From p.j.a.cock at googlemail.com  Wed Jun  1 03:43:43 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 1 Jun 2011 08:43:43 +0100
Subject: [Biopython] missing dtd in Bio.Entrez
In-Reply-To: <BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
References: <mailman.16532.1306902457.2958.biopython-dev@lists.open-bio.org>
	<BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
Message-ID: <BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>

Hi Guy,

You have to have subscribed to the mailing list in order
to post to it - sadly this became necessary due to spam.

Thank you for your email, but could you give a little more
detail. Which version of Biopython do you have? Use:

import Bio
print Bio.__version__

The DTD file pubmed_110101.dtd was added to our
repository in September 2010, so should have been in
Biopython 1.56 and 1.57:-

https://github.com/biopython/biopython/commit/9ea066c5de4e8d64d16f2774bed78e0b69777b8a#Bio/Entrez/DTDs/pubmed_110101.dtd

Regards,

Peter

On Wed, Jun 1, 2011 at 5:32 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> ---------- Forwarded message ----------
> From:?Guy Eakin <guyeakin at gmail.com>
> To:?biopython-dev at biopython.org
> Date:?Wed, 1 Jun 2011 00:27:15 -0400
> Subject:?missing dtd in Bio.Entrez
> http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_110101.dtd
>
> The above is missing from the current biopython distribution. The
> error message requests that this email address be notified.
>
> Thanks,
> Guy Eakin
>
>


From guyeakin at gmail.com  Wed Jun  1 04:33:55 2011
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 1 Jun 2011 04:33:55 -0400
Subject: [Biopython] missing dtd in Bio.Entrez
In-Reply-To: <BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>
References: <mailman.16532.1306902457.2958.biopython-dev@lists.open-bio.org>
	<BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
	<BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>
Message-ID: <BANLkTik92b=dHN76mjb9dP6juLsGm4pLBw@mail.gmail.com>

Well, I suppose that explains it.  version 1.54 is what I am using.  I
downloaded it from the Ubuntu software center earlier tonight. I had
just assumed that was most recent. Sorry for the red herring.

guy

On Wed, Jun 1, 2011 at 3:43 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi Guy,
>
> You have to have subscribed to the mailing list in order
> to post to it - sadly this became necessary due to spam.
>
> Thank you for your email, but could you give a little more
> detail. Which version of Biopython do you have? Use:
>
> import Bio
> print Bio.__version__
>
> The DTD file pubmed_110101.dtd was added to our
> repository in September 2010, so should have been in
> Biopython 1.56 and 1.57:-
>
> https://github.com/biopython/biopython/commit/9ea066c5de4e8d64d16f2774bed78e0b69777b8a#Bio/Entrez/DTDs/pubmed_110101.dtd
>
> Regards,
>
> Peter
>
> On Wed, Jun 1, 2011 at 5:32 AM, Guy Eakin <guyeakin at gmail.com> wrote:
>> ---------- Forwarded message ----------
>> From:?Guy Eakin <guyeakin at gmail.com>
>> To:?biopython-dev at biopython.org
>> Date:?Wed, 1 Jun 2011 00:27:15 -0400
>> Subject:?missing dtd in Bio.Entrez
>> http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_110101.dtd
>>
>> The above is missing from the current biopython distribution. The
>> error message requests that this email address be notified.
>>
>> Thanks,
>> Guy Eakin
>>
>>
>


From p.j.a.cock at googlemail.com  Wed Jun  1 04:42:47 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 1 Jun 2011 09:42:47 +0100
Subject: [Biopython] missing dtd in Bio.Entrez
In-Reply-To: <BANLkTik92b=dHN76mjb9dP6juLsGm4pLBw@mail.gmail.com>
References: <mailman.16532.1306902457.2958.biopython-dev@lists.open-bio.org>
	<BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
	<BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>
	<BANLkTik92b=dHN76mjb9dP6juLsGm4pLBw@mail.gmail.com>
Message-ID: <BANLkTi=xKZEgdaLogkcT4aV0cCpF7WPc5A@mail.gmail.com>

On Wed, Jun 1, 2011 at 9:33 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> Well, I suppose that explains it. ?version 1.54 is what I am using. ?I
> downloaded it from the Ubuntu software center earlier tonight. I had
> just assumed that was most recent. Sorry for the red herring.
>
> guy

Yes, that makes sense.

