if we drop the .tag attribute on
> each XML element. If we drop .tag, then all elements that do not
> have attributes (which are most of them) can be presented as a
> simple list, dictionary, string, and so on instead of a ListElement,
> DictionaryElement, StringElement. Then the *Element classes are
> used only in those cases where there actually are attributes. Or is
> that too inconsistent?

I've not played with the code yet to see what you mean about the
tag attribute.

There is an inconsistency with DictionaryElement vs DictElement
(deliberate for space?) and StructureElement vs DictElement (typo?).

Peter

From mjldehoon at yahoo.com  Sun Jul 18 09:59:41 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sun, 18 Jul 2010 06:59:41 -0700 (PDT)
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTik-iQeekeXWmLTfkBESYUUIYPlx1Cw2G_WvhWeM@mail.gmail.com>
Message-ID: <650816.80191.qm@web62406.mail.re1.yahoo.com>



--- On Sun, 7/18/10, Peter <biopython at maubp.freeserve.co.uk> wrote:
> I've not played with the code yet to see what you mean
> about the tag attribute. 

Here's an example:

<eInfoResult>
<DbList>
        <DbName>pubmed</DbName>
        <DbName>protein</DbName>
        <DbName>nucleotide</DbName>
        <DbName>nuccore</DbName>
        <DbName>nucgss</DbName>
....



>>> record['DbList'][0]       
'pubmed'
>>> record['DbList'][0].tag
u'DbName'
>>> record['DbList'][0].attributes
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'StringElement' object has no attribute 'attributes'
>>> 

So currently record['DbList'] is a list of StringElements (actually, a ListElement of StringElements) where the XML tag name is stored in a .tag attribute. If we don't store the .tag attribute, then record['DbList'] would become a list of plain strings.

--Michiel.


      

From bala.biophysics at gmail.com  Mon Jul 19 05:39:11 2010
From: bala.biophysics at gmail.com (Bala subramanian)
Date: Mon, 19 Jul 2010 11:39:11 +0200
Subject: [Biopython] clustering pdb
Message-ID: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>

Friends,
I have around 3000 pdb files obtained from MD simulations. I would like to
know if it is possible to cluster the pdb files using any of the biopython's
bio.PDB or other modules. If so, i would appreciate if you could provide me
a sample code.

Is there any utility in Biopython to handle MD trajectories obtained from
common packages like gromacs, amber etc ?

Thank you,
Bala

From biopython at maubp.freeserve.co.uk  Mon Jul 19 05:49:26 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 19 Jul 2010 10:49:26 +0100
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
Message-ID: <AANLkTilzTT_1kOVsQpi76fDittiGf8rGkZBJ6Urflkzz@mail.gmail.com>

On Mon, Jul 19, 2010 at 10:39 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Friends,
> I have around 3000 pdb files obtained from MD simulations. I would like to
> know if it is possible to cluster the pdb files using any of the biopython's
> bio.PDB or other modules. If so, i would appreciate if you could provide me
> a sample code.

What kind of clustering do you want to do? By folds/structure? By sequence?

> Is there any utility in Biopython to handle MD trajectories obtained from
> common packages like gromacs, amber etc ?

No, we don't do any molecular dynamics - try The Molecular Modelling Toolkit
(MMTK) by Konran Hinsen for a Python MD toolkit:
http://dirac.cnrs-orleans.fr/MMTK/

Peter

From schaefer at rostlab.org  Mon Jul 19 05:56:45 2010
From: schaefer at rostlab.org (Christian Schaefer)
Date: Mon, 19 Jul 2010 11:56:45 +0200
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
Message-ID: <4C44215D.5050401@rostlab.org>

On 07/19/2010 11:39 AM, Bala subramanian wrote:
> Friends,
> I have around 3000 pdb files obtained from MD simulations. I would like to
> know if it is possible to cluster the pdb files using any of the biopython's
> bio.PDB or other modules. If so, i would appreciate if you could provide me
> a sample code.

It depends on what you mean by 'clustering'. If you refer to sequence 
clustering, i.e. redundancy reduction on sequence level, there are 
several tools out there (like CDHit) for that purpose. Not sure if 
there's a native implementation in BioPython for that.

Chris

-- 
Dipl.-Bioinf. Christian Schaefer
Technical University Munich
Department for Bioinformatics
Faculty of Computer Science/I12
Boltzmannstr. 3
D-85748 Garching b. Muenchen
Germany
http://www.rostlab.org/~schaefer

From biopython at maubp.freeserve.co.uk  Mon Jul 19 06:07:49 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 19 Jul 2010 11:07:49 +0100
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTimujbfw33zV4bG3y6J8fRu0yocwJ2XryN2W7El5@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
	<AANLkTilzTT_1kOVsQpi76fDittiGf8rGkZBJ6Urflkzz@mail.gmail.com>
	<AANLkTimujbfw33zV4bG3y6J8fRu0yocwJ2XryN2W7El5@mail.gmail.com>
Message-ID: <AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>

On Mon, Jul 19, 2010 at 10:59 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Hello peter,
> Sorry for the incomplete information. I want to cluster the structures say
> for example using rmsd between the pdb.
>
> Thanks,
> Bala

Provided you can specify the atomic mapping between the structures,
you can calculate RMSD using Bio.PDB, see for example:
http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/
One way to do this would be pairwise sequence alignments. There
are probably specialised tools out there for this sort of clustering...

Peter

P.S. Please try to CC the mailing list in replies.

From anaryin at gmail.com  Mon Jul 19 07:08:12 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Mon, 19 Jul 2010 13:08:12 +0200
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com> 
	<AANLkTilzTT_1kOVsQpi76fDittiGf8rGkZBJ6Urflkzz@mail.gmail.com> 
	<AANLkTimujbfw33zV4bG3y6J8fRu0yocwJ2XryN2W7El5@mail.gmail.com> 
	<AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>
Message-ID: <AANLkTim8G--ZDzxOGnQYdcx-DICLa7pMBFqkJzCs_iZg@mail.gmail.com>

Hey,

You can try this:
http://sbcb.bioch.ox.ac.uk/oliver/software/GromacsWrapper/html/edpdb.html

Best!

Jo?o [...] Rodrigues
@ http://doeidoei.wordpress.org



On Mon, Jul 19, 2010 at 12:07 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Mon, Jul 19, 2010 at 10:59 AM, Bala subramanian
> <bala.biophysics at gmail.com> wrote:
> > Hello peter,
> > Sorry for the incomplete information. I want to cluster the structures
> say
> > for example using rmsd between the pdb.
> >
> > Thanks,
> > Bala
>
> Provided you can specify the atomic mapping between the structures,
> you can calculate RMSD using Bio.PDB, see for example:
> http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/
> One way to do this would be pairwise sequence alignments. There
> are probably specialised tools out there for this sort of clustering...
>
> Peter
>
> P.S. Please try to CC the mailing list in replies.
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From schaefer at rostlab.org  Mon Jul 19 09:22:09 2010
From: schaefer at rostlab.org (Christian Schaefer)
Date: Mon, 19 Jul 2010 15:22:09 +0200
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>	<AANLkTilzTT_1kOVsQpi76fDittiGf8rGkZBJ6Urflkzz@mail.gmail.com>	<AANLkTimujbfw33zV4bG3y6J8fRu0yocwJ2XryN2W7El5@mail.gmail.com>
	<AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>
Message-ID: <4C445181.6070801@rostlab.org>

On 07/19/2010 12:07 PM, Peter wrote:
> Provided you can specify the atomic mapping between the structures,
> you can calculate RMSD using Bio.PDB, see for example:
> http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/
> One way to do this would be pairwise sequence alignments. There
> are probably specialised tools out there for this sort of clustering...

Thanks Peter for that. I didn't know that Biopython provides 
superimpositioning of two pdb structures. I'd need that badly for my 
current project, and I used ProFit [1] so far. A native python 
implementation is of course very convenient in my case.

Chris

[1] http://www.bioinf.org.uk/

-- 
Dipl.-Bioinf. Christian Schaefer
Technical University Munich
Department for Bioinformatics
Faculty of Computer Science/I12
Boltzmannstr. 3
D-85748 Garching b. Muenchen
Germany
http://www.rostlab.org/~schaefer

From calhoun.bradley at gmail.com  Mon Jul 19 12:01:22 2010
From: calhoun.bradley at gmail.com (Brad Calhoun)
Date: Mon, 19 Jul 2010 11:01:22 -0500
Subject: [Biopython] missing DTD file
Message-ID: <AANLkTikrB1kNGYw-YIiA5DO2tlgTte5u_3SsH0tp6ASc@mail.gmail.com>

To whom it may concern,

The function of Biopython (currently using version 1.52) is severely limited
by a missing DTD file: "eLink_090910.dtd"  which I am unable to locate at
the suggested locations.

Any instruction to resolve this issue would be greatly appreciated.

Regards,
BTC

From biopython at maubp.freeserve.co.uk  Mon Jul 19 12:21:46 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 19 Jul 2010 17:21:46 +0100
Subject: [Biopython] missing DTD file
In-Reply-To: <AANLkTikrB1kNGYw-YIiA5DO2tlgTte5u_3SsH0tp6ASc@mail.gmail.com>
References: <AANLkTikrB1kNGYw-YIiA5DO2tlgTte5u_3SsH0tp6ASc@mail.gmail.com>
Message-ID: <AANLkTim3WXBCOPpDbNGvVKAxNDWkUFp06GUbwSWMaZ5a@mail.gmail.com>

On Mon, Jul 19, 2010 at 5:01 PM, Brad Calhoun <calhoun.bradley at gmail.com> wrote:
> To whom it may concern,
>
> The function of Biopython (currently using version 1.52) is severely limited
> by a missing DTD file: "eLink_090910.dtd" ?which I am unable to locate at
> the suggested locations.
>
> Any instruction to resolve this issue would be greatly appreciated.

Hi Brad,

This was included in Biopython 1.54 (it wasn't noticed quite in time for
Biopython 1.53). You can update your Biopython or get this and other
DTD files from the NCBI. In this case the file is here:

http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/eLink_090910.dtd

Peter

P.S. Googling for "biopython eLink_090910.dtd" worked pretty well ;)


From fredgca at hotmail.com  Mon Jul 19 12:37:30 2010
From: fredgca at hotmail.com (Frederico Arnoldi)
Date: Mon, 19 Jul 2010 16:37:30 +0000
Subject: [Biopython] clustering pdb
In-Reply-To: <mailman.1.1279555202.24200.biopython@lists.open-bio.org>
References: <mailman.1.1279555202.24200.biopython@lists.open-bio.org>
Message-ID: <SNT136-w639ECE8C3471B2BBC20C57BFBF0@phx.gbl>


Dear Bala,

As indicated by Rodrigues, you can use GromacsWrapper for peforming MD. I do not know any package for python that you could use to handle MD trajectories. However, it is possible to use RPy and Bio3D (http://mccammon.ucsd.edu/~bgrant/bio3d/index.html).

Att.,
Frederico Arnoldi

?
> Message: 1
> Date: Mon, 19 Jul 2010 11:39:11 +0200
> From: Bala subramanian 
> Subject: [Biopython] clustering pdb
> To: biopython at lists.open-bio.org
> Message-ID:
> 
> Content-Type: text/plain; charset=ISO-8859-1
>
> Friends,
> I have around 3000 pdb files obtained from MD simulations. I would like to
> know if it is possible to cluster the pdb files using any of the biopython's
> bio.PDB or other modules. If so, i would appreciate if you could provide me
> a sample code.
>
> Is there any utility in Biopython to handle MD trajectories obtained from
> common packages like gromacs, amber etc ?
>
> Thank you,
> Bala
>
 		 	   		  
_________________________________________________________________
PREPARE-SE: O SEU HOTMAIL VAI FICAR MELHOR DO QUE NUNCA. CLIQUE E VEJA AS NOVIDADES.
http://www.windowslive.com.br/public/product.aspx/view/1?ocid=Hotmail:Live:Hotmail:Tagline:senDimensao:PREPARE-SE83:-

From anaryin at gmail.com  Mon Jul 19 12:47:56 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Mon, 19 Jul 2010 18:47:56 +0200
Subject: [Biopython] clustering pdb
In-Reply-To: <SNT136-w639ECE8C3471B2BBC20C57BFBF0@phx.gbl>
References: <mailman.1.1279555202.24200.biopython@lists.open-bio.org> 
	<SNT136-w639ECE8C3471B2BBC20C57BFBF0@phx.gbl>
Message-ID: <AANLkTin_jZkHyiNf9jJht_QBJC9mUqHmWKUcc7EvsxLQ@mail.gmail.com>

edPDB actually allows some analysis of the trajectories (to some degree).
You might want to start looking there and then maybe bridge it with MMTK's
functionalities?

From pingou at pingoured.fr  Wed Jul 21 04:47:53 2010
From: pingou at pingoured.fr (Pierre-Yves)
Date: Wed, 21 Jul 2010 10:47:53 +0200
Subject: [Biopython] AssertionError
Message-ID: <1279702073.26644.8.camel@lab.localdomain>

Hi,

I am running into a problem which I can't figure why.

I parse a fasta file using biopython:
for seq_record in SeqIO.parse(fastafile, "fasta"):
     if seq_record.id == name:
            print seq_record.id
            return seq_record

This seq_record becomes seq and I try to extract only a subpart of the
sequence:
s = Seq(seq.seq[start:stop], generic_dna)
seq_out = SeqRecord(s, id = row[col_name])

Print of start and stop shows me:
251944 253441
which is what I expect.

But the creation of the sequence object fails with the following error:
Traceback (most recent call last):
  File "FastaExtractor.py", line 91, in <module>
    s = Seq(seq.seq[start:stop], generic_dna)
  File "/usr/lib64/python2.6/site-packages/Bio/Seq.py", line 87, in
__init__
    type(data) == type(u""))  # but can be a unicode string
AssertionError

When I try to create an object by hand using the python consol, it works
perfectly well.
Any idea what could be wrong ?

Thanks,

Pierre


From pingou at pingoured.fr  Wed Jul 21 05:10:35 2010
From: pingou at pingoured.fr (Pierre-Yves)
Date: Wed, 21 Jul 2010 11:10:35 +0200
Subject: [Biopython] AssertionError
In-Reply-To: <1279702073.26644.8.camel@lab.localdomain>
References: <1279702073.26644.8.camel@lab.localdomain>
Message-ID: <1279703435.26644.10.camel@lab.localdomain>

On Wed, 2010-07-21 at 10:47 +0200, Pierre-Yves wrote:
> s = Seq(seq.seq[start:stop], generic_dna)
> seq_out = SeqRecord(s, id = row[col_name])
I found the solution:
s = Seq(str(seq.seq[start:stop]), generic_dna)

Sorry for the noise,

Pierre


From biopython at maubp.freeserve.co.uk  Wed Jul 21 05:17:21 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 21 Jul 2010 10:17:21 +0100
Subject: [Biopython] AssertionError
In-Reply-To: <1279702073.26644.8.camel@lab.localdomain>
References: <1279702073.26644.8.camel@lab.localdomain>
Message-ID: <AANLkTinLG5zoyfVhSvJFWEx4eLFin7ZexhdaBvn9N4bY@mail.gmail.com>

On Wed, Jul 21, 2010 at 9:47 AM, Pierre-Yves <pingou at pingoured.fr> wrote:
> Hi,
>
> I am running into a problem which I can't figure why.
>
> I parse a fasta file using biopython:
> for seq_record in SeqIO.parse(fastafile, "fasta"):
> ? ? if seq_record.id == name:
> ? ? ? ? ? ?print seq_record.id
> ? ? ? ? ? ?return seq_record
>
> This seq_record becomes seq and I try to extract only a subpart of the
> sequence:
> s = Seq(seq.seq[start:stop], generic_dna)
> seq_out = SeqRecord(s, id = row[col_name])


If seq is a SeqRecord (a variable name I avoid), then seq.seq is
a Seq object, and slicing a Seq object gives another Seq object.
This means you shouldn't do this:

 Seq(seq.seq[start:stop], generic_dna)

Just do this:

seq.seq[start:stop]

Your work around seems overly complicated,

Seq(str(seq.seq[start:stop]), generic_dna)

If your reason for doing this is to specify the alphabet, just tell
Bio.SeqIO.parse() the alphabet instead.

You can also slice the original SeqRecord instead, to give a new
SeqRecord, and change its id to what you want.

>
> But the creation of the sequence object fails with the following error:
> Traceback (most recent call last):
> ?File "FastaExtractor.py", line 91, in <module>
> ? ?s = Seq(seq.seq[start:stop], generic_dna)
> ?File "/usr/lib64/python2.6/site-packages/Bio/Seq.py", line 87, in
> __init__
> ? ?type(data) == type(u"")) ?# but can be a unicode string
> AssertionError

That should be a clearer error message, the Seq object is not
expecting you to give it a Seq object - but a string or unicode.

Peter


From pingou at pingoured.fr  Wed Jul 21 05:22:12 2010
From: pingou at pingoured.fr (Pierre-Yves)
Date: Wed, 21 Jul 2010 11:22:12 +0200
Subject: [Biopython] AssertionError
In-Reply-To: <AANLkTinLG5zoyfVhSvJFWEx4eLFin7ZexhdaBvn9N4bY@mail.gmail.com>
References: <1279702073.26644.8.camel@lab.localdomain>
	<AANLkTinLG5zoyfVhSvJFWEx4eLFin7ZexhdaBvn9N4bY@mail.gmail.com>
Message-ID: <1279704132.26644.13.camel@lab.localdomain>

On Wed, 2010-07-21 at 10:17 +0100, Peter wrote:

> If seq is a SeqRecord (a variable name I avoid),
Changed.