If you want a more recent version, uou can probably ask for the latest
version to be offered on an Ubuntu backport repository - otherwise natty
has Biopython 1.56 and oneiric has 1.57 according to this:

http://packages.ubuntu.com/search?suite=all&searchon=names&keywords=python-biopython

Alternatively, try:

sudo apt-get remove python-biopython python-biopython-doc python-biopython-sql
sudo apt-get build-dep python-biopython python-biopython-doc
python-biopython-sql

and then install from source.

Peter


From guyeakin at gmail.com  Wed Jun  1 04:51:13 2011
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 1 Jun 2011 04:51:13 -0400
Subject: [Biopython] missing dtd in Bio.Entrez
In-Reply-To: <BANLkTi=xKZEgdaLogkcT4aV0cCpF7WPc5A@mail.gmail.com>
References: <mailman.16532.1306902457.2958.biopython-dev@lists.open-bio.org>
	<BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
	<BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>
	<BANLkTik92b=dHN76mjb9dP6juLsGm4pLBw@mail.gmail.com>
	<BANLkTi=xKZEgdaLogkcT4aV0cCpF7WPc5A@mail.gmail.com>
Message-ID: <BANLkTimSXquetU1LEnghhL959UjnH0dhcA@mail.gmail.com>

Thanks for the help.  I'll upgrade soon. Bio as well as the OS. I am
an infrequent user of linux and biopython so have been doubly lazy.
Guy

On Wed, Jun 1, 2011 at 4:42 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Wed, Jun 1, 2011 at 9:33 AM, Guy Eakin <guyeakin at gmail.com> wrote:
>> Well, I suppose that explains it. ?version 1.54 is what I am using. ?I
>> downloaded it from the Ubuntu software center earlier tonight. I had
>> just assumed that was most recent. Sorry for the red herring.
>>
>> guy
>
> Yes, that makes sense.
>
> If you want a more recent version, uou can probably ask for the latest
> version to be offered on an Ubuntu backport repository - otherwise natty
> has Biopython 1.56 and oneiric has 1.57 according to this:
>
> http://packages.ubuntu.com/search?suite=all&searchon=names&keywords=python-biopython
>
> Alternatively, try:
>
> sudo apt-get remove python-biopython python-biopython-doc python-biopython-sql
> sudo apt-get build-dep python-biopython python-biopython-doc
> python-biopython-sql
>
> and then install from source.
>
> Peter
>


From chaouki.amir at gmail.com  Wed Jun  1 09:46:43 2011
From: chaouki.amir at gmail.com (amir chaouki)
Date: Wed, 1 Jun 2011 14:46:43 +0100
Subject: [Biopython] (no subject)
Message-ID: <BANLkTinJ0YK0ePF_LTDtGFBE7JfYfMGw0w@mail.gmail.com>

biopython does the alignement or only reads alignement files formats????

-- 
*Amir Chaouki*

From p.j.a.cock at googlemail.com  Thu Jun  2 09:17:57 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 2 Jun 2011 14:17:57 +0100
Subject: [Biopython] (no subject)
In-Reply-To: <BANLkTinJ0YK0ePF_LTDtGFBE7JfYfMGw0w@mail.gmail.com>
References: <BANLkTinJ0YK0ePF_LTDtGFBE7JfYfMGw0w@mail.gmail.com>
Message-ID: <BANLkTikoE=Kn8zJMVtmzxEp+c1nLw2C1ZQ@mail.gmail.com>

On Wed, Jun 1, 2011 at 2:46 PM, amir chaouki <chaouki.amir at gmail.com> wrote:
> biopython does the alignement or only reads alignement files formats????
>
> --
> *Amir Chaouki*

Hi Amir,

Biopython's Bio.AlignIO module reads alignment files, and there
are wrappers to help call some command line alignment tools in
Bio.Align.Applications as well. Unless you are doing research on
alignment algorithms, there doesn't seem to be much need for
actually implementing this kind of thing in Python directly.

Also, there is a pairwise alignment module, Bio.pairwise2, which
might be of interest.

Peter

P.S. Please give your emails a subject

From from.d.putto at gmail.com  Mon Jun  6 09:29:24 2011
From: from.d.putto at gmail.com (Sheila the angel)
Date: Mon, 6 Jun 2011 15:29:24 +0200
Subject: [Biopython] processing XML files in Biopython
Message-ID: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>

Hi All,

I am new to BioPython. I have simple question 'How can I process XML files
in Biopython?'
For example I have NCBI Reference Sequence ID 'NP_997807.1'
I want to download the 'xml' file and want to extract certain information
(e.g. GeneID, amino acid length etc.).
To download the file I did

from Bio import Entrez
handle = Entrez.efetch(db="protein", id= "NP_997807.1", retmode="xml")
record = Entrez.read(handle)
handle.close()

Now I have no clue how to extract certain information (like GeneID) :(
plz help

--
Cheers

Sheila d. Angela

From p.j.a.cock at googlemail.com  Mon Jun  6 09:35:15 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 14:35:15 +0100
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
Message-ID: <BANLkTikys4hhxviVq3WUd_Toon_6uHU8cw@mail.gmail.com>

On Mon, Jun 6, 2011 at 2:29 PM, Sheila the angel <from.d.putto at gmail.com> wrote:
> Hi All,
>
> I am new to BioPython. I have simple question 'How can I process XML files
> in Biopython?'
> For example I have NCBI Reference Sequence ID 'NP_997807.1'

Personally I still download the plain text GenBank format file, and
use Biopython's Bio.SeqIO module to parse that.

> I want to download the 'xml' file and want to extract certain information
> (e.g. GeneID, amino acid length etc.).
> To download the file I did
>
> from Bio import Entrez
> handle = Entrez.efetch(db="protein", id= "NP_997807.1", retmode="xml")
> record = Entrez.read(handle)
> handle.close()
>
> Now I have no clue how to extract certain information (like GeneID) :(
> plz help

If you want to use the XML, then the Bio.Entrez.parse() function should
turn it into a nested structure of Python objects (dicts and lists). Or,
there are several built in XML parsers that come with Python, such
as ElementTree. That could be more efficient if you just wanted to
get one or two bits of information like a GeneID.

Peter

From reece at harts.net  Mon Jun  6 10:30:57 2011
From: reece at harts.net (Reece Hart)
Date: Mon, 6 Jun 2011 07:30:57 -0700
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTikys4hhxviVq3WUd_Toon_6uHU8cw@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
	<BANLkTikys4hhxviVq3WUd_Toon_6uHU8cw@mail.gmail.com>
Message-ID: <BANLkTimoFeXDjd5LEfszx5hA3HeQbKE8KQ@mail.gmail.com>

On Mon, Jun 6, 2011 at 6:35 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> If you want to use the XML, then the Bio.Entrez.parse() function should
> turn it into a nested structure of Python objects (dicts and lists). Or,
> there are several built in XML parsers that come with Python, such
> as ElementTree. That could be more efficient if you just wanted to
> get one or two bits of information like a GeneID.
>

In addition, the Bio.Entrez parser is not namespace-aware and therefore
won't parse some NCBI XML at all (e.g., downloaded dbSNP files). Can someone
with more experience here please corroborate?

And, if that is correct, what is the advantage of using Bio.Entrez.parse
over using another Python XML lib?