>  then seq.seq is
> a Seq object, and slicing a Seq object gives another Seq object.
> This means you shouldn't do this:
> 
>  Seq(seq.seq[start:stop], generic_dna)
> 
> Just do this:
> 
> seq.seq[start:stop]

Indeed:
 seq_out = SeqRecord( seq_record.seq[start:stop],
                      id = row[col_name]
                    )
just works.

> >
> > But the creation of the sequence object fails with the following error:
> > Traceback (most recent call last):
> >  File "FastaExtractor.py", line 91, in <module>
> >    s = Seq(seq.seq[start:stop], generic_dna)
> >  File "/usr/lib64/python2.6/site-packages/Bio/Seq.py", line 87, in
> > __init__
> >    type(data) == type(u""))  # but can be a unicode string
> > AssertionError
> 
> That should be a clearer error message, the Seq object is not
> expecting you to give it a Seq object - but a string or unicode.

A clearer error message would indeed be nice.


Pierre


From biopython at maubp.freeserve.co.uk  Wed Jul 21 05:46:18 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 21 Jul 2010 10:46:18 +0100
Subject: [Biopython] AssertionError
In-Reply-To: <1279704132.26644.13.camel@lab.localdomain>
References: <1279702073.26644.8.camel@lab.localdomain>
	<AANLkTinLG5zoyfVhSvJFWEx4eLFin7ZexhdaBvn9N4bY@mail.gmail.com>
	<1279704132.26644.13.camel@lab.localdomain>
Message-ID: <AANLkTimjjqo0MRcH8OTkWNouclXVpEZg0HccuUGhujiW@mail.gmail.com>

On Wed, Jul 21, 2010 at 10:22 AM, Pierre-Yves <pingou at pingoured.fr> wrote:
>>
>> That should be a clearer error message, the Seq object is not
>> expecting you to give it a Seq object - but a string or unicode.
>
> A clearer error message would indeed be nice.
>

It will give a TypeError in the next release. Thanks for the feedback.

Peter

From bala.biophysics at gmail.com  Wed Jul 21 10:51:07 2010
From: bala.biophysics at gmail.com (Bala subramanian)
Date: Wed, 21 Jul 2010 16:51:07 +0200
Subject: [Biopython] running naccess
Message-ID: <AANLkTimgjZ3cgwELxQyHoJF7tOrK9Y_9wpWGTVFYZMiy@mail.gmail.com>

Friends,
I am trying to run naccess as follows.

from Bio.PDB.PDBParser import PDBParser
par = PDBParser()
structure = par.get_structure('test','12_25.pdb')
import Bio.PDB.NACCESS as nac
data=nac.run_naccess(structure[0],'12_25.pdb')

It seems that there is an issue with tmp dir creation. I could nt run
naccess even if i define *temp_path='.'* with run_naccess function. Kindly
write me how to resolve the issue.


*I get the following error:*

IOError                                   Traceback (most recent call last)

/tmp/tmpqQLhRl/<ipython console> in <module>()

/apps/py_modules/gcc/lib/python2.6/site-packages/Bio/PDB/NACCESS.pyc in
run_naccess(model, pdb_file, probe_size, z_slice, naccess, temp_path)
     56     # get the output, then delete the temp directory

     57     rsa_file = tmp_pdb_file[:-4] + '.rsa'
---> 58     rf = open(rsa_file)
     59     rsa_data = rf.readlines()
     60     rf.close()

IOError: [Errno 2] No such file or directory: '/tmp/tmpqQLhRl/tmpaOkRlK.rsa'

From biopython at maubp.freeserve.co.uk  Wed Jul 21 11:02:44 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 21 Jul 2010 16:02:44 +0100
Subject: [Biopython] running naccess
In-Reply-To: <AANLkTimgjZ3cgwELxQyHoJF7tOrK9Y_9wpWGTVFYZMiy@mail.gmail.com>
References: <AANLkTimgjZ3cgwELxQyHoJF7tOrK9Y_9wpWGTVFYZMiy@mail.gmail.com>
Message-ID: <AANLkTin6dOYlq5l00ZjzTkX2bcHRz8RogIoBVe9PMxC0@mail.gmail.com>

On Wed, Jul 21, 2010 at 3:51 PM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Friends,
> I am trying to run naccess as follows.
>
> from Bio.PDB.PDBParser import PDBParser
> par = PDBParser()
> structure = par.get_structure('test','12_25.pdb')
> import Bio.PDB.NACCESS as nac
> data=nac.run_naccess(structure[0],'12_25.pdb')
>
> It seems that there is an issue with tmp dir creation. I could nt run
> naccess even if i define *temp_path='.'* with run_naccess function. Kindly
> write me how to resolve the issue.
>
>
> *I get the following error:*
>
> IOError ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Traceback (most recent call last)
>
> /tmp/tmpqQLhRl/<ipython console> in <module>()
>
> /apps/py_modules/gcc/lib/python2.6/site-packages/Bio/PDB/NACCESS.pyc in
> run_naccess(model, pdb_file, probe_size, z_slice, naccess, temp_path)
> ? ? 56 ? ? # get the output, then delete the temp directory
>
> ? ? 57 ? ? rsa_file = tmp_pdb_file[:-4] + '.rsa'
> ---> 58 ? ? rf = open(rsa_file)
> ? ? 59 ? ? rsa_data = rf.readlines()
> ? ? 60 ? ? rf.close()
>
> IOError: [Errno 2] No such file or directory: '/tmp/tmpqQLhRl/tmpaOkRlK.rsa'

Try putting some debug print statements into NACCESS.py, in
particular see what stdout and stderr contain. My guess is there
is a problem running the tool.

Also try running the NACCESS command line tool by hand at
the command prompt, to make sure it is installed and working
correctly.

Peter


From 2huggie at gmail.com  Fri Jul 23 03:04:13 2010
From: 2huggie at gmail.com (Timothy Wu)
Date: Fri, 23 Jul 2010 15:04:13 +0800
Subject: [Biopython] Gene ontology parsing
Message-ID: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>

Hi

Is there a parser in BioPython for OBO v1.2?

If there isn't (at least I couldn't find it a while back), maybe I could
contribute a little. I've casually wrote an OntologyIO package with
"OboRecord", a scanner and consumer files. I may have not handles all the
stuff written on http://www.geneontology.org/GO.format.obo-1_2.shtml, but it
did suit my own purpose before. I don't know if anyone in the project will
be interested in it. I also do not know if my code will pass the quality
standard set forth by BioPython. I've also wrote a GoGraph structure that
allow me to look for stuff in the DAG, treating it much like a tree, looking
for "common ancestor" given two nodes, parent, child, etc. I've never
contributed code to any project before, so if these code can indeed be
contributed, perhaps some help from someone in the project would be needed,
thanks.

Timothy

From bartek at rezolwenta.eu.org  Fri Jul 23 03:50:45 2010
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Fri, 23 Jul 2010 09:50:45 +0200
Subject: [Biopython] Gene ontology parsing
In-Reply-To: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>
References: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>
Message-ID: <AANLkTikq8U_NoZrbrj0Ajg7V+ZFjAPd3hOkuPwqLX=wP@mail.gmail.com>

hi Timothy,

I, for one, would be interested in Gene Ontology parsing. I could also help
with reviewing the code if you worry about whether it fits to the rest of
biopython.

I think the easiest for all would be if you could make a branch of biopython
on github including your proposed enhancements. This would allow everybody
to see what's in there and also make changes and finally mergi it into the
trunk.

thanks for your offer

Bartek
On Fri, Jul 23, 2010 at 9:04 AM, Timothy Wu <2huggie at gmail.com> wrote:

> Hi
>
> Is there a parser in BioPython for OBO v1.2?
>
> If there isn't (at least I couldn't find it a while back), maybe I could
> contribute a little. I've casually wrote an OntologyIO package with
> "OboRecord", a scanner and consumer files. I may have not handles all the
> stuff written on http://www.geneontology.org/GO.format.obo-1_2.shtml, but
> it
> did suit my own purpose before. I don't know if anyone in the project will
> be interested in it. I also do not know if my code will pass the quality
> standard set forth by BioPython. I've also wrote a GoGraph structure that
> allow me to look for stuff in the DAG, treating it much like a tree,
> looking
> for "common ancestor" given two nodes, parent, child, etc. I've never
> contributed code to any project before, so if these code can indeed be
> contributed, perhaps some help from someone in the project would be needed,
> thanks.
>
> Timothy
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>


-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433

From biopython at maubp.freeserve.co.uk  Fri Jul 23 05:45:11 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 23 Jul 2010 10:45:11 +0100
Subject: [Biopython] Gene ontology parsing
In-Reply-To: <AANLkTikq8U_NoZrbrj0Ajg7V+ZFjAPd3hOkuPwqLX=wP@mail.gmail.com>
References: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>
	<AANLkTikq8U_NoZrbrj0Ajg7V+ZFjAPd3hOkuPwqLX=wP@mail.gmail.com>
Message-ID: <AANLkTikt_2b3=mz6kuFxUrpx7grujhNbx4WSkJasRvqy@mail.gmail.com>

On Fri, Jul 23, 2010 at 8:50 AM, Bartek Wilczynski
<bartek at rezolwenta.eu.org> wrote:
> hi Timothy,
>
> I, for one, would be interested in Gene Ontology parsing. I could also help
> with reviewing the code if you worry about whether it fits to the rest of
> biopython.
>
> I think the easiest for all would be if you could make a branch of biopython
> on github including your proposed enhancements. This would allow everybody
> to see what's in there and also make changes and finally mergi it into the
> trunk.
>
> thanks for your offer
>
> Bartek

Hi Timothy & Bartek,

There are already several people working on GO stuff in branches on github,
e.g. Chris Lasher, Kyle Ellrott, Tam?s Nepusz. I don't know if any of them are
doing OBO v1.2, but it would be sensible to check and try and combine efforts.

Peter


From amaher at fas.harvard.edu  Fri Jul 23 11:22:32 2010
From: amaher at fas.harvard.edu (Andrew Maher)
Date: Fri, 23 Jul 2010 11:22:32 -0400
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
Message-ID: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>

I'm a beginner with python, and I'm having trouble with something relatively
simple:

I'm trying to find the isoelectric point of a protein with the
sequence: VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC

So, when I load python 2.6.2 with bipython v1.54 and then type in "from
Bio.SeqUtils import ProtParam" on one line and then "X =
ProteinAnalysis("VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC")
on the next line, I get the following error message:

NameError: name 'ProteinAnalysis' is not defined

But, looking at the source code for ProtParam (
http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis),
isn't the ProteinAnalysis class clearly defined? What am I doing wrong?

From anaryin at gmail.com  Fri Jul 23 11:25:47 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 23 Jul 2010 17:25:47 +0200
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>
Message-ID: <AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>

Hello Andrew,

Try this: ProtParam.ProteinAnalysis(Sequence)

Best,

Jo?o [...] Rodrigues
@ http://doeidoei.wordpress.org



On Fri, Jul 23, 2010 at 5:22 PM, Andrew Maher <amaher at fas.harvard.edu>wrote:

> I'm a beginner with python, and I'm having trouble with something
> relatively
> simple:
>
> I'm trying to find the isoelectric point of a protein with the
> sequence:
> VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC
>
> So, when I load python 2.6.2 with bipython v1.54 and then type in "from
> Bio.SeqUtils import ProtParam" on one line and then "X =
>
> ProteinAnalysis("VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC")
> on the next line, I get the following error message:
>
> NameError: name 'ProteinAnalysis' is not defined
>
> But, looking at the source code for ProtParam (
>
> http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis
> ),
> isn't the ProteinAnalysis class clearly defined? What am I doing wrong?
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From amaher at fas.harvard.edu  Fri Jul 23 11:31:59 2010
From: amaher at fas.harvard.edu (Andrew Maher)
Date: Fri, 23 Jul 2010 11:31:59 -0400
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com> 
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>
Message-ID: <AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>

Sorry, now I get this:

-bash-3.1$ python
Python 2.6.2 (r262:71600, Jul 27 2009, 17:05:24)
[GCC 4.1.2 20070626 (Red Hat 4.1.2-14)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio.SeqUtils.ProtParam
>>>
ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'ProtParam' is not defined
>>>

I wonder what's wrong...

On Fri, Jul 23, 2010 at 11:25 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hello Andrew,
>
> Try this: ProtParam.ProteinAnalysis(Sequence)
>
> Best,
>
> Jo?o [...] Rodrigues
> @ http://doeidoei.wordpress.org
>
>
>
> On Fri, Jul 23, 2010 at 5:22 PM, Andrew Maher <amaher at fas.harvard.edu>wrote:
>
>> I'm a beginner with python, and I'm having trouble with something
>> relatively
>> simple:
>>
>> I'm trying to find the isoelectric point of a protein with the
>> sequence:
>> VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC
>>
>> So, when I load python 2.6.2 with bipython v1.54 and then type in "from
>> Bio.SeqUtils import ProtParam" on one line and then "X =
>>
>> ProteinAnalysis("VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC")
>> on the next line, I get the following error message:
>>
>> NameError: name 'ProteinAnalysis' is not defined
>>
>> But, looking at the source code for ProtParam (
>>
>> http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis
>> ),
>> isn't the ProteinAnalysis class clearly defined? What am I doing wrong?
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>


From anaryin at gmail.com  Fri Jul 23 11:34:49 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 23 Jul 2010 17:34:49 +0200
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com> 
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com> 
	<AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
Message-ID: <AANLkTinnR+eC_kEyasuQWekDANKfcCZk-JSRJTA77uEq@mail.gmail.com>

No problem, you just switched the import statement.

from Bio.SeqUtils import ProtParam

sequence = ''DTKTLIKTIVT"

ProtParam.ProteinAnalysis(sequence)

or

import Bio.SeqUtils.ProtParam

sequence = ''DTKTLIKTIVT"

ProteinAnalysis(sequence)


It's a namespace issue :)

Best!

Jo?o


From biopython at maubp.freeserve.co.uk  Fri Jul 23 11:39:40 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 23 Jul 2010 16:39:40 +0100
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>
	<AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
Message-ID: <AANLkTimjfWxktsDc75FGZvNC+V_8yH546N1ynoCG0JN4@mail.gmail.com>

On Fri, Jul 23, 2010 at 4:31 PM, Andrew Maher <amaher at fas.harvard.edu> wrote:
> Sorry, now I get this:

Maybe reading up on Python's import statement and name spaces will help.
You are close...

One approach is to import the module:

from Bio.SeqUtils import ProtParam
x = ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')

Or, you might prefer to import just the class - probably a good plan if you
only need one or two things from this module:

from Bio.SeqUtils.ProtParam import ProteinAnalysis
x = ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')

Peter

P.S.

You can even do this - but I don't think it is very clear:

import Bio.SeqUtils.ProtParam
x = Bio.SeqUtils.ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')

From amaher at fas.harvard.edu  Fri Jul 23 11:49:06 2010
From: amaher at fas.harvard.edu (Andrew Maher)
Date: Fri, 23 Jul 2010 11:49:06 -0400
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTimjfWxktsDc75FGZvNC+V_8yH546N1ynoCG0JN4@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com> 
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com> 
	<AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com> 
	<AANLkTimjfWxktsDc75FGZvNC+V_8yH546N1ynoCG0JN4@mail.gmail.com>
Message-ID: <AANLkTi=_MYE7m=NgcptdMzvi_pEqbJ6HuJ=_9jb3vEMY@mail.gmail.com>

Thanks a lot!

Also, I've noticed that when using this module to get an isoelectric point,
x.pi() does not work, but x.isoelectric_point() does. Perhaps someone should
note that somewhere.

-Andrew

On Fri, Jul 23, 2010 at 11:39 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Fri, Jul 23, 2010 at 4:31 PM, Andrew Maher <amaher at fas.harvard.edu>
> wrote:
> > Sorry, now I get this:
>
> Maybe reading up on Python's import statement and name spaces will help.
> You are close...
>
> One approach is to import the module:
>
> from Bio.SeqUtils import ProtParam
> x = ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')
>
> Or, you might prefer to import just the class - probably a good plan if you
> only need one or two things from this module:
>
> from Bio.SeqUtils.ProtParam import ProteinAnalysis
> x = ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')
>
> Peter
>
> P.S.
>
> You can even do this - but I don't think it is very clear:
>
> import Bio.SeqUtils.ProtParam
> x =
> Bio.SeqUtils.ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')
>
>

From biopython at maubp.freeserve.co.uk  Fri Jul 23 11:52:53 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 23 Jul 2010 16:52:53 +0100
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTi=_MYE7m=NgcptdMzvi_pEqbJ6HuJ=_9jb3vEMY@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>
	<AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
	<AANLkTimjfWxktsDc75FGZvNC+V_8yH546N1ynoCG0JN4@mail.gmail.com>
	<AANLkTi=_MYE7m=NgcptdMzvi_pEqbJ6HuJ=_9jb3vEMY@mail.gmail.com>
Message-ID: <AANLkTimt4468w4Ph8uiKN-zN7tK8iSjoC3ODB2quC8-D@mail.gmail.com>

On Fri, Jul 23, 2010 at 4:49 PM, Andrew Maher <amaher at fas.harvard.edu> wrote:
> Thanks a lot!
>
> Also, I've noticed that when using this module to get an isoelectric point,
> x.pi() does not work, but x.isoelectric_point() does. Perhaps someone should
> note that somewhere.

That looks like a typo in the ProtParam module documentation - I'll
fix that. Thanks!