Thanks,
Reece

From p.j.a.cock at googlemail.com  Mon Jun  6 10:37:53 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 15:37:53 +0100
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTimoFeXDjd5LEfszx5hA3HeQbKE8KQ@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
	<BANLkTikys4hhxviVq3WUd_Toon_6uHU8cw@mail.gmail.com>
	<BANLkTimoFeXDjd5LEfszx5hA3HeQbKE8KQ@mail.gmail.com>
Message-ID: <BANLkTikaPRc=34QkHdB5VzHz7k0ynCk=kw@mail.gmail.com>

On Mon, Jun 6, 2011 at 3:30 PM, Reece Hart <reece at harts.net> wrote:
> On Mon, Jun 6, 2011 at 6:35 AM, Peter Cock wrote:
>>
>> If you want to use the XML, then the Bio.Entrez.parse() function should
>> turn it into a nested structure of Python objects (dicts and lists). Or,
>> there are several built in XML parsers that come with Python, such
>> as ElementTree. That could be more efficient if you just wanted to
>> get one or two bits of information like a GeneID.
>
> In addition, the?Bio.Entrez parser is not namespace-aware and therefore
> won't parse some NCBI XML at all (e.g., downloaded dbSNP files). Can
> someone with more experience here please corroborate?

See http://bugzilla.open-bio.org/show_bug.cgi?id=2771 for dbSNP.
Do you have any other problem databases with Entrez XML?

> And, if that is correct, what is the advantage of using Bio.Entrez.parse
> over using another Python XML lib?

If you're not scared of XML, not much.

Peter


From david.suarez at yahoo.com  Mon Jun  6 10:37:43 2011
From: david.suarez at yahoo.com (=?ISO-8859-1?Q?David_Su=E1rez_Pascal?=)
Date: Mon, 6 Jun 2011 09:37:43 -0500
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
Message-ID: <BANLkTi=p0WEJ_DTk_o-5LmrY=5tJk-u9Vg@mail.gmail.com>

Sheila,
I don't think you have to deal with XML files. Indeed I tried your code and
what I detected was that Entrez.read already parsed the data.
What I get when I try your code is a list:
>>> type(record)
<class 'Bio.Entrez.Parser.ListElement'>

which contains a dict with the following keys:
>>> record[0].keys()
[u'GBSeq_moltype',
 u'GBSeq_source',
 u'GBSeq_sequence',
 u'GBSeq_primary-accession',
 u'GBSeq_definition',
 u'GBSeq_accession-version',
 u'GBSeq_topology',
 u'GBSeq_length',
 u'GBSeq_feature-table',
 u'GBSeq_create-date',
 u'GBSeq_other-seqids',
 u'GBSeq_division',
 u'GBSeq_taxonomy',
 u'GBSeq_comment',
 u'GBSeq_source-db',
 u'GBSeq_references',
 u'GBSeq_update-date',
 u'GBSeq_organism',
 u'GBSeq_locus']

If you got the same response, then you can just do:
>>> record[0]['GBSeq_locus']
'NP_997807'

I hope this helps.

David

2011/6/6 Sheila the angel <from.d.putto at gmail.com>

> Hi All,
>
> I am new to BioPython. I have simple question 'How can I process XML files
> in Biopython?'
> For example I have NCBI Reference Sequence ID 'NP_997807.1'
> I want to download the 'xml' file and want to extract certain information
> (e.g. GeneID, amino acid length etc.).
> To download the file I did
>
> from Bio import Entrez
> handle = Entrez.efetch(db="protein", id= "NP_997807.1", retmode="xml")
> record = Entrez.read(handle)
> handle.close()
>
> Now I have no clue how to extract certain information (like GeneID) :(
> plz help
>
> --
> Cheers
>
> Sheila d. Angela
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>

From from.d.putto at gmail.com  Mon Jun  6 11:10:04 2011
From: from.d.putto at gmail.com (Sheila the angel)
Date: Mon, 6 Jun 2011 17:10:04 +0200
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTi=p0WEJ_DTk_o-5LmrY=5tJk-u9Vg@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
	<BANLkTi=p0WEJ_DTk_o-5LmrY=5tJk-u9Vg@mail.gmail.com>
Message-ID: <BANLkTi=xNcQKa0MuKAdfK2dOyjLmCBcYcg@mail.gmail.com>

@David- Yes it works but few small question
1. how to extract the information not sored in directly in record[0].keys()
for an example
record[0]['GBSeq_feature-table']
gives output which seems parsed in XML. From this how can I extract the
'GBQualifier_name' ?