Peter

From kellrott at gmail.com  Fri Jul 23 12:17:19 2010
From: kellrott at gmail.com (Kyle)
Date: Fri, 23 Jul 2010 09:17:19 -0700
Subject: [Biopython] Gene ontology parsing
In-Reply-To: <AANLkTikt_2b3=mz6kuFxUrpx7grujhNbx4WSkJasRvqy@mail.gmail.com>
References: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>
	<AANLkTikq8U_NoZrbrj0Ajg7V+ZFjAPd3hOkuPwqLX=wP@mail.gmail.com>
	<AANLkTikt_2b3=mz6kuFxUrpx7grujhNbx4WSkJasRvqy@mail.gmail.com>
Message-ID: <AANLkTim_b2zOC3DwA3GwuBnB5gmgOvfOdFYFPayDt3-m@mail.gmail.com>

> There are already several people working on GO stuff in branches on github,
> e.g. Chris Lasher, Kyle Ellrott, Tam?s Nepusz. I don't know if any of them are
> doing OBO v1.2, but it would be sensible to check and try and combine efforts.

The branch at http://github.com/kellrott/biopython/tree/gosupport
should parse most of the information held in OBO v1.2.
Chris's original version was targeted only for the GO OBO file, as
there was a typecheck to make sure the node ID's started with 'GO:'.
That's disable in my branch, and I've used the package to parse a few
of the other ontologies found at www.obofoundry.org.
The module is currently called Bio.GO, but maybe it should be
re-factored to represent the fact that it covers general OBO files,
and not just the GO file specifically.

The main things things keeping it from merging into the main branch
are proper documentation, complete unit tests, and making sure that it
covers all of the standard usage practices.

If you can try it out, and let me know which function are missing (and
maybe contribute some code), we can push this thing forward.

Kyle


From bouchard.lysiane at gmail.com  Fri Jul 23 15:54:29 2010
From: bouchard.lysiane at gmail.com (Lysiane Bouchard)
Date: Fri, 23 Jul 2010 15:54:29 -0400
Subject: [Biopython] NaN values, lowess
Message-ID: <AANLkTikK+NdqWOAwSa56Oh+tOjOQekKqx8jRF6f56vOz@mail.gmail.com>

Hi,

I am experimenting problems with the lowess function, from Bio.Statistics
module, version 1.53.
It seems that when the data trajectory is fairly constant, NaN / infinite
values are returned as estimated trend.  I wonder if someone encountered a
similar problem ?

Thank you,

Lysiane

From pengyu.ut at gmail.com  Wed Jul 28 00:08:37 2010
From: pengyu.ut at gmail.com (Peng Yu)
Date: Tue, 27 Jul 2010 23:08:37 -0500
Subject: [Biopython] Where is alphebet of Bio.Seq documented
Message-ID: <AANLkTintQX20Q2vE8sMfx9111tWXNyGwAF_2EqZWkkBS@mail.gmail.com>

Hi,

Seq class has a member alphabet if I'm correct about the terminology.
But I don't see it in help(Bio.Seq). Is it documented in python
help()?

from Bio.Seq import Seq
my_seq = Seq("AGTACACTGGT")
print my_seq
print my_seq.alphabet

-- 
Regards,
Peng

From biopython at maubp.freeserve.co.uk  Wed Jul 28 06:51:26 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 28 Jul 2010 11:51:26 +0100
Subject: [Biopython] Where is alphebet of Bio.Seq documented
In-Reply-To: <AANLkTintQX20Q2vE8sMfx9111tWXNyGwAF_2EqZWkkBS@mail.gmail.com>
References: <AANLkTintQX20Q2vE8sMfx9111tWXNyGwAF_2EqZWkkBS@mail.gmail.com>
Message-ID: <AANLkTinNr6LgT8u5UiSZR0TuTmgaBNJ=UirtpS-eQ18n@mail.gmail.com>

On Wed, Jul 28, 2010 at 5:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
> Hi,
>
> Seq class has a member alphabet if I'm correct about the terminology.
> But I don't see it in help(Bio.Seq). Is it documented in python
> help()?
>
> from Bio.Seq import Seq
> my_seq = Seq("AGTACACTGGT")
> print my_seq
> print my_seq.alphabet

Hi Peng,

The main tutorial does explain this, but you are right that the Seq docstrings
should describe the alphabet property/attribute of the Seq objects. It is just
an Alphabet object as defined in the Bio.Alphabet module.

Peter

From Achim.Treumann at NEPAF.com  Sat Jul 31 02:05:09 2010
From: Achim.Treumann at NEPAF.com (Achim Treumann)
Date: Sat, 31 Jul 2010 07:05:09 +0100
Subject: [Biopython] problem with SeqIO.index() and get_raw
Message-ID: <01798D2396253A449511F31F1CDE83550C3E6C@srv1.NEPAF.local>

Dear all, 

I am new to biopython and trying to familiarise myself with its utilities. When I was trying to parse a swissprot.dat file to then copy the full data back using the get_raw attribute, I got stuck (Biopython 1.53, Python 2.6 on WinXP). 

I was using the following code:

<code>
from Bio import SeqIO
from Bio import Swissprot
InputFile = "D:\data\uniprot_sprot.short.dat"

handle = open(InputFile)
uniprot = SeqIO.index(InputFile, "swiss")
acclist=[]
for record in Swissprot.parse(handle):
    accList.append(record.accessions[0])
handle.close()
out_handle = open("D:\data\uniprot_sprot.temp.dat", "w")
for acc in accList:
    out_handle.write(uniprot.get_raw(acc)
out_handle.close()
</code>

The input file is a sprot-formatted file with 39 entries. 

When I try to run this, I get the following error:
Traceback (most recent call last):
  File"<pyshell#52>", line 2, in <module>
    handle.write(uniprot.getraw(acc))
Attribute error: 'SwissDict' object has no attribute 'get_raw'

Where am I going wrong? I have tried to replicate the corresponding example from the tutorial and got stuck at the same point with the same error message. Any help would be greatly appreciated. 

As I am typing, I realise that get_raw might only have been implemented in Biopython 1.54... I will post this anyway, and if upgrading sorts it, I will send a reply. 

Many thanks for comments and advice, 
Achim


From biopython at maubp.freeserve.co.uk  Sat Jul 31 05:16:38 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 31 Jul 2010 10:16:38 +0100
Subject: [Biopython] problem with SeqIO.index() and get_raw
In-Reply-To: <01798D2396253A449511F31F1CDE83550C3E6C@srv1.NEPAF.local>
References: <01798D2396253A449511F31F1CDE83550C3E6C@srv1.NEPAF.local>
Message-ID: <AANLkTi=BnC51gXDeQ-a-GuMwVyqpO7C4MuwwuTyByeFb@mail.gmail.com>

On Sat, Jul 31, 2010 at 7:05 AM, Achim Treumann
<Achim.Treumann at nepaf.com> wrote:
> Dear all,
>
> I am new to biopython and trying to familiarise myself with its utilities.
> When I was trying to parse a swissprot.dat file to then copy the full
> data back using the get_raw attribute, I got stuck (Biopython 1.53,
> Python 2.6 on WinXP).
>
>...
>
> As I am typing, I realise that get_raw might only have been
> implemented in Biopython 1.54... I will post this anyway, and if
> upgrading sorts it, I will send a reply.

Hi Achim,

Well guessed. Yes, get_raw was added in Biopython 1.54, see
http://news.open-bio.org/news/2010/05/biopython-release-154/

Are you reading the current tutorial on line (rather than the
version shipped with Biopython 1.53)? It does mention this,
although maybe it could be in the FAQ as well... would that
help?

Peter

From Achim.Treumann at NEPAF.com  Sat Jul 31 21:53:17 2010
From: Achim.Treumann at NEPAF.com (Achim Treumann)
Date: Sun, 1 Aug 2010 02:53:17 +0100
Subject: [Biopython] problem with SeqIO.index() and get_raw
References: <01798D2396253A449511F31F1CDE83550C3E6C@srv1.NEPAF.local>
	<AANLkTi=BnC51gXDeQ-a-GuMwVyqpO7C4MuwwuTyByeFb@mail.gmail.com>
Message-ID: <01798D2396253A449511F31F1CDE83550C3E6D@srv1.NEPAF.local>

Hi Peter, Jordan andd others, 

many thanks for the fast replies. 

You are obviously right - installing 1.54 got me rolling. 

I now noticed that the tutorial I was working with was indeed 1.54 (should have checked that when I downloaded it separately from the distribution). When I was going through the tutorial I did not realise that the version I was working with was not 1.54... Don't think that it would be essential to put this into the FAQ - neither google nor searching this discussion list brought up other people who were struggling with this, I must have been the only one too thick to check version numbers :-)

Thanks a lot again for your rapid help, 
Achim

-----Original Message-----
From: p.j.a.cock at googlemail.com on behalf of Peter
Sent: Sat 31/07/2010 18:16
To: Achim Treumann
Cc: biopython at lists.open-bio.org
Subject: Re: [Biopython] problem with SeqIO.index() and get_raw
 
On Sat, Jul 31, 2010 at 7:05 AM, Achim Treumann
<Achim.Treumann at nepaf.com> wrote:
> Dear all,
>
> I am new to biopython and trying to familiarise myself with its utilities.
> When I was trying to parse a swissprot.dat file to then copy the full
> data back using the get_raw attribute, I got stuck (Biopython 1.53,
> Python 2.6 on WinXP).
>
>...
>
> As I am typing, I realise that get_raw might only have been
> implemented in Biopython 1.54... I will post this anyway, and if
> upgrading sorts it, I will send a reply.

Hi Achim,

Well guessed. Yes, get_raw was added in Biopython 1.54, see
http://news.open-bio.org/news/2010/05/biopython-release-154/

Are you reading the current tutorial on line (rather than the
version shipped with Biopython 1.53)? It does mention this,
although maybe it could be in the FAQ as well... would that
help?

Peter



From reece at berkeley.edu  Thu Jul  1 00:05:05 2010
From: reece at berkeley.edu (Reece Hart)
Date: Wed, 30 Jun 2010 17:05:05 -0700
Subject: [Biopython] BioJava-like seqres alignment for Bio.PDB
In-Reply-To: <AANLkTilaZJ-aVaFCTVw97P3ryBnLXE75najLkzoWcJgf@mail.gmail.com>
References: <AANLkTimQy0Ez8l4p6udUvqzf469IpBov4Fh-6OEefQep@mail.gmail.com>	<4C2A7C09.2020204@berkeley.edu>
	<AANLkTilaZJ-aVaFCTVw97P3ryBnLXE75najLkzoWcJgf@mail.gmail.com>
Message-ID: <4C2BDBB1.7070503@berkeley.edu>

On 06/30/2010 06:44 AM, Peter wrote:
> That looks like a good reason to have a PDB XML parser (as trying to do
> this from the plain text PDB is probably fiddly).
>    

The only way to do this from the PDB text file is to infer the mapping 
by aligning the seqres block and the ATOM residues. Fiddly is a generous 
description of the problems one will encounter.

mmCIF and XML are the authoritative sources, AFAIK.

-Reece



From lunt at ctbp.ucsd.edu  Thu Jul  1 03:06:41 2010
From: lunt at ctbp.ucsd.edu (Bryan Lunt)
Date: Wed, 30 Jun 2010 20:06:41 -0700
Subject: [Biopython] (least) Favorite PDB models?
Message-ID: <AANLkTin1WHAN80BOdUQY4jX7fvHiMj4_kbzdR4vB62SJ@mail.gmail.com>

Greetings All,

So I have finished (for now) the section of my program that maps PDB
model residues to SEQRES residues...

And every programmer's favorite thing is QA, right?

Does anyone have some suggestions of particularly ugly PDB models
(discontinuous, strange residue numberings, etc)
that I can test it on?

Thanks All!
-Bryan Lunt


From p.j.a.cock at googlemail.com  Thu Jul  1 09:33:04 2010
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 1 Jul 2010 10:33:04 +0100
Subject: [Biopython] (least) Favorite PDB models?
In-Reply-To: <AANLkTin1WHAN80BOdUQY4jX7fvHiMj4_kbzdR4vB62SJ@mail.gmail.com>
References: <AANLkTin1WHAN80BOdUQY4jX7fvHiMj4_kbzdR4vB62SJ@mail.gmail.com>
Message-ID: <AANLkTil3tYrKIOcXU8233gfYP5HsiZlVJAJAYiURCVZT@mail.gmail.com>

On Thu, Jul 1, 2010 at 4:06 AM, Bryan Lunt <lunt at ctbp.ucsd.edu> wrote:
> Greetings All,
>
> So I have finished (for now) the section of my program that maps PDB
> model residues to SEQRES residues...
>
> And every programmer's favorite thing is QA, right?

It should be ;)

Unit tests are good!

> Does anyone have some suggestions of particularly ugly PDB models
> (discontinuous, strange residue numberings, etc)
> that I can test it on?

There are a few odd files listed here,

http://www.warwick.ac.uk/go/peter_cock/python/ramachandran/top500/

For example 1DIN and 2HMZ showed some interesting behaviour
with fractional occupancy - these should be hard to map onto a single
sequence!

Peter


From anaryin at gmail.com  Fri Jul  2 19:25:21 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 2 Jul 2010 14:25:21 -0500
Subject: [Biopython] BioJava-like seqres alignment for Bio.PDB
In-Reply-To: <AANLkTilaZJ-aVaFCTVw97P3ryBnLXE75najLkzoWcJgf@mail.gmail.com>
References: <AANLkTimQy0Ez8l4p6udUvqzf469IpBov4Fh-6OEefQep@mail.gmail.com> 
	<4C2A7C09.2020204@berkeley.edu>
	<AANLkTilaZJ-aVaFCTVw97P3ryBnLXE75najLkzoWcJgf@mail.gmail.com>
Message-ID: <AANLkTil-8vv40FatNKCRIxzqJrCn9Ogv4IbDg_pSmpVE@mail.gmail.com>

Hey!

>> Does anyone have any code for easy alignment between the SEQRES entry
> >> in a pdb file and the actual ATOM/HETATM entries in the chain?
>

There's not parsing for SEQRES yet in parse_header_pdb but it wouldn't be
hard to.


>  >> In biojava, this is just one of the options when you parse a PDB file,
> >> it would certainly be useful.
>

Indeed it would.


That looks like a good reason to have a PDB XML parser (as trying to do
> this from the plain text PDB is probably fiddly).
>

I don't know if people have started working on such a parser but I have some
sort of a head start. Check here:

http://github.com/JoaoRodrigues/biopython/blob/GSOC2010/Bio/Struct/WWW/WHATIFXML.py

Warning, very ugly :)



> > In any case, having function that provides this mapping (both directions)
> in
> > BioPython would be extremely useful.
>
> Maybe something for the GSoC project TODO list? ;)
>

Hmm, I was working on something more or less like this a while back and it
didn't work that well. But it might be a good idea. It seems however that
Bryan already did it :) No?

Jo?o



From rodrigo_faccioli at uol.com.br  Fri Jul  2 21:50:58 2010
From: rodrigo_faccioli at uol.com.br (Rodrigo Faccioli)
Date: Fri, 2 Jul 2010 18:50:58 -0300
Subject: [Biopython] BioJava-like seqres alignment for Bio.PDB
In-Reply-To: <AANLkTil-8vv40FatNKCRIxzqJrCn9Ogv4IbDg_pSmpVE@mail.gmail.com>
References: <AANLkTimQy0Ez8l4p6udUvqzf469IpBov4Fh-6OEefQep@mail.gmail.com>
	<4C2A7C09.2020204@berkeley.edu>
	<AANLkTilaZJ-aVaFCTVw97P3ryBnLXE75najLkzoWcJgf@mail.gmail.com>
	<AANLkTil-8vv40FatNKCRIxzqJrCn9Ogv4IbDg_pSmpVE@mail.gmail.com>
Message-ID: <AANLkTimEkMSUPowJ3eGhKS_zf-8yv2ms1DKLHA5UyUR3@mail.gmail.com>

Hi,

About the SEQRES implementation for BioPython, I've developed it. Please,
see it in [1]. I hope this implementation could help you.

[1]
http://github.com/rodrigofaccioli/ContributeToBioPython/blob/master/fcfrp/PDBParser.py

Best,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Fri, Jul 2, 2010 at 4:25 PM, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hey!
>
> >> Does anyone have any code for easy alignment between the SEQRES entry
> > >> in a pdb file and the actual ATOM/HETATM entries in the chain?
> >
>
> There's not parsing for SEQRES yet in parse_header_pdb but it wouldn't be
> hard to.
>
>
> >  >> In biojava, this is just one of the options when you parse a PDB
> file,
> > >> it would certainly be useful.
> >
>
> Indeed it would.
>
>
> That looks like a good reason to have a PDB XML parser (as trying to do
> > this from the plain text PDB is probably fiddly).
> >
>
> I don't know if people have started working on such a parser but I have
> some
> sort of a head start. Check here:
>
>
> http://github.com/JoaoRodrigues/biopython/blob/GSOC2010/Bio/Struct/WWW/WHATIFXML.py
>
> Warning, very ugly :)
>
>
>
> > > In any case, having function that provides this mapping (both
> directions)
> > in
> > > BioPython would be extremely useful.
> >
> > Maybe something for the GSoC project TODO list? ;)
> >
>
> Hmm, I was working on something more or less like this a while back and it
> didn't work that well. But it might be a good idea. It seems however that
> Bryan already did it :) No?
>
> Jo?o
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



From biopython at maubp.freeserve.co.uk  Mon Jul  5 17:53:41 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 5 Jul 2010 18:53:41 +0100
Subject: [Biopython] Is Bio.Crystal still useful (for NDB files)?
Message-ID: <AANLkTinMfklMpOJ2o7KGH_8mqlgJOP3oQbYI4XyHvdir@mail.gmail.com>

Hello all,

Is anyone using Bio.Crystal? It is a parser for a subset of the PDB format
which used to be used by the The Nucleic Acid Database Project. My
impression from their website is that they are moving all their data to
the PDB format - but still have some structures that are present only
in the NDB format:

http://ndbserver.rutgers.edu/download_data/index.html

I'm asking because Bio.Crystal needs some updating to avoid
deprecation warnings in the latest versions of Python - and it
might be simpler just to deprecate it instead.

Peter


From rjalves at igc.gulbenkian.pt  Mon Jul  5 20:00:17 2010
From: rjalves at igc.gulbenkian.pt (Renato Alves)
Date: Mon, 05 Jul 2010 21:00:17 +0100
Subject: [Biopython] Finding what is the most recent Pubmed ID or list of
	all valid PMIDs
Message-ID: <4C3239D1.7040708@igc.gulbenkian.pt>

Greetings All,

I'm trying to figure out a way to have a more or less up-to-date list of
Pubmed IDs for validation purposes. This has to be performed on a
programmatic way.

My first attempt was to look for this in NCBI's FTP. I could find
ftp://ftp.ncbi.nih.gov/pubmed/deleted_pmids.txt but not information
about the most recent PMID.

I also tried to use EInfo but the count section under PubMed seems
either outdated or completely unrelated to the total number of assigned
PMIDs. Even when adding the total of deleted_pmids + the number from
EInfo I couldn't get accurate information.

So my question is, does anyone know how to get either a list of all the
valid PMIDs or simply the most recent PMID?

Thanks,
Renato

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From biopython at maubp.freeserve.co.uk  Mon Jul  5 20:54:37 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 5 Jul 2010 21:54:37 +0100
Subject: [Biopython] Finding what is the most recent Pubmed ID or list
	of all valid PMIDs
In-Reply-To: <4C3239D1.7040708@igc.gulbenkian.pt>
References: <4C3239D1.7040708@igc.gulbenkian.pt>
Message-ID: <AANLkTil82BTTFYGnw42ZSMy0MsL_kUWdxM3wl6CmO6Xm@mail.gmail.com>

On Mon, Jul 5, 2010 at 9:00 PM, Renato Alves <rjalves at igc.gulbenkian.pt> wrote:
> Greetings All,
>
> I'm trying to figure out a way to have a more or less up-to-date list of
> Pubmed IDs for validation purposes. This has to be performed on a
> programmatic way.
>
> My first attempt was to look for this in NCBI's FTP. I could find
> ftp://ftp.ncbi.nih.gov/pubmed/deleted_pmids.txt but not information
> about the most recent PMID.
>
> I also tried to use EInfo but the count section under PubMed seems
> either outdated or completely unrelated to the total number of assigned
> PMIDs. Even when adding the total of deleted_pmids + the number from
> EInfo I couldn't get accurate information.
>
> So my question is, does anyone know how to get either a list of all the
> valid PMIDs or simply the most recent PMID?

To try and work out the latest PMID, I'd start by trying a PubMed search
by date, using a recent threshold.

What number of PMIDs are you trying to validate? Would it make
sense to use Entrez to do the validation (in batches)?

Peter


From rjalves at igc.gulbenkian.pt  Mon Jul  5 22:13:34 2010
From: rjalves at igc.gulbenkian.pt (Renato Alves)
Date: Mon, 05 Jul 2010 23:13:34 +0100
Subject: [Biopython] Finding what is the most recent Pubmed ID or list
 of all valid PMIDs
In-Reply-To: <AANLkTil82BTTFYGnw42ZSMy0MsL_kUWdxM3wl6CmO6Xm@mail.gmail.com>
References: <4C3239D1.7040708@igc.gulbenkian.pt>
	<AANLkTil82BTTFYGnw42ZSMy0MsL_kUWdxM3wl6CmO6Xm@mail.gmail.com>
Message-ID: <4C32590E.6020609@igc.gulbenkian.pt>

From Peter on 07/05/2010 09:54 PM:
> On Mon, Jul 5, 2010 at 9:00 PM, Renato Alves <rjalves at igc.gulbenkian.pt> wrote:
>> Greetings All,
>>
>> I'm trying to figure out a way to have a more or less up-to-date list of
>> Pubmed IDs for validation purposes. This has to be performed on a
>> programmatic way.
>>
>> My first attempt was to look for this in NCBI's FTP. I could find
>> ftp://ftp.ncbi.nih.gov/pubmed/deleted_pmids.txt but not information
>> about the most recent PMID.
>>
>> I also tried to use EInfo but the count section under PubMed seems
>> either outdated or completely unrelated to the total number of assigned
>> PMIDs. Even when adding the total of deleted_pmids + the number from
>> EInfo I couldn't get accurate information.
>>
>> So my question is, does anyone know how to get either a list of all the
>> valid PMIDs or simply the most recent PMID?
> 
> To try and work out the latest PMID, I'd start by trying a PubMed search
> by date, using a recent threshold.
> 
> What number of PMIDs are you trying to validate? Would it make
> sense to use Entrez to do the validation (in batches)?
> 
> Peter
I've thought of using Entrez but I was trying to avoid it by using
information available locally. I've no idea how many and what PMIDs will
be requested.

But indeed searching by date I can get a rough idea of what might be the
most recent PMID.

Thanks Peter

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From biopython at maubp.freeserve.co.uk  Tue Jul  6 08:23:28 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 09:23:28 +0100
Subject: [Biopython] Is Bio.Crystal still useful (for NDB files)?
In-Reply-To: <20100706084942.10823rdn5pazwcg6@horde.genesilico.pl>
References: <AANLkTinMfklMpOJ2o7KGH_8mqlgJOP3oQbYI4XyHvdir@mail.gmail.com>
	<20100706084942.10823rdn5pazwcg6@horde.genesilico.pl>
Message-ID: <AANLkTikQrCeXAH0IkYxoNvlsLF1sLFQbKDfjHH8vheh0@mail.gmail.com>

On Tue, Jul 6, 2010 at 7:49 AM, Kristian Rother <krother at genesilico.pl> wrote:
>
>
> Hi Peter,
>
> none of us here is using Bio.Crystal - and we use NDB structures a lot.
>
> Best,
> ? Kristian

Hi Kristian,

What kind of files are you using from the NDB? Standard PDB or mmCIF maybe?

Peter



From biopython at maubp.freeserve.co.uk  Tue Jul  6 08:43:18 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 09:43:18 +0100
Subject: [Biopython] Is Bio.Crystal still useful (for NDB files)?
In-Reply-To: <20100706102515.18063fisv68bqesr@horde.genesilico.pl>
References: <AANLkTinMfklMpOJ2o7KGH_8mqlgJOP3oQbYI4XyHvdir@mail.gmail.com>
	<20100706084942.10823rdn5pazwcg6@horde.genesilico.pl>
	<AANLkTikQrCeXAH0IkYxoNvlsLF1sLFQbKDfjHH8vheh0@mail.gmail.com>
	<20100706102515.18063fisv68bqesr@horde.genesilico.pl>
Message-ID: <AANLkTilSG4QA-pxSX2xo6iC2gjdGUoGZbKhTYqkBieE3@mail.gmail.com>

> Quoting Peter <biopython at maubp.freeserve.co.uk>:
>> Hi Kristian,
>>
>> What kind of files are you using from the NDB? Standard PDB or mmCIF
>> maybe?
>>
>> Peter

On Tue, Jul 6, 2010 at 9:25 AM, Kristian Rother wrote:
> Hi Peter,
>
> Standard PDB.
> We're gradually shifting to the PDB database for queries though, because the
> XML-based API for querying subsets of structures is much better there.
>
> Kristian

Thanks - maybe we can depreacte Bio.Crystal then...

Peter


From biopython at maubp.freeserve.co.uk  Tue Jul  6 10:36:39 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 11:36:39 +0100
Subject: [Biopython] Deprecating Bio.Crystal in next release?
Message-ID: <AANLkTilkAMk07WN4NQSy2yH0CL_Dd9r7XbG7VGBW8MoM@mail.gmail.com>

Hi all,

Given recent discussion (and the lack of interest on the dev list on previous
occasions), is there any objection to deprecating Bio.Crystal in the
next release
of Biopython?

http://lists.open-bio.org/pipermail/biopython/2010-July/006633.html
http://lists.open-bio.org/pipermail/biopython-dev/2008-October/004405.html
http://lists.open-bio.org/pipermail/biopython-dev/2007-July/002901.html

Thanks,

Peter


From biopython at maubp.freeserve.co.uk  Tue Jul  6 10:46:12 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 11:46:12 +0100
Subject: [Biopython] Is Bio.Crystal still useful (for NDB files)?
In-Reply-To: <20100706123045.12993suli0ec27dh@horde.genesilico.pl>
References: <AANLkTinMfklMpOJ2o7KGH_8mqlgJOP3oQbYI4XyHvdir@mail.gmail.com>
	<20100706084942.10823rdn5pazwcg6@horde.genesilico.pl>
	<AANLkTikQrCeXAH0IkYxoNvlsLF1sLFQbKDfjHH8vheh0@mail.gmail.com>
	<20100706123045.12993suli0ec27dh@horde.genesilico.pl>
Message-ID: <AANLkTik2tC64zDcLoprfRr1Dw44RS6k0KxtyuB8n9SKu@mail.gmail.com>

On Tue, Jul 6, 2010 at 11:30 AM, Kristian Rother <krother at genesilico.pl> wrote:
>
>> What kind of files are you using from the NDB? Standard PDB or mmCIF
>> maybe?
>
> Ah... sorry.. just PDB.
>
> Kristian

That's useful to know - thanks.

Peter

P.S. Please try to CC the mailing list ;)


From biopython at maubp.freeserve.co.uk  Tue Jul  6 13:40:51 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 14:40:51 +0100
Subject: [Biopython] Deprecating Bio.InterPro
Message-ID: <AANLkTiloI5mXX-jv22_PN5pe7NhSkx-tta2RfaYJhacG@mail.gmail.com>

Hi all,

Another old module which hasn't been updated for some time is Bio.InterPro,
a parser for the HTML (webpages) at the EBI, e.g.

http://www.ebi.ac.uk/interpro/IEntry?ac=IPR001064

The parser doesn't work with the current website, and also uses a Python
library called sgmllib which was deprecated as of Python 2.6. Website
parsers are in general a bad idea because the tend to need a lot of work
to keep up to date. Perhaps in this case there are suitable plain text files
on the FTP site which might be used?

Unless anyone has a good reason not to, we are going to deprecate the
Bio.IntrerPro module in the next release of Biopython.

Peter


From biopython at maubp.freeserve.co.uk  Tue Jul  6 15:20:38 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 6 Jul 2010 16:20:38 +0100
Subject: [Biopython] Deprecating Bio.Index?
Message-ID: <AANLkTim5HG78UMCWqGX_d-Ht6eEquEo_woaVD3ZRiCbb@mail.gmail.com>

Hello all,

Is anyone using the Bio.Index module in Biopython in their own code?

This supported file indexing and was used in other parts of Biopython which
have all now been deprecated (e.g. Bio.SwissProt.SProt and Bio.Prosite) or
removed. The more recent Bio.SeqIO module provides a general approach
to indexing sequence files.

Would it inconvenience anyone if Bio.Index was deprecated in the next
release (triggering warnings when imported, but still functional), and then
removed later on?

Thanks,

Peter


From guyeakin at gmail.com  Thu Jul  8 00:52:49 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 7 Jul 2010 20:52:49 -0400
Subject: [Biopython] Bio.Entrez/Medline DTD problems - missing DTD
	nlmmedlinecitationset_100301.dtd
Message-ID: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com>

 I am learning biopython and seem to be having trouble parsing efetch
generated xml.

Maybe I am confused here, but I can't for the life of me Get my xml to parse
correctly, and it seems to be coming up with a missing dtd error using both
Medline.parse and Entrez.parse. (traceback for medline below below)

 nlmmedlinecitationset_100301.
dtd and pubmed_100301.dtd seem to be missing from my biopython
installation, and unavailable from the following NCBI sites:

http://www.ncbi.nlm.nih.gov/dtd/ or
http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/

My apologies if this is user error; i do not see reference to this DTD issue
in the archives so am posting the incident. Is this just bad luck during my
learning curve, or am I missing something conceptual here?

 Thanks,

Guy



Traceback (most recent call last):

 File
"C:\Python26\Lib\site-packages\pythonwin\pywin\framework\scriptutils.py",
line 312, in RunScript

   exec codeObject in __main__.__dict__

 File "C:\ieye\ieye\citations\pubmed_search_fxn.py", line 36, in <module>

   parsed_results = Entrez.read(fetch_handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\__init__.py", line 262, in
read

   record = handler.read(handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 108, in
read

   self.parser.ParseFile(handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 381, in
externalEntityRefHandler

   parser.ParseFile(handle)

 File "C:\Python26\lib\site-packages\Bio\Entrez\Parser.py", line 377, in
externalEntityRefHandler

   raise RuntimeError(message)

RuntimeError: Unable to load DTD file nlmmedlinecitationset_100301.dtd.


From biopython at maubp.freeserve.co.uk  Thu Jul  8 07:42:32 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 8 Jul 2010 08:42:32 +0100
Subject: [Biopython] Bio.Entrez/Medline DTD problems - missing DTD
	nlmmedlinecitationset_100301.dtd
In-Reply-To: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com>
References: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com>
Message-ID: <AANLkTikdmzaHip2tdRKu_CiY__lyADvRjGoGv6rtySz-@mail.gmail.com>

On Thu, Jul 8, 2010 at 1:52 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> ?I am learning biopython and seem to be having trouble parsing efetch
> generated xml.
>
> Maybe I am confused here, but I can't for the life of me Get my xml to parse
> correctly, and it seems to be coming up with a missing dtd error using both
> Medline.parse and Entrez.parse. (traceback for medline below below)
>
> ?nlmmedlinecitationset_100301.
> dtd and pubmed_100301.dtd seem to be missing from my biopython
> installation, and unavailable from the following NCBI sites:
>
> http://www.ncbi.nlm.nih.gov/dtd/ or
> http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/
>
> My apologies if this is user error; i do not see reference to this DTD issue
> in the archives so am posting the incident. Is this just bad luck during my
> learning curve, or am I missing something conceptual here?

The problem is with the NCBI "hiding" the file by not showing the raw
contents of that folder, but just an HTML page with a partial list. You
need this file:

http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/nlmmedlinecitationset_100301.dtd

I've added this to our repository so the next version of Biopython will
include it. Please let us know if anything else is missing - what was
the Entrez request you used to get the XML using this DTD file?

Regards,

Peter



From guyeakin at gmail.com  Thu Jul  8 11:28:17 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Thu, 8 Jul 2010 07:28:17 -0400
Subject: [Biopython] Bio.Entrez/Medline DTD problems - missing DTD
	nlmmedlinecitationset_100301.dtd
In-Reply-To: <AANLkTikdmzaHip2tdRKu_CiY__lyADvRjGoGv6rtySz-@mail.gmail.com>
References: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com> 
	<AANLkTikdmzaHip2tdRKu_CiY__lyADvRjGoGv6rtySz-@mail.gmail.com>
Message-ID: <AANLkTim82RfW0K8Q9W3LOEc1U9l6z2hLbqN44VUw9j93@mail.gmail.com>

Peter,

Many thanks.

this is a query statement that generated the
nlmmedlinecitationset_100301.dtd error: Entrez.esearch(db="pubmed",
                        term= ('glaucom*'),
                        retmax=2, usehistory="y",
                        reldate=7, datetype="edat")


fetch_handle = Entrez.efetch(db="pubmed", retmode="xml",rettype='medline',
                             webenv=webenv, query_key=query_key)


You will also want to add pubmed_100301.dtd to your repository.  I do not
have the query that generated it's dependent XML, but got an separate error
related to its absence yesterday.  Oddly, I was able to download the
"hidden" pubmed_100301.dtd, but could not replicate the error.   All
following errors focused on the nlmmedlinecitationset_100301.dtd file which
I could not locate until this morning. Perhaps it was just recently posted
to the site. Either way, thanks for the confirmation that I was on the right
track.

regards,
guy

On Thu, Jul 8, 2010 at 3:42 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Thu, Jul 8, 2010 at 1:52 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> >  I am learning biopython and seem to be having trouble parsing efetch
> > generated xml.
> >
> > Maybe I am confused here, but I can't for the life of me Get my xml to
> parse
> > correctly, and it seems to be coming up with a missing dtd error using
> both
> > Medline.parse and Entrez.parse. (traceback for medline below below)
> >
> >  nlmmedlinecitationset_100301.
> > dtd and pubmed_100301.dtd seem to be missing from my biopython
> > installation, and unavailable from the following NCBI sites:
> >
> > http://www.ncbi.nlm.nih.gov/dtd/ or
> > http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/
> >
> > My apologies if this is user error; i do not see reference to this DTD
> issue
> > in the archives so am posting the incident. Is this just bad luck during
> my
> > learning curve, or am I missing something conceptual here?
>
> The problem is with the NCBI "hiding" the file by not showing the raw
> contents of that folder, but just an HTML page with a partial list. You
> need this file:
>
>
> http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/nlmmedlinecitationset_100301.dtd
>
> I've added this to our repository so the next version of Biopython will
> include it. Please let us know if anything else is missing - what was
> the Entrez request you used to get the XML using this DTD file?
>
> Regards,
>
> Peter
>


From biopython at maubp.freeserve.co.uk  Thu Jul  8 11:53:30 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 8 Jul 2010 12:53:30 +0100
Subject: [Biopython] Bio.Entrez/Medline DTD problems - missing DTD
	nlmmedlinecitationset_100301.dtd
In-Reply-To: <AANLkTim82RfW0K8Q9W3LOEc1U9l6z2hLbqN44VUw9j93@mail.gmail.com>
References: <AANLkTimMit800wrR5nI7199MXTc1_Yzc1twvPR2kLJjy@mail.gmail.com>
	<AANLkTikdmzaHip2tdRKu_CiY__lyADvRjGoGv6rtySz-@mail.gmail.com>
	<AANLkTim82RfW0K8Q9W3LOEc1U9l6z2hLbqN44VUw9j93@mail.gmail.com>
Message-ID: <AANLkTinKqg5q7WGf0CS-mTR53Jz5u-i3saslHjIaMU2g@mail.gmail.com>

On Thu, Jul 8, 2010 at 12:28 PM, Guy Eakin <guyeakin at gmail.com> wrote:
> Peter,
>
> Many thanks.
>
> this is a query statement that generated the
> nlmmedlinecitationset_100301.dtd error: Entrez.esearch(db="pubmed",
> ? ? ? ? ? ? ? ? ? ? ? ?term= ('glaucom*'),
> ? ? ? ? ? ? ? ? ? ? ? ?retmax=2, usehistory="y",
> ? ? ? ? ? ? ? ? ? ? ? ?reldate=7, datetype="edat")
>
>
> fetch_handle = Entrez.efetch(db="pubmed", retmode="xml",rettype='medline',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? webenv=webenv, query_key=query_key)
>

Great. A more complete version is:

from Bio import Entrez
Entrez.email = "A.N.Other at example.com"

s = Entrez.read(Entrez.esearch(db="pubmed",term=
('glaucom*'),retmax=2, usehistory="y",reldate=7, datetype="edat"))

r = Entrez.read(Entrez.efetch(db="pubmed",
retmode="xml",rettype='medline', webenv=s["WebEnv"],
query_key=s["QueryKey"]))


>
> You will also want to add pubmed_100301.dtd to your repository. ...
>

Yes, we needed the new pubmed_100301.dtd and also bookdoc_100301.dtd

It looks like the NCBI did some updates recently - hopefully they'll update that
webpage soon and we can see if we need to add anymore (other than finding
out from error messages).

Thanks for the report, and please let us know if you find any more missing DTD
files.

Peter



From guyeakin at gmail.com  Wed Jul 14 20:48:41 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 14 Jul 2010 16:48:41 -0400
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
Message-ID: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>

I am using Bio.Entrez.read to parse XML returned from pubmed.

This results in a dictionary for which one of the keys is ArticleIDList,
e.g,
Example
PubmedData': {u'ArticleIdList': ['S0735-6757(09)00464-1',
'10.1016/j.ajem.2009.09.013', '20579576'], blah: blah, etc.}

In the original XML Each <ArticleID> in <ArticleIDList> contains an IDtype
attribute that names the ID. for example
<ArtcleID IDType="doi">10.1016/j.ajem.2009.09.013</ArticleID>

the IDtype is useful, but I can't find it in the Bio.Entrez.read output, so
I have no *easy* way of determining whether the ID# is
pii, pmc, pmid, etc.

Is there a better way to get the IDtype attribute, or other XML tag
attributes from the Entrez.read output?

Thanks.
Guy

Code below

---------------
from Bio import Medline
from Bio import Entrez
import routine_pubmed_query_terms as pubmedterms #this is a separate .py
file that I use to hold query terms, email address, etc.

  s = Entrez.read(Entrez.esearch(db="pubmed",
                                   term=pubmedterms.entrezquery(program),
                                   retmax=pubmedterms.maxlimit,
                                   usehistory="y",
                                   reldate=pubmedterms.datelimit,
                                   datetype="edat"))
    print "found %s records, returning %s" % (int(s["Count"]),
                                                  len(s["IdList"]))

    r = Entrez.read(Entrez.efetch(db="pubmed",retmode="xml",
                                  rettype='medline', webenv=s["WebEnv"],
                                  query_key=s["QueryKey"]))


From biopython at maubp.freeserve.co.uk  Wed Jul 14 21:18:34 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 14 Jul 2010 22:18:34 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>
Message-ID: <AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com>

On Wed, Jul 14, 2010 at 9:48 PM, Guy Eakin <guyeakin at gmail.com> wrote:
> I am using Bio.Entrez.read to parse XML returned from pubmed.
>
> This results in a dictionary for which one of the keys is ArticleIDList,
> e.g,
> Example
> PubmedData': {u'ArticleIdList': ['S0735-6757(09)00464-1',
> '10.1016/j.ajem.2009.09.013', '20579576'], blah: blah, etc.}
>
> In the original XML Each <ArticleID> in <ArticleIDList> contains an IDtype
> attribute that names the ID. for example
> <ArtcleID IDType="doi">10.1016/j.ajem.2009.09.013</ArticleID>
>
> the IDtype is useful, but I can't find it in the Bio.Entrez.read output, so
> I have no *easy* way of determining whether the ID# is
> pii, pmc, pmid, etc.
>
> Is there a better way to get the IDtype attribute, or other XML tag
> attributes from the Entrez.read output?
>

Hi,

This information is in the tutorial, but could perhaps be clearer.
It might look like you get strings back, but in fact it is a subclass
with an attributes property (a dictionary). e.g.

from Bio import Entrez
handle = Entrez.efetch(db="pubmed",retmode="xml",rettype='medline',id='19304878')
r = Entrez.read(handle)
handle.close()
print r[0]['PubmedData']['ArticleIdList'][1]
print r[0]['PubmedData']['ArticleIdList'][1].attributes

Michiel - maybe we need to override the __repr__ method so it shows
this information?

Peter


From biopython at maubp.freeserve.co.uk  Wed Jul 14 21:33:06 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 14 Jul 2010 22:33:06 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>
	<AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com>
	<AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com>
Message-ID: <AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com>

On Wed, Jul 14, 2010 at 10:21 PM, Guy Eakin <guyeakin at gmail.com> wrote:
> thanks.? I understood that it had a? .tag feature,but missed the
> .attributes!
> Awesome. And thank you for the quick reply.
>
> Guy

No problem. Now you know the answer, can you suggest
any clarifications to the documentation?

Peter

P.S. Try and CC the mailing list in replies.



From guyeakin at gmail.com  Thu Jul 15 02:52:44 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 14 Jul 2010 22:52:44 -0400
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com> 
	<AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com> 
	<AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com> 
	<AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com>
Message-ID: <AANLkTinquPR9P36p952-PavSh7_9wLdWkDZ_08w2n9P7@mail.gmail.com>

Sure, I am new, so there are probably errors, but how about something like a
demonstration appended to the end of the tutorial section at
http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc105

At core, the simple demonstration that type(record) calls a class object
rather than a list, and that foo.attributes, and foo.tag exist would be
helpful.  I am not using any of the sequence utilities, so admit that my
reading of those sections was brief.  Reiteration in the entrez parsing
sections is probably helpful for people like me.

A more verbose demonstration follows.

Again, thanks for the help.
Guy

8.11.1  Parsing Medline records [intervening text omitted]

At this point let?s address what these elements contain.  Consider
information found in the following statement.

>>> records[0]['PubmedData']

{u'ArticleIdList': ['btp163', '10.1093/bioinformatics/btp163', '19304878',
'PMC2682512'], u'PublicationStatus': 'ppublish', u'History': [{u'Month':
'3', u'Day': '20', u'Year': '2009'}, {u'Minute': '0', u'Month': '3', u'Day':
'24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month': '3',
u'Day': '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month':
'7', u'Day': '10', u'Hour': '9', u'Year': '2009'}]}

It is important to recall that each item is a biopython class, rather than a
simply a dictionary or list item.  This can be verified by

>>>type(records[0]['PubmedData']['ArticleIdList']

Which returns <class 'Bio.Entrez.Parser.ListElement'> rather than <type
'list'>

This is important,  as the class item contains additional auxiliary
information as noted earlier.  One such piece of important auxillary info is
the XML tag attributes from the parsed XML.

In this case, the  original XML contained the following tags:

<ArticleIdList>

            <ArticleId IdType="pii">btp163</ArticleId>

            <ArticleId IdType="doi">10.1093/bioinformatics/btp163</ArticleId>

            <ArticleId IdType="pubmed">19304878</ArticleId>

            <ArticleId IdType="pmc">PMC2682512</ArticleId>

</ArticleIdList>



which have now been parsed into the u'ArticleIdList' dictionary key:

>>> L =records[0]['PubmedData']['ArticleIdList']

['btp163', '10.1093/bioinformatics/btp163', '19304878', 'PMC2682512']

Viewed as a simple list, these elements appear to lack the IdType
information.  However,  the IdType attribute from the <ArticleId> tag is
stored in the parsed data, and can be retrieved by calling ?attributes? on
the biopython class object.

>>> for item in L:

...            print "%s - %s" % (item, item.attributes)

...

btp163 - {u'IdType': u'pii'}

10.1093/bioinformatics/btp163 - {u'IdType': u'doi'}

19304878 - {u'IdType': u'pubmed'}

PMC2682512 - {u'IdType': u'pmc'}


On Wed, Jul 14, 2010 at 5:33 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Wed, Jul 14, 2010 at 10:21 PM, Guy Eakin <guyeakin at gmail.com> wrote:
> > thanks.  I understood that it had a  .tag feature,but missed the
> > .attributes!
> > Awesome. And thank you for the quick reply.
> >
> > Guy
>
> No problem. Now you know the answer, can you suggest
> any clarifications to the documentation?
>
> Peter
>
> P.S. Try and CC the mailing list in replies.
>



From biopython at maubp.freeserve.co.uk  Thu Jul 15 09:44:06 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 15 Jul 2010 10:44:06 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTinquPR9P36p952-PavSh7_9wLdWkDZ_08w2n9P7@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com>
	<AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com>
	<AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com>
	<AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com>
	<AANLkTinquPR9P36p952-PavSh7_9wLdWkDZ_08w2n9P7@mail.gmail.com>
Message-ID: <AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>

On Thu, Jul 15, 2010 at 3:52 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> Sure, I am new, so there are probably errors, but how about something like a
> demonstration appended to the end of the tutorial section at
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc105
>
> At core, the simple demonstration that type(record) calls a class object
> rather than a list, and that foo.attributes, and foo.tag exist would be
> helpful. ?I am not using any of the sequence utilities, so admit that my
> reading of those sections was brief. ?Reiteration in the entrez parsing
> sections is probably helpful for people like me.
>
> A more verbose demonstration follows.
>
> Again, thanks for the help.
> Guy

Thank you for the detailed suggested text.

> 8.11.1 ?Parsing Medline records [intervening text omitted]
>
> At this point let?s address what these elements contain. ?Consider
> information found in the following statement.
>
>>>> records[0]['PubmedData']
>
> {u'ArticleIdList': ['btp163', '10.1093/bioinformatics/btp163', '19304878',
> 'PMC2682512'], u'PublicationStatus': 'ppublish', u'History': [{u'Month':
> '3', u'Day': '20', u'Year': '2009'}, {u'Minute': '0', u'Month': '3', u'Day':
> '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month': '3',
> u'Day': '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month':
> '7', u'Day': '10', u'Hour': '9', u'Year': '2009'}]}
>
> It is important to recall that each item is a biopython class, rather than a
> simply a dictionary or list item. ?This can be verified by
>
>>>>type(records[0]['PubmedData']['ArticleIdList']
>
> Which returns <class 'Bio.Entrez.Parser.ListElement'> rather than <type
> 'list'>

This is why I was suggesting to Michiel that we override the __repr__
for our subclassed objects, so that rather than seeing things like this:

['btp163', '10.1093/bioinformatics/btp163', '19304878', 'PMC2682512']

we get something like:

ListElement(['btp163', '10.1093/bioinformatics/btp163', '19304878',
'PMC2682512'], attributes={...})

On deeper reflection, the trouble with this is that all the children within
the list would get longer, so the full representation of a ListElement (or
any container) would become very very long - swamping the console
output. Even if we literally show the attributes with a dot dot dot :(

Maybe we'll have to settle for just documentation improvements.
Michiel - this is your code - what do you think?

Peter



From guyeakin at gmail.com  Thu Jul 15 13:32:43 2010
From: guyeakin at gmail.com (Guy Eakin)
Date: Thu, 15 Jul 2010 09:32:43 -0400
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>
References: <AANLkTiknXlNTcZ8yOehGoxkt7NP0IX_5rQIxY0Zc2gsK@mail.gmail.com> 
	<AANLkTimhkDux142fltn2KjAD3QEBOKN9f3PrLyXR2Bo4@mail.gmail.com> 
	<AANLkTimvXxL24sd2nikI6-uOZfaSmOe__fGdLNBdmmWk@mail.gmail.com> 
	<AANLkTim-1I6SrVADmZTvnsPp6lAHvAW9oKNXS6KX3dzs@mail.gmail.com> 
	<AANLkTinquPR9P36p952-PavSh7_9wLdWkDZ_08w2n9P7@mail.gmail.com> 
	<AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>
Message-ID: <AANLkTilabI_j5OEg5XCgf438y0kntjCBpH34mfnnh5WN@mail.gmail.com>

>From the naive first-time user perspective, the current implementation is
fine for the computer, but could benefit from a viewer output that creates a
more human readable representation.  I found myself cross referencing the
console output to the original XML in most cases.

That says to me that there might be benefit to a function that recapitulates
the original XML's nested structure, listing attribute values.  I would
think something along the following would be quite useful, and if limited to
particular range of records would not necessarily be unwieldy.

(apologies for the admittedly unwieldy markup)

>>> Bio.Entrez.viewer(recordlist, range=(0:(len(recordlist)),
ShowMedlineCitation = True, ShowPubmedData = True)

<Parent1> - (Attributes = Parent1.atribute) -  \n                       #(80
characters/line)
..............value
..............indented text allows word wrap of entries > 80 char.
........<Children>1 - Attribute - \n
.......................value


that's an off the cuff representation before I dash to a meeting, but I
think you can see what I am suggesting.

Guy


Guy
On Thu, Jul 15, 2010 at 5:44 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Thu, Jul 15, 2010 at 3:52 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> > Sure, I am new, so there are probably errors, but how about something
> like a
> > demonstration appended to the end of the tutorial section at
> > http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc105
> >
> > At core, the simple demonstration that type(record) calls a class object
> > rather than a list, and that foo.attributes, and foo.tag exist would be
> > helpful.  I am not using any of the sequence utilities, so admit that my
> > reading of those sections was brief.  Reiteration in the entrez parsing
> > sections is probably helpful for people like me.
> >
> > A more verbose demonstration follows.
> >
> > Again, thanks for the help.
> > Guy
>
> Thank you for the detailed suggested text.
>
> > 8.11.1  Parsing Medline records [intervening text omitted]
> >
> > At this point let?s address what these elements contain.  Consider
> > information found in the following statement.
> >
> >>>> records[0]['PubmedData']
> >
> > {u'ArticleIdList': ['btp163', '10.1093/bioinformatics/btp163',
> '19304878',
> > 'PMC2682512'], u'PublicationStatus': 'ppublish', u'History': [{u'Month':
> > '3', u'Day': '20', u'Year': '2009'}, {u'Minute': '0', u'Month': '3',
> u'Day':
> > '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month': '3',
> > u'Day': '24', u'Hour': '9', u'Year': '2009'}, {u'Minute': '0', u'Month':
> > '7', u'Day': '10', u'Hour': '9', u'Year': '2009'}]}
> >
> > It is important to recall that each item is a biopython class, rather
> than a
> > simply a dictionary or list item.  This can be verified by
> >
> >>>>type(records[0]['PubmedData']['ArticleIdList']
> >
> > Which returns <class 'Bio.Entrez.Parser.ListElement'> rather than <type
> > 'list'>
>
> This is why I was suggesting to Michiel that we override the __repr__
> for our subclassed objects, so that rather than seeing things like this:
>
> ['btp163', '10.1093/bioinformatics/btp163', '19304878', 'PMC2682512']
>
> we get something like:
>
> ListElement(['btp163', '10.1093/bioinformatics/btp163', '19304878',
> 'PMC2682512'], attributes={...})
>
> On deeper reflection, the trouble with this is that all the children within
> the list would get longer, so the full representation of a ListElement (or
> any container) would become very very long - swamping the console
> output. Even if we literally show the attributes with a dot dot dot :(
>
> Maybe we'll have to settle for just documentation improvements.
> Michiel - this is your code - what do you think?
>
> Peter
>



From mjldehoon at yahoo.com  Thu Jul 15 13:36:19 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Thu, 15 Jul 2010 06:36:19 -0700 (PDT)
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>
Message-ID: <436965.79909.qm@web62402.mail.re1.yahoo.com>



--- On Thu, 7/15/10, Peter <biopython at maubp.freeserve.co.uk> wrote:
> This is why I was suggesting to Michiel that we override
> than seeing the __repr__ for our subclassed objects, so
> that rather things like this:
> 
> ['btp163', '10.1093/bioinformatics/btp163', '19304878',
> 'PMC2682512']
> 
> we get something like:
> 
> ListElement(['btp163', '10.1093/bioinformatics/btp163',
> '19304878', 'PMC2682512'], attributes={...})
> 
> On deeper reflection, the trouble with this is that all the
> children within the list would get longer, so the full
> representation of a ListElement (or
> any container) would become very very long - swamping the
> console output.

The attributes are almost always only a small fraction of the Entrez XML file. So while it's true that each element gets larger, it's a small relative increase. The elements that are very long after adding the attributes are also very long without the attributes. So I am in favor of your original suggestion. If there are no other suggestions, I'll make the change in Bio.Entrez over the weekend (or feel free to do so before that).

Best,
--Michiel


      


From biopython at maubp.freeserve.co.uk  Thu Jul 15 13:50:41 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 15 Jul 2010 14:50:41 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <436965.79909.qm@web62402.mail.re1.yahoo.com>
References: <AANLkTilPLwCI8ZlmqBGMETd9wHrpYRN6v4eiwNKm-7Jk@mail.gmail.com>
	<436965.79909.qm@web62402.mail.re1.yahoo.com>
Message-ID: <AANLkTilYvSgosb1zMHQFXzXy5AMAmn9125vVdst6BI__@mail.gmail.com>

On Thu, Jul 15, 2010 at 2:36 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>
> --- On Thu, 7/15/10, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> This is why I was suggesting to Michiel that we override
>> than seeing the __repr__ for our subclassed objects, so
>> that rather things like this:
>>
>> ['btp163', '10.1093/bioinformatics/btp163', '19304878',
>> 'PMC2682512']
>>
>> we get something like:
>>
>> ListElement(['btp163', '10.1093/bioinformatics/btp163',
>> '19304878', 'PMC2682512'], attributes={...})
>>
>> On deeper reflection, the trouble with this is that all the
>> children within the list would get longer, so the full
>> representation of a ListElement (or  any container) would
>> become very very long - swamping the console output.
>
> The attributes are almost always only a small fraction of the Entrez XML file.
> So while it's true that each element gets larger, it's a small relative increase.
> The elements that are very long after adding the attributes are also very long
> without the attributes. So I am in favor of your original suggestion. If there are
> no other suggestions, I'll make the change in Bio.Entrez over the weekend
> (or feel free to do so before that).

Maybe you can keep the basic data type repr if there are no attributes,
and only expand it if needed? It would be inconsistent but would keep the
total string length down.

Peter


From bjorn_johansson at bio.uminho.pt  Sat Jul 17 11:32:12 2010
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Sat, 17 Jul 2010 12:32:12 +0100
Subject: [Biopython] format fasta files to genbank: problem with too long
	Locus identifier
Message-ID: <AANLkTinI0xNF1jDLFlyrW5WI1lh-bTDJ6X1j1F3O7jk7@mail.gmail.com>

Hi all, this is an example of parsing a fasta file and then trying to
convert it to genbank.
It seems that the fasta header file is not split between the "|", and all
that is in the fasta header ends up as "LOCUS" in the genbank file. Is this
the expected behavior? Can this be set somehow?

Thanks for any help on this!
/bjorn



>>> from Bio import SeqIO
>>> a=SeqIO.read("newfile.fasta", "fasta")
>>> a
SeqRecord(seq=Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...GGG',
SingleLetterAlphabet()), id='gi|2765658|emb|Z78533.1|CIZ78533',
name='gi|2765658|emb|Z78533.1|CIZ78533',
description='gi|2765658|emb|Z78533.1|CIZ78533 C.irapeanum 5.8S rRNA gene and
ITS1 and ITS2 DNA', dbxrefs=[])
>>> a.format('fasta')
'>gi|2765658|emb|Z78533.1|CIZ78533 C.irapeanum 5.8S rRNA gene and ITS1 and
ITS2
DNA\nCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGGAATAAA\nCGATCGAGTGAATCCGGAGGACCGGTGTACTCAGCTCACCGGGGGCATTGCTCCCGTGGT\nGACCCTGATTTGTTGTTGGG\n'
>>> a.format('genbank')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqRecord.py", line 638,
in format
    return self.__format__(format)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqRecord.py", line 652,
in __format__
    SeqIO.write([self], handle, format_spec)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/__init__.py", line
398, in write
    count = writer_class(handle).write_file(sequences)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/Interfaces.py",
line 271, in write_file
    count = self.write_records(records)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/Interfaces.py",
line 256, in write_records
    self.write_record(record)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/InsdcIO.py", line
628, in write_record
    self._write_the_first_line(record)
  File "/usr/local/lib/python2.6/dist-packages/Bio/SeqIO/InsdcIO.py", line
453, in _write_the_first_line
    raise ValueError("Locus identifier %s is too long" % repr(locus))
ValueError: Locus identifier 'gi|2765658|emb|Z78533.1|CIZ78533' is too long
>>>


From biopython at maubp.freeserve.co.uk  Sat Jul 17 11:50:50 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 17 Jul 2010 12:50:50 +0100
Subject: [Biopython] format fasta files to genbank: problem with too
	long Locus identifier
In-Reply-To: <AANLkTinI0xNF1jDLFlyrW5WI1lh-bTDJ6X1j1F3O7jk7@mail.gmail.com>
References: <AANLkTinI0xNF1jDLFlyrW5WI1lh-bTDJ6X1j1F3O7jk7@mail.gmail.com>
Message-ID: <AANLkTikx0ziKAL2Sd2ABYbySSHdXxUsRaqfvaXwuqQ6g@mail.gmail.com>

2010/7/17 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> Hi all, this is an example of parsing a fasta file and then trying to
> convert it to genbank.
> It seems that the fasta header file is not split between the "|", and all
> that is in the fasta header ends up as "LOCUS" in the genbank file. Is this
> the expected behavior? Can this be set somehow?
>
> Thanks for any help on this!
> /bjorn

Hi Bjorn,

Yes this is expected behaviour. There are no standards for FASTA
identifiers, the NCBI conventions are just one of dozens of styles.
Therefore we don't try and parse the identifiers in FASTA files (we
can't do it reliably). Then for GenBank files, the identifier field in
the LOCUS line is very limited - you'll have to shorten your ID
manually, Try something like this:

from Bio import SeqIO
a=SeqIO.read("newfile.fasta", "fasta")
a.id = a.id.split("|")[3]
print a.format('genbank')

(untested)

Peter



From biopython at maubp.freeserve.co.uk  Sat Jul 17 19:59:46 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 17 Jul 2010 20:59:46 +0100
Subject: [Biopython] format fasta files to genbank: problem with too
	long Locus identifier
In-Reply-To: <AANLkTilIcFjK-8pW_6RmcqpiuCyUWHC36X_jiGAp0XEY@mail.gmail.com>
References: <AANLkTinI0xNF1jDLFlyrW5WI1lh-bTDJ6X1j1F3O7jk7@mail.gmail.com>
	<AANLkTikx0ziKAL2Sd2ABYbySSHdXxUsRaqfvaXwuqQ6g@mail.gmail.com>
	<AANLkTilIcFjK-8pW_6RmcqpiuCyUWHC36X_jiGAp0XEY@mail.gmail.com>
Message-ID: <AANLkTimN1h85UeV_0D3Xb6F-Tc52r24beGhD2Lju5f2G@mail.gmail.com>

2010/7/17 Bj?rn Johansson <bjorn_johansson at bio.uminho.pt>:
> Thanks for the quick reply!
>
> it seems that it is the a.name field that needs to be shortened
> (and ends up in the LOCUS field). the a.id seems to be the
> entire fasta header and ends up as DEFINITION.
>
> /bjorn

Sounds right - I should have tested it after all ;)

Peter



From mjldehoon at yahoo.com  Sun Jul 18 08:43:45 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sun, 18 Jul 2010 01:43:45 -0700 (PDT)
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTilYvSgosb1zMHQFXzXy5AMAmn9125vVdst6BI__@mail.gmail.com>
Message-ID: <190917.68159.qm@web62405.mail.re1.yahoo.com>

> Maybe you can keep the basic data type repr if there are no
> attributes, and only expand it if needed? It would be inconsistent
> but would keep the total string length down.
> 
Done.

The code can be further simplified if we drop the .tag attribute on each XML element. If we drop .tag, then all elements that do not have attributes (which are most of them) can be presented as a simple list, dictionary, string, and so on instead of a ListElement, DictionaryElement, StringElement. Then the *Element classes are used only in those cases where there actually are attributes. Or is that too inconsistent?

--Michiel.


      


From biopython at maubp.freeserve.co.uk  Sun Jul 18 10:59:02 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sun, 18 Jul 2010 11:59:02 +0100
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <190917.68159.qm@web62405.mail.re1.yahoo.com>
References: <AANLkTilYvSgosb1zMHQFXzXy5AMAmn9125vVdst6BI__@mail.gmail.com>
	<190917.68159.qm@web62405.mail.re1.yahoo.com>
Message-ID: <AANLkTik-iQeekeXWmLTfkBESYUUIYPlx1Cw2G_WvhWeM@mail.gmail.com>

On Sun, Jul 18, 2010 at 9:43 AM, Michiel de Hoon wrote:
>> Maybe you can keep the basic data type repr if there are no
>> attributes, and only expand it if needed? It would be inconsistent
>> but would keep the total string length down.
>>
> Done.
>
> The code can be further simplified if we drop the .tag attribute on
> each XML element. If we drop .tag, then all elements that do not
> have attributes (which are most of them) can be presented as a
> simple list, dictionary, string, and so on instead of a ListElement,
> DictionaryElement, StringElement. Then the *Element classes are
> used only in those cases where there actually are attributes. Or is
> that too inconsistent?

I've not played with the code yet to see what you mean about the
tag attribute.

There is an inconsistency with DictionaryElement vs DictElement
(deliberate for space?) and StructureElement vs DictElement (typo?).

Peter


From mjldehoon at yahoo.com  Sun Jul 18 13:59:41 2010
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sun, 18 Jul 2010 06:59:41 -0700 (PDT)
Subject: [Biopython] Pubmeddata XML parsing with Entrez .fetch and .read
In-Reply-To: <AANLkTik-iQeekeXWmLTfkBESYUUIYPlx1Cw2G_WvhWeM@mail.gmail.com>
Message-ID: <650816.80191.qm@web62406.mail.re1.yahoo.com>



--- On Sun, 7/18/10, Peter <biopython at maubp.freeserve.co.uk> wrote:
> I've not played with the code yet to see what you mean
> about the tag attribute. 

Here's an example:

<eInfoResult>
<DbList>
        <DbName>pubmed</DbName>
        <DbName>protein</DbName>
        <DbName>nucleotide</DbName>
        <DbName>nuccore</DbName>
        <DbName>nucgss</DbName>
....



>>> record['DbList'][0]       
'pubmed'
>>> record['DbList'][0].tag
u'DbName'
>>> record['DbList'][0].attributes
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'StringElement' object has no attribute 'attributes'
>>> 

So currently record['DbList'] is a list of StringElements (actually, a ListElement of StringElements) where the XML tag name is stored in a .tag attribute. If we don't store the .tag attribute, then record['DbList'] would become a list of plain strings.

--Michiel.


      


From bala.biophysics at gmail.com  Mon Jul 19 09:39:11 2010
From: bala.biophysics at gmail.com (Bala subramanian)
Date: Mon, 19 Jul 2010 11:39:11 +0200
Subject: [Biopython] clustering pdb
Message-ID: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>

Friends,
I have around 3000 pdb files obtained from MD simulations. I would like to
know if it is possible to cluster the pdb files using any of the biopython's
bio.PDB or other modules. If so, i would appreciate if you could provide me
a sample code.

Is there any utility in Biopython to handle MD trajectories obtained from
common packages like gromacs, amber etc ?

Thank you,
Bala


From biopython at maubp.freeserve.co.uk  Mon Jul 19 09:49:26 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 19 Jul 2010 10:49:26 +0100
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
Message-ID: <AANLkTilzTT_1kOVsQpi76fDittiGf8rGkZBJ6Urflkzz@mail.gmail.com>

On Mon, Jul 19, 2010 at 10:39 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Friends,
> I have around 3000 pdb files obtained from MD simulations. I would like to
> know if it is possible to cluster the pdb files using any of the biopython's
> bio.PDB or other modules. If so, i would appreciate if you could provide me
> a sample code.

What kind of clustering do you want to do? By folds/structure? By sequence?

> Is there any utility in Biopython to handle MD trajectories obtained from
> common packages like gromacs, amber etc ?

No, we don't do any molecular dynamics - try The Molecular Modelling Toolkit
(MMTK) by Konran Hinsen for a Python MD toolkit:
http://dirac.cnrs-orleans.fr/MMTK/

Peter


From schaefer at rostlab.org  Mon Jul 19 09:56:45 2010
From: schaefer at rostlab.org (Christian Schaefer)
Date: Mon, 19 Jul 2010 11:56:45 +0200
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
Message-ID: <4C44215D.5050401@rostlab.org>

On 07/19/2010 11:39 AM, Bala subramanian wrote:
> Friends,
> I have around 3000 pdb files obtained from MD simulations. I would like to
> know if it is possible to cluster the pdb files using any of the biopython's
> bio.PDB or other modules. If so, i would appreciate if you could provide me
> a sample code.

It depends on what you mean by 'clustering'. If you refer to sequence 
clustering, i.e. redundancy reduction on sequence level, there are 
several tools out there (like CDHit) for that purpose. Not sure if 
there's a native implementation in BioPython for that.

Chris

-- 
Dipl.-Bioinf. Christian Schaefer
Technical University Munich
Department for Bioinformatics
Faculty of Computer Science/I12
Boltzmannstr. 3
D-85748 Garching b. Muenchen
Germany
http://www.rostlab.org/~schaefer


From biopython at maubp.freeserve.co.uk  Mon Jul 19 10:07:49 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 19 Jul 2010 11:07:49 +0100
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTimujbfw33zV4bG3y6J8fRu0yocwJ2XryN2W7El5@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>
	<AANLkTilzTT_1kOVsQpi76fDittiGf8rGkZBJ6Urflkzz@mail.gmail.com>
	<AANLkTimujbfw33zV4bG3y6J8fRu0yocwJ2XryN2W7El5@mail.gmail.com>
Message-ID: <AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>

On Mon, Jul 19, 2010 at 10:59 AM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Hello peter,
> Sorry for the incomplete information. I want to cluster the structures say
> for example using rmsd between the pdb.
>
> Thanks,
> Bala

Provided you can specify the atomic mapping between the structures,
you can calculate RMSD using Bio.PDB, see for example:
http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/
One way to do this would be pairwise sequence alignments. There
are probably specialised tools out there for this sort of clustering...

Peter

P.S. Please try to CC the mailing list in replies.


From anaryin at gmail.com  Mon Jul 19 11:08:12 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Mon, 19 Jul 2010 13:08:12 +0200
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com> 
	<AANLkTilzTT_1kOVsQpi76fDittiGf8rGkZBJ6Urflkzz@mail.gmail.com> 
	<AANLkTimujbfw33zV4bG3y6J8fRu0yocwJ2XryN2W7El5@mail.gmail.com> 
	<AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>
Message-ID: <AANLkTim8G--ZDzxOGnQYdcx-DICLa7pMBFqkJzCs_iZg@mail.gmail.com>

Hey,

You can try this:
http://sbcb.bioch.ox.ac.uk/oliver/software/GromacsWrapper/html/edpdb.html

Best!

Jo?o [...] Rodrigues
@ http://doeidoei.wordpress.org



On Mon, Jul 19, 2010 at 12:07 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Mon, Jul 19, 2010 at 10:59 AM, Bala subramanian
> <bala.biophysics at gmail.com> wrote:
> > Hello peter,
> > Sorry for the incomplete information. I want to cluster the structures
> say
> > for example using rmsd between the pdb.
> >
> > Thanks,
> > Bala
>
> Provided you can specify the atomic mapping between the structures,
> you can calculate RMSD using Bio.PDB, see for example:
> http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/
> One way to do this would be pairwise sequence alignments. There
> are probably specialised tools out there for this sort of clustering...
>
> Peter
>
> P.S. Please try to CC the mailing list in replies.
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



From schaefer at rostlab.org  Mon Jul 19 13:22:09 2010
From: schaefer at rostlab.org (Christian Schaefer)
Date: Mon, 19 Jul 2010 15:22:09 +0200
Subject: [Biopython] clustering pdb
In-Reply-To: <AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>
References: <AANLkTilOGqJmS6n3HW3R67VCuWVfxvS2RoqJNBrYMdx0@mail.gmail.com>	<AANLkTilzTT_1kOVsQpi76fDittiGf8rGkZBJ6Urflkzz@mail.gmail.com>	<AANLkTimujbfw33zV4bG3y6J8fRu0yocwJ2XryN2W7El5@mail.gmail.com>
	<AANLkTin4xOZBDKt7tbklfumhT28WsEOUmVtuO2sJ_H4x@mail.gmail.com>
Message-ID: <4C445181.6070801@rostlab.org>

On 07/19/2010 12:07 PM, Peter wrote:
> Provided you can specify the atomic mapping between the structures,
> you can calculate RMSD using Bio.PDB, see for example:
> http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/
> One way to do this would be pairwise sequence alignments. There
> are probably specialised tools out there for this sort of clustering...

Thanks Peter for that. I didn't know that Biopython provides 
superimpositioning of two pdb structures. I'd need that badly for my 
current project, and I used ProFit [1] so far. A native python 
implementation is of course very convenient in my case.

Chris

[1] http://www.bioinf.org.uk/

-- 
Dipl.-Bioinf. Christian Schaefer
Technical University Munich
Department for Bioinformatics
Faculty of Computer Science/I12
Boltzmannstr. 3
D-85748 Garching b. Muenchen
Germany
http://www.rostlab.org/~schaefer


From calhoun.bradley at gmail.com  Mon Jul 19 16:01:22 2010
From: calhoun.bradley at gmail.com (Brad Calhoun)
Date: Mon, 19 Jul 2010 11:01:22 -0500
Subject: [Biopython] missing DTD file
Message-ID: <AANLkTikrB1kNGYw-YIiA5DO2tlgTte5u_3SsH0tp6ASc@mail.gmail.com>

To whom it may concern,

The function of Biopython (currently using version 1.52) is severely limited
by a missing DTD file: "eLink_090910.dtd"  which I am unable to locate at
the suggested locations.

Any instruction to resolve this issue would be greatly appreciated.

Regards,
BTC


From biopython at maubp.freeserve.co.uk  Mon Jul 19 16:21:46 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 19 Jul 2010 17:21:46 +0100
Subject: [Biopython] missing DTD file
In-Reply-To: <AANLkTikrB1kNGYw-YIiA5DO2tlgTte5u_3SsH0tp6ASc@mail.gmail.com>
References: <AANLkTikrB1kNGYw-YIiA5DO2tlgTte5u_3SsH0tp6ASc@mail.gmail.com>
Message-ID: <AANLkTim3WXBCOPpDbNGvVKAxNDWkUFp06GUbwSWMaZ5a@mail.gmail.com>

On Mon, Jul 19, 2010 at 5:01 PM, Brad Calhoun <calhoun.bradley at gmail.com> wrote:
> To whom it may concern,
>
> The function of Biopython (currently using version 1.52) is severely limited
> by a missing DTD file: "eLink_090910.dtd" ?which I am unable to locate at
> the suggested locations.
>
> Any instruction to resolve this issue would be greatly appreciated.

Hi Brad,

This was included in Biopython 1.54 (it wasn't noticed quite in time for
Biopython 1.53). You can update your Biopython or get this and other
DTD files from the NCBI. In this case the file is here:

http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/eLink_090910.dtd

Peter

P.S. Googling for "biopython eLink_090910.dtd" worked pretty well ;)



From fredgca at hotmail.com  Mon Jul 19 16:37:30 2010
From: fredgca at hotmail.com (Frederico Arnoldi)
Date: Mon, 19 Jul 2010 16:37:30 +0000
Subject: [Biopython] clustering pdb
In-Reply-To: <mailman.1.1279555202.24200.biopython@lists.open-bio.org>
References: <mailman.1.1279555202.24200.biopython@lists.open-bio.org>
Message-ID: <SNT136-w639ECE8C3471B2BBC20C57BFBF0@phx.gbl>


Dear Bala,

As indicated by Rodrigues, you can use GromacsWrapper for peforming MD. I do not know any package for python that you could use to handle MD trajectories. However, it is possible to use RPy and Bio3D (http://mccammon.ucsd.edu/~bgrant/bio3d/index.html).

Att.,
Frederico Arnoldi

?
> Message: 1
> Date: Mon, 19 Jul 2010 11:39:11 +0200
> From: Bala subramanian 
> Subject: [Biopython] clustering pdb
> To: biopython at lists.open-bio.org
> Message-ID:
> 
> Content-Type: text/plain; charset=ISO-8859-1
>
> Friends,
> I have around 3000 pdb files obtained from MD simulations. I would like to
> know if it is possible to cluster the pdb files using any of the biopython's
> bio.PDB or other modules. If so, i would appreciate if you could provide me
> a sample code.
>
> Is there any utility in Biopython to handle MD trajectories obtained from
> common packages like gromacs, amber etc ?
>
> Thank you,
> Bala
>
 		 	   		  
_________________________________________________________________
PREPARE-SE: O SEU HOTMAIL VAI FICAR MELHOR DO QUE NUNCA. CLIQUE E VEJA AS NOVIDADES.
http://www.windowslive.com.br/public/product.aspx/view/1?ocid=Hotmail:Live:Hotmail:Tagline:senDimensao:PREPARE-SE83:-


From anaryin at gmail.com  Mon Jul 19 16:47:56 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Mon, 19 Jul 2010 18:47:56 +0200
Subject: [Biopython] clustering pdb
In-Reply-To: <SNT136-w639ECE8C3471B2BBC20C57BFBF0@phx.gbl>
References: <mailman.1.1279555202.24200.biopython@lists.open-bio.org> 
	<SNT136-w639ECE8C3471B2BBC20C57BFBF0@phx.gbl>
Message-ID: <AANLkTin_jZkHyiNf9jJht_QBJC9mUqHmWKUcc7EvsxLQ@mail.gmail.com>

edPDB actually allows some analysis of the trajectories (to some degree).
You might want to start looking there and then maybe bridge it with MMTK's
functionalities?


From pingou at pingoured.fr  Wed Jul 21 08:47:53 2010
From: pingou at pingoured.fr (Pierre-Yves)
Date: Wed, 21 Jul 2010 10:47:53 +0200
Subject: [Biopython] AssertionError
Message-ID: <1279702073.26644.8.camel@lab.localdomain>

Hi,

I am running into a problem which I can't figure why.

I parse a fasta file using biopython:
for seq_record in SeqIO.parse(fastafile, "fasta"):
     if seq_record.id == name:
            print seq_record.id
            return seq_record

This seq_record becomes seq and I try to extract only a subpart of the
sequence:
s = Seq(seq.seq[start:stop], generic_dna)
seq_out = SeqRecord(s, id = row[col_name])

Print of start and stop shows me:
251944 253441
which is what I expect.

But the creation of the sequence object fails with the following error:
Traceback (most recent call last):
  File "FastaExtractor.py", line 91, in <module>
    s = Seq(seq.seq[start:stop], generic_dna)
  File "/usr/lib64/python2.6/site-packages/Bio/Seq.py", line 87, in
__init__
    type(data) == type(u""))  # but can be a unicode string
AssertionError

When I try to create an object by hand using the python consol, it works
perfectly well.
Any idea what could be wrong ?

Thanks,

Pierre



From pingou at pingoured.fr  Wed Jul 21 09:10:35 2010
From: pingou at pingoured.fr (Pierre-Yves)
Date: Wed, 21 Jul 2010 11:10:35 +0200
Subject: [Biopython] AssertionError
In-Reply-To: <1279702073.26644.8.camel@lab.localdomain>
References: <1279702073.26644.8.camel@lab.localdomain>
Message-ID: <1279703435.26644.10.camel@lab.localdomain>

On Wed, 2010-07-21 at 10:47 +0200, Pierre-Yves wrote:
> s = Seq(seq.seq[start:stop], generic_dna)
> seq_out = SeqRecord(s, id = row[col_name])
I found the solution:
s = Seq(str(seq.seq[start:stop]), generic_dna)

Sorry for the noise,

Pierre



From biopython at maubp.freeserve.co.uk  Wed Jul 21 09:17:21 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 21 Jul 2010 10:17:21 +0100
Subject: [Biopython] AssertionError
In-Reply-To: <1279702073.26644.8.camel@lab.localdomain>
References: <1279702073.26644.8.camel@lab.localdomain>
Message-ID: <AANLkTinLG5zoyfVhSvJFWEx4eLFin7ZexhdaBvn9N4bY@mail.gmail.com>

On Wed, Jul 21, 2010 at 9:47 AM, Pierre-Yves <pingou at pingoured.fr> wrote:
> Hi,
>
> I am running into a problem which I can't figure why.
>
> I parse a fasta file using biopython:
> for seq_record in SeqIO.parse(fastafile, "fasta"):
> ? ? if seq_record.id == name:
> ? ? ? ? ? ?print seq_record.id
> ? ? ? ? ? ?return seq_record
>
> This seq_record becomes seq and I try to extract only a subpart of the
> sequence:
> s = Seq(seq.seq[start:stop], generic_dna)
> seq_out = SeqRecord(s, id = row[col_name])


If seq is a SeqRecord (a variable name I avoid), then seq.seq is
a Seq object, and slicing a Seq object gives another Seq object.
This means you shouldn't do this:

 Seq(seq.seq[start:stop], generic_dna)

Just do this:

seq.seq[start:stop]

Your work around seems overly complicated,

Seq(str(seq.seq[start:stop]), generic_dna)

If your reason for doing this is to specify the alphabet, just tell
Bio.SeqIO.parse() the alphabet instead.

You can also slice the original SeqRecord instead, to give a new
SeqRecord, and change its id to what you want.

>
> But the creation of the sequence object fails with the following error:
> Traceback (most recent call last):
> ?File "FastaExtractor.py", line 91, in <module>
> ? ?s = Seq(seq.seq[start:stop], generic_dna)
> ?File "/usr/lib64/python2.6/site-packages/Bio/Seq.py", line 87, in
> __init__
> ? ?type(data) == type(u"")) ?# but can be a unicode string
> AssertionError

That should be a clearer error message, the Seq object is not
expecting you to give it a Seq object - but a string or unicode.

Peter



From pingou at pingoured.fr  Wed Jul 21 09:22:12 2010
From: pingou at pingoured.fr (Pierre-Yves)
Date: Wed, 21 Jul 2010 11:22:12 +0200
Subject: [Biopython] AssertionError
In-Reply-To: <AANLkTinLG5zoyfVhSvJFWEx4eLFin7ZexhdaBvn9N4bY@mail.gmail.com>
References: <1279702073.26644.8.camel@lab.localdomain>
	<AANLkTinLG5zoyfVhSvJFWEx4eLFin7ZexhdaBvn9N4bY@mail.gmail.com>
Message-ID: <1279704132.26644.13.camel@lab.localdomain>

On Wed, 2010-07-21 at 10:17 +0100, Peter wrote:

> If seq is a SeqRecord (a variable name I avoid),
Changed.

>  then seq.seq is
> a Seq object, and slicing a Seq object gives another Seq object.
> This means you shouldn't do this:
> 
>  Seq(seq.seq[start:stop], generic_dna)
> 
> Just do this:
> 
> seq.seq[start:stop]

Indeed:
 seq_out = SeqRecord( seq_record.seq[start:stop],
                      id = row[col_name]
                    )
just works.

> >
> > But the creation of the sequence object fails with the following error:
> > Traceback (most recent call last):
> >  File "FastaExtractor.py", line 91, in <module>
> >    s = Seq(seq.seq[start:stop], generic_dna)
> >  File "/usr/lib64/python2.6/site-packages/Bio/Seq.py", line 87, in
> > __init__
> >    type(data) == type(u""))  # but can be a unicode string
> > AssertionError
> 
> That should be a clearer error message, the Seq object is not
> expecting you to give it a Seq object - but a string or unicode.

A clearer error message would indeed be nice.


Pierre



From biopython at maubp.freeserve.co.uk  Wed Jul 21 09:46:18 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 21 Jul 2010 10:46:18 +0100
Subject: [Biopython] AssertionError
In-Reply-To: <1279704132.26644.13.camel@lab.localdomain>
References: <1279702073.26644.8.camel@lab.localdomain>
	<AANLkTinLG5zoyfVhSvJFWEx4eLFin7ZexhdaBvn9N4bY@mail.gmail.com>
	<1279704132.26644.13.camel@lab.localdomain>
Message-ID: <AANLkTimjjqo0MRcH8OTkWNouclXVpEZg0HccuUGhujiW@mail.gmail.com>

On Wed, Jul 21, 2010 at 10:22 AM, Pierre-Yves <pingou at pingoured.fr> wrote:
>>
>> That should be a clearer error message, the Seq object is not
>> expecting you to give it a Seq object - but a string or unicode.
>
> A clearer error message would indeed be nice.
>

It will give a TypeError in the next release. Thanks for the feedback.

Peter


From bala.biophysics at gmail.com  Wed Jul 21 14:51:07 2010
From: bala.biophysics at gmail.com (Bala subramanian)
Date: Wed, 21 Jul 2010 16:51:07 +0200
Subject: [Biopython] running naccess
Message-ID: <AANLkTimgjZ3cgwELxQyHoJF7tOrK9Y_9wpWGTVFYZMiy@mail.gmail.com>

Friends,
I am trying to run naccess as follows.

from Bio.PDB.PDBParser import PDBParser
par = PDBParser()
structure = par.get_structure('test','12_25.pdb')
import Bio.PDB.NACCESS as nac
data=nac.run_naccess(structure[0],'12_25.pdb')

It seems that there is an issue with tmp dir creation. I could nt run
naccess even if i define *temp_path='.'* with run_naccess function. Kindly
write me how to resolve the issue.


*I get the following error:*

IOError                                   Traceback (most recent call last)

/tmp/tmpqQLhRl/<ipython console> in <module>()

/apps/py_modules/gcc/lib/python2.6/site-packages/Bio/PDB/NACCESS.pyc in
run_naccess(model, pdb_file, probe_size, z_slice, naccess, temp_path)
     56     # get the output, then delete the temp directory

     57     rsa_file = tmp_pdb_file[:-4] + '.rsa'
---> 58     rf = open(rsa_file)
     59     rsa_data = rf.readlines()
     60     rf.close()

IOError: [Errno 2] No such file or directory: '/tmp/tmpqQLhRl/tmpaOkRlK.rsa'


From biopython at maubp.freeserve.co.uk  Wed Jul 21 15:02:44 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 21 Jul 2010 16:02:44 +0100
Subject: [Biopython] running naccess
In-Reply-To: <AANLkTimgjZ3cgwELxQyHoJF7tOrK9Y_9wpWGTVFYZMiy@mail.gmail.com>
References: <AANLkTimgjZ3cgwELxQyHoJF7tOrK9Y_9wpWGTVFYZMiy@mail.gmail.com>
Message-ID: <AANLkTin6dOYlq5l00ZjzTkX2bcHRz8RogIoBVe9PMxC0@mail.gmail.com>

On Wed, Jul 21, 2010 at 3:51 PM, Bala subramanian
<bala.biophysics at gmail.com> wrote:
> Friends,
> I am trying to run naccess as follows.
>
> from Bio.PDB.PDBParser import PDBParser
> par = PDBParser()
> structure = par.get_structure('test','12_25.pdb')
> import Bio.PDB.NACCESS as nac
> data=nac.run_naccess(structure[0],'12_25.pdb')
>
> It seems that there is an issue with tmp dir creation. I could nt run
> naccess even if i define *temp_path='.'* with run_naccess function. Kindly
> write me how to resolve the issue.
>
>
> *I get the following error:*
>
> IOError ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Traceback (most recent call last)
>
> /tmp/tmpqQLhRl/<ipython console> in <module>()
>
> /apps/py_modules/gcc/lib/python2.6/site-packages/Bio/PDB/NACCESS.pyc in
> run_naccess(model, pdb_file, probe_size, z_slice, naccess, temp_path)
> ? ? 56 ? ? # get the output, then delete the temp directory
>
> ? ? 57 ? ? rsa_file = tmp_pdb_file[:-4] + '.rsa'
> ---> 58 ? ? rf = open(rsa_file)
> ? ? 59 ? ? rsa_data = rf.readlines()
> ? ? 60 ? ? rf.close()
>
> IOError: [Errno 2] No such file or directory: '/tmp/tmpqQLhRl/tmpaOkRlK.rsa'

Try putting some debug print statements into NACCESS.py, in
particular see what stdout and stderr contain. My guess is there
is a problem running the tool.

Also try running the NACCESS command line tool by hand at
the command prompt, to make sure it is installed and working
correctly.

Peter



From 2huggie at gmail.com  Fri Jul 23 07:04:13 2010
From: 2huggie at gmail.com (Timothy Wu)
Date: Fri, 23 Jul 2010 15:04:13 +0800
Subject: [Biopython] Gene ontology parsing
Message-ID: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>

Hi

Is there a parser in BioPython for OBO v1.2?

If there isn't (at least I couldn't find it a while back), maybe I could
contribute a little. I've casually wrote an OntologyIO package with
"OboRecord", a scanner and consumer files. I may have not handles all the
stuff written on http://www.geneontology.org/GO.format.obo-1_2.shtml, but it
did suit my own purpose before. I don't know if anyone in the project will
be interested in it. I also do not know if my code will pass the quality
standard set forth by BioPython. I've also wrote a GoGraph structure that
allow me to look for stuff in the DAG, treating it much like a tree, looking
for "common ancestor" given two nodes, parent, child, etc. I've never
contributed code to any project before, so if these code can indeed be
contributed, perhaps some help from someone in the project would be needed,
thanks.

Timothy


From bartek at rezolwenta.eu.org  Fri Jul 23 07:50:45 2010
From: bartek at rezolwenta.eu.org (Bartek Wilczynski)
Date: Fri, 23 Jul 2010 09:50:45 +0200
Subject: [Biopython] Gene ontology parsing
In-Reply-To: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>
References: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>
Message-ID: <AANLkTikq8U_NoZrbrj0Ajg7V+ZFjAPd3hOkuPwqLX=wP@mail.gmail.com>

hi Timothy,

I, for one, would be interested in Gene Ontology parsing. I could also help
with reviewing the code if you worry about whether it fits to the rest of
biopython.

I think the easiest for all would be if you could make a branch of biopython
on github including your proposed enhancements. This would allow everybody
to see what's in there and also make changes and finally mergi it into the
trunk.

thanks for your offer

Bartek
On Fri, Jul 23, 2010 at 9:04 AM, Timothy Wu <2huggie at gmail.com> wrote:

> Hi
>
> Is there a parser in BioPython for OBO v1.2?
>
> If there isn't (at least I couldn't find it a while back), maybe I could
> contribute a little. I've casually wrote an OntologyIO package with
> "OboRecord", a scanner and consumer files. I may have not handles all the
> stuff written on http://www.geneontology.org/GO.format.obo-1_2.shtml, but
> it
> did suit my own purpose before. I don't know if anyone in the project will
> be interested in it. I also do not know if my code will pass the quality
> standard set forth by BioPython. I've also wrote a GoGraph structure that
> allow me to look for stuff in the DAG, treating it much like a tree,
> looking
> for "common ancestor" given two nodes, parent, child, etc. I've never
> contributed code to any project before, so if these code can indeed be
> contributed, perhaps some help from someone in the project would be needed,
> thanks.
>
> Timothy
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>


-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
Meyerhoffstrasse 1,
69012 Heidelberg,
Germany
tel: +49 6221 387 8433


From biopython at maubp.freeserve.co.uk  Fri Jul 23 09:45:11 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 23 Jul 2010 10:45:11 +0100
Subject: [Biopython] Gene ontology parsing
In-Reply-To: <AANLkTikq8U_NoZrbrj0Ajg7V+ZFjAPd3hOkuPwqLX=wP@mail.gmail.com>
References: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>
	<AANLkTikq8U_NoZrbrj0Ajg7V+ZFjAPd3hOkuPwqLX=wP@mail.gmail.com>
Message-ID: <AANLkTikt_2b3=mz6kuFxUrpx7grujhNbx4WSkJasRvqy@mail.gmail.com>

On Fri, Jul 23, 2010 at 8:50 AM, Bartek Wilczynski
<bartek at rezolwenta.eu.org> wrote:
> hi Timothy,
>
> I, for one, would be interested in Gene Ontology parsing. I could also help
> with reviewing the code if you worry about whether it fits to the rest of
> biopython.
>
> I think the easiest for all would be if you could make a branch of biopython
> on github including your proposed enhancements. This would allow everybody
> to see what's in there and also make changes and finally mergi it into the
> trunk.
>
> thanks for your offer
>
> Bartek

Hi Timothy & Bartek,

There are already several people working on GO stuff in branches on github,
e.g. Chris Lasher, Kyle Ellrott, Tam?s Nepusz. I don't know if any of them are
doing OBO v1.2, but it would be sensible to check and try and combine efforts.

Peter



From amaher at fas.harvard.edu  Fri Jul 23 15:22:32 2010
From: amaher at fas.harvard.edu (Andrew Maher)
Date: Fri, 23 Jul 2010 11:22:32 -0400
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
Message-ID: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>

I'm a beginner with python, and I'm having trouble with something relatively
simple:

I'm trying to find the isoelectric point of a protein with the
sequence: VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC

So, when I load python 2.6.2 with bipython v1.54 and then type in "from
Bio.SeqUtils import ProtParam" on one line and then "X =
ProteinAnalysis("VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC")
on the next line, I get the following error message:

NameError: name 'ProteinAnalysis' is not defined

But, looking at the source code for ProtParam (
http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis),
isn't the ProteinAnalysis class clearly defined? What am I doing wrong?


From anaryin at gmail.com  Fri Jul 23 15:25:47 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 23 Jul 2010 17:25:47 +0200
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>
Message-ID: <AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>

Hello Andrew,

Try this: ProtParam.ProteinAnalysis(Sequence)

Best,

Jo?o [...] Rodrigues
@ http://doeidoei.wordpress.org



On Fri, Jul 23, 2010 at 5:22 PM, Andrew Maher <amaher at fas.harvard.edu>wrote:

> I'm a beginner with python, and I'm having trouble with something
> relatively
> simple:
>
> I'm trying to find the isoelectric point of a protein with the
> sequence:
> VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC
>
> So, when I load python 2.6.2 with bipython v1.54 and then type in "from
> Bio.SeqUtils import ProtParam" on one line and then "X =
>
> ProteinAnalysis("VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC")
> on the next line, I get the following error message:
>
> NameError: name 'ProteinAnalysis' is not defined
>
> But, looking at the source code for ProtParam (
>
> http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis
> ),
> isn't the ProteinAnalysis class clearly defined? What am I doing wrong?
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



From amaher at fas.harvard.edu  Fri Jul 23 15:31:59 2010
From: amaher at fas.harvard.edu (Andrew Maher)
Date: Fri, 23 Jul 2010 11:31:59 -0400
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com> 
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>
Message-ID: <AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>

Sorry, now I get this:

-bash-3.1$ python
Python 2.6.2 (r262:71600, Jul 27 2009, 17:05:24)
[GCC 4.1.2 20070626 (Red Hat 4.1.2-14)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio.SeqUtils.ProtParam
>>>
ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'ProtParam' is not defined
>>>

I wonder what's wrong...

On Fri, Jul 23, 2010 at 11:25 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hello Andrew,
>
> Try this: ProtParam.ProteinAnalysis(Sequence)
>
> Best,
>
> Jo?o [...] Rodrigues
> @ http://doeidoei.wordpress.org
>
>
>
> On Fri, Jul 23, 2010 at 5:22 PM, Andrew Maher <amaher at fas.harvard.edu>wrote:
>
>> I'm a beginner with python, and I'm having trouble with something
>> relatively
>> simple:
>>
>> I'm trying to find the isoelectric point of a protein with the
>> sequence:
>> VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC
>>
>> So, when I load python 2.6.2 with bipython v1.54 and then type in "from
>> Bio.SeqUtils import ProtParam" on one line and then "X =
>>
>> ProteinAnalysis("VPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPEASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC")
>> on the next line, I get the following error message:
>>
>> NameError: name 'ProteinAnalysis' is not defined
>>
>> But, looking at the source code for ProtParam (
>>
>> http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis
>> ),
>> isn't the ProteinAnalysis class clearly defined? What am I doing wrong?
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>



From anaryin at gmail.com  Fri Jul 23 15:34:49 2010
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Fri, 23 Jul 2010 17:34:49 +0200
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com> 
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com> 
	<AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
Message-ID: <AANLkTinnR+eC_kEyasuQWekDANKfcCZk-JSRJTA77uEq@mail.gmail.com>

No problem, you just switched the import statement.

from Bio.SeqUtils import ProtParam

sequence = ''DTKTLIKTIVT"

ProtParam.ProteinAnalysis(sequence)

or

import Bio.SeqUtils.ProtParam

sequence = ''DTKTLIKTIVT"

ProteinAnalysis(sequence)


It's a namespace issue :)

Best!

Jo?o



From biopython at maubp.freeserve.co.uk  Fri Jul 23 15:39:40 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 23 Jul 2010 16:39:40 +0100
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>
	<AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
Message-ID: <AANLkTimjfWxktsDc75FGZvNC+V_8yH546N1ynoCG0JN4@mail.gmail.com>

On Fri, Jul 23, 2010 at 4:31 PM, Andrew Maher <amaher at fas.harvard.edu> wrote:
> Sorry, now I get this:

Maybe reading up on Python's import statement and name spaces will help.
You are close...

One approach is to import the module:

from Bio.SeqUtils import ProtParam
x = ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')

Or, you might prefer to import just the class - probably a good plan if you
only need one or two things from this module:

from Bio.SeqUtils.ProtParam import ProteinAnalysis
x = ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')

Peter

P.S.

You can even do this - but I don't think it is very clear:

import Bio.SeqUtils.ProtParam
x = Bio.SeqUtils.ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')


From amaher at fas.harvard.edu  Fri Jul 23 15:49:06 2010
From: amaher at fas.harvard.edu (Andrew Maher)
Date: Fri, 23 Jul 2010 11:49:06 -0400
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTimjfWxktsDc75FGZvNC+V_8yH546N1ynoCG0JN4@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com> 
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com> 
	<AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com> 
	<AANLkTimjfWxktsDc75FGZvNC+V_8yH546N1ynoCG0JN4@mail.gmail.com>
Message-ID: <AANLkTi=_MYE7m=NgcptdMzvi_pEqbJ6HuJ=_9jb3vEMY@mail.gmail.com>

Thanks a lot!

Also, I've noticed that when using this module to get an isoelectric point,
x.pi() does not work, but x.isoelectric_point() does. Perhaps someone should
note that somewhere.

-Andrew

On Fri, Jul 23, 2010 at 11:39 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Fri, Jul 23, 2010 at 4:31 PM, Andrew Maher <amaher at fas.harvard.edu>
> wrote:
> > Sorry, now I get this:
>
> Maybe reading up on Python's import statement and name spaces will help.
> You are close...
>
> One approach is to import the module:
>
> from Bio.SeqUtils import ProtParam
> x = ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')
>
> Or, you might prefer to import just the class - probably a good plan if you
> only need one or two things from this module:
>
> from Bio.SeqUtils.ProtParam import ProteinAnalysis
> x = ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')
>
> Peter
>
> P.S.
>
> You can even do this - but I don't think it is very clear:
>
> import Bio.SeqUtils.ProtParam
> x =
> Bio.SeqUtils.ProtParam.ProteinAnalysis('VPIQKVQDDTKTLIKTIVTRINDISHTQSVSS')
>
>


From biopython at maubp.freeserve.co.uk  Fri Jul 23 15:52:53 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 23 Jul 2010 16:52:53 +0100
Subject: [Biopython] Using the Bio.SeqUtils.ProtParam module
In-Reply-To: <AANLkTi=_MYE7m=NgcptdMzvi_pEqbJ6HuJ=_9jb3vEMY@mail.gmail.com>
References: <AANLkTin4AFn6GN1UMDAfb8D8EL2mG9M+NGRArzSf3Y4M@mail.gmail.com>
	<AANLkTik_ZRrV4VuthESzhF04k-eGW-5DXBeY1w-3CQdo@mail.gmail.com>
	<AANLkTim_vaMt2qT0OqtK8MEavtNu5KjdGfrdgMoixew=@mail.gmail.com>
	<AANLkTimjfWxktsDc75FGZvNC+V_8yH546N1ynoCG0JN4@mail.gmail.com>
	<AANLkTi=_MYE7m=NgcptdMzvi_pEqbJ6HuJ=_9jb3vEMY@mail.gmail.com>
Message-ID: <AANLkTimt4468w4Ph8uiKN-zN7tK8iSjoC3ODB2quC8-D@mail.gmail.com>

On Fri, Jul 23, 2010 at 4:49 PM, Andrew Maher <amaher at fas.harvard.edu> wrote:
> Thanks a lot!
>
> Also, I've noticed that when using this module to get an isoelectric point,
> x.pi() does not work, but x.isoelectric_point() does. Perhaps someone should
> note that somewhere.

That looks like a typo in the ProtParam module documentation - I'll
fix that. Thanks!

Peter


From kellrott at gmail.com  Fri Jul 23 16:17:19 2010
From: kellrott at gmail.com (Kyle)
Date: Fri, 23 Jul 2010 09:17:19 -0700
Subject: [Biopython] Gene ontology parsing
In-Reply-To: <AANLkTikt_2b3=mz6kuFxUrpx7grujhNbx4WSkJasRvqy@mail.gmail.com>
References: <AANLkTinWFFg=0dN9rJ0S3GKpCGMn7A67Y1s6B=sjaUjR@mail.gmail.com>
	<AANLkTikq8U_NoZrbrj0Ajg7V+ZFjAPd3hOkuPwqLX=wP@mail.gmail.com>
	<AANLkTikt_2b3=mz6kuFxUrpx7grujhNbx4WSkJasRvqy@mail.gmail.com>
Message-ID: <AANLkTim_b2zOC3DwA3GwuBnB5gmgOvfOdFYFPayDt3-m@mail.gmail.com>

> There are already several people working on GO stuff in branches on github,
> e.g. Chris Lasher, Kyle Ellrott, Tam?s Nepusz. I don't know if any of them are
> doing OBO v1.2, but it would be sensible to check and try and combine efforts.

The branch at http://github.com/kellrott/biopython/tree/gosupport
should parse most of the information held in OBO v1.2.
Chris's original version was targeted only for the GO OBO file, as
there was a typecheck to make sure the node ID's started with 'GO:'.
That's disable in my branch, and I've used the package to parse a few
of the other ontologies found at www.obofoundry.org.
The module is currently called Bio.GO, but maybe it should be
re-factored to represent the fact that it covers general OBO files,
and not just the GO file specifically.

The main things things keeping it from merging into the main branch
are proper documentation, complete unit tests, and making sure that it
covers all of the standard usage practices.

If you can try it out, and let me know which function are missing (and
maybe contribute some code), we can push this thing forward.

Kyle



From bouchard.lysiane at gmail.com  Fri Jul 23 19:54:29 2010
From: bouchard.lysiane at gmail.com (Lysiane Bouchard)
Date: Fri, 23 Jul 2010 15:54:29 -0400
Subject: [Biopython] NaN values, lowess
Message-ID: <AANLkTikK+NdqWOAwSa56Oh+tOjOQekKqx8jRF6f56vOz@mail.gmail.com>

Hi,

I am experimenting problems with the lowess function, from Bio.Statistics
module, version 1.53.
It seems that when the data trajectory is fairly constant, NaN / infinite
values are returned as estimated trend.  I wonder if someone encountered a
similar problem ?

Thank you,

Lysiane


From pengyu.ut at gmail.com  Wed Jul 28 04:08:37 2010
From: pengyu.ut at gmail.com (Peng Yu)
Date: Tue, 27 Jul 2010 23:08:37 -0500
Subject: [Biopython] Where is alphebet of Bio.Seq documented
Message-ID: <AANLkTintQX20Q2vE8sMfx9111tWXNyGwAF_2EqZWkkBS@mail.gmail.com>

Hi,

Seq class has a member alphabet if I'm correct about the terminology.
But I don't see it in help(Bio.Seq). Is it documented in python
help()?

from Bio.Seq import Seq
my_seq = Seq("AGTACACTGGT")
print my_seq
print my_seq.alphabet

-- 
Regards,
Peng


From biopython at maubp.freeserve.co.uk  Wed Jul 28 10:51:26 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 28 Jul 2010 11:51:26 +0100
Subject: [Biopython] Where is alphebet of Bio.Seq documented
In-Reply-To: <AANLkTintQX20Q2vE8sMfx9111tWXNyGwAF_2EqZWkkBS@mail.gmail.com>
References: <AANLkTintQX20Q2vE8sMfx9111tWXNyGwAF_2EqZWkkBS@mail.gmail.com>
Message-ID: <AANLkTinNr6LgT8u5UiSZR0TuTmgaBNJ=UirtpS-eQ18n@mail.gmail.com>

On Wed, Jul 28, 2010 at 5:08 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
> Hi,
>
> Seq class has a member alphabet if I'm correct about the terminology.
> But I don't see it in help(Bio.Seq). Is it documented in python
> help()?
>
> from Bio.Seq import Seq
> my_seq = Seq("AGTACACTGGT")
> print my_seq
> print my_seq.alphabet

Hi Peng,

The main tutorial does explain this, but you are right that the Seq docstrings
should describe the alphabet property/attribute of the Seq objects. It is just
an Alphabet object as defined in the Bio.Alphabet module.

Peter


From Achim.Treumann at NEPAF.com  Sat Jul 31 06:05:09 2010
From: Achim.Treumann at NEPAF.com (Achim Treumann)
Date: Sat, 31 Jul 2010 07:05:09 +0100
Subject: [Biopython] problem with SeqIO.index() and get_raw
Message-ID: <01798D2396253A449511F31F1CDE83550C3E6C@srv1.NEPAF.local>

Dear all, 

I am new to biopython and trying to familiarise myself with its utilities. When I was trying to parse a swissprot.dat file to then copy the full data back using the get_raw attribute, I got stuck (Biopython 1.53, Python 2.6 on WinXP). 

I was using the following code:

<code>
from Bio import SeqIO
from Bio import Swissprot
InputFile = "D:\data\uniprot_sprot.short.dat"

handle = open(InputFile)
uniprot = SeqIO.index(InputFile, "swiss")
acclist=[]
for record in Swissprot.parse(handle):
    accList.append(record.accessions[0])
handle.close()
out_handle = open("D:\data\uniprot_sprot.temp.dat", "w")
for acc in accList:
    out_handle.write(uniprot.get_raw(acc)
out_handle.close()
</code>

The input file is a sprot-formatted file with 39 entries. 

When I try to run this, I get the following error:
Traceback (most recent call last):
  File"<pyshell#52>", line 2, in <module>
    handle.write(uniprot.getraw(acc))
Attribute error: 'SwissDict' object has no attribute 'get_raw'

Where am I going wrong? I have tried to replicate the corresponding example from the tutorial and got stuck at the same point with the same error message. Any help would be greatly appreciated. 

As I am typing, I realise that get_raw might only have been implemented in Biopython 1.54... I will post this anyway, and if upgrading sorts it, I will send a reply. 

Many thanks for comments and advice, 
Achim



From biopython at maubp.freeserve.co.uk  Sat Jul 31 09:16:38 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 31 Jul 2010 10:16:38 +0100
Subject: [Biopython] problem with SeqIO.index() and get_raw
In-Reply-To: <01798D2396253A449511F31F1CDE83550C3E6C@srv1.NEPAF.local>
References: <01798D2396253A449511F31F1CDE83550C3E6C@srv1.NEPAF.local>
Message-ID: <AANLkTi=BnC51gXDeQ-a-GuMwVyqpO7C4MuwwuTyByeFb@mail.gmail.com>

On Sat, Jul 31, 2010 at 7:05 AM, Achim Treumann
<Achim.Treumann at nepaf.com> wrote:
> Dear all,
>
> I am new to biopython and trying to familiarise myself with its utilities.
> When I was trying to parse a swissprot.dat file to then copy the full
> data back using the get_raw attribute, I got stuck (Biopython 1.53,
> Python 2.6 on WinXP).
>
>...
>
> As I am typing, I realise that get_raw might only have been
> implemented in Biopython 1.54... I will post this anyway, and if
> upgrading sorts it, I will send a reply.

Hi Achim,

Well guessed. Yes, get_raw was added in Biopython 1.54, see
http://news.open-bio.org/news/2010/05/biopython-release-154/

Are you reading the current tutorial on line (rather than the
version shipped with Biopython 1.53)? It does mention this,
although maybe it could be in the FAQ as well... would that
help?

Peter