2. just out of curiosity  'why we use record[0] to extract information e.g.
record[0]['GBSeq_definition']  '



On Mon, Jun 6, 2011 at 4:37 PM, David Su?rez Pascal
<david.suarez at yahoo.com>wrote:

> Sheila,
> I don't think you have to deal with XML files. Indeed I tried your code and
> what I detected was that Entrez.read already parsed the data.
> What I get when I try your code is a list:
> >>> type(record)
> <class 'Bio.Entrez.Parser.ListElement'>
>
> which contains a dict with the following keys:
> >>> record[0].keys()
> [u'GBSeq_moltype',
>  u'GBSeq_source',
>  u'GBSeq_sequence',
>  u'GBSeq_primary-accession',
>  u'GBSeq_definition',
>  u'GBSeq_accession-version',
>  u'GBSeq_topology',
>  u'GBSeq_length',
>  u'GBSeq_feature-table',
>  u'GBSeq_create-date',
>  u'GBSeq_other-seqids',
>  u'GBSeq_division',
>  u'GBSeq_taxonomy',
>  u'GBSeq_comment',
>  u'GBSeq_source-db',
>  u'GBSeq_references',
>  u'GBSeq_update-date',
>  u'GBSeq_organism',
>  u'GBSeq_locus']
>
> If you got the same response, then you can just do:
> >>> record[0]['GBSeq_locus']
> 'NP_997807'
>
> I hope this helps.
>
> David
>
> 2011/6/6 Sheila the angel <from.d.putto at gmail.com>
>
>> Hi All,
>>
>> I am new to BioPython. I have simple question 'How can I process XML files
>> in Biopython?'
>> For example I have NCBI Reference Sequence ID 'NP_997807.1'
>> I want to download the 'xml' file and want to extract certain information
>> (e.g. GeneID, amino acid length etc.).
>> To download the file I did
>>
>> from Bio import Entrez
>> handle = Entrez.efetch(db="protein", id= "NP_997807.1", retmode="xml")
>> record = Entrez.read(handle)
>> handle.close()
>>
>> Now I have no clue how to extract certain information (like GeneID) :(
>> plz help
>>
>> --
>> Cheers
>>
>> Sheila d. Angela
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>


From p.j.a.cock at googlemail.com  Mon Jun  6 11:16:23 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 16:16:23 +0100
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTi=xNcQKa0MuKAdfK2dOyjLmCBcYcg@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
	<BANLkTi=p0WEJ_DTk_o-5LmrY=5tJk-u9Vg@mail.gmail.com>
	<BANLkTi=xNcQKa0MuKAdfK2dOyjLmCBcYcg@mail.gmail.com>
Message-ID: <BANLkTinLipX-71yTynSRF3+DGytyacoR+Q@mail.gmail.com>

On Mon, Jun 6, 2011 at 4:10 PM, Sheila the angel <from.d.putto at gmail.com> wrote:
> @David- Yes it works but few small question
> 1. how to extract the information not sored in directly in record[0].keys()
> for an example
> record[0]['GBSeq_feature-table']
> gives output which seems parsed in XML. From this how can I extract the
> 'GBQualifier_name' ?
>
> 2. just out of curiosity ?'why we use record[0] to extract information e.g.
> record[0]['GBSeq_definition'] ?'

This is because the parser gave you a list, and we want the first element
(element zero), which was a dictionary, and we picked the key GBSeq_definition
This is what I meant by the Bio.Entrez parser turns the XML into Python
objects (lists and dicts containing strings/numbers). The structure comes
from the XML itself.

As I said, if you know beforehand exactly which XML element you want,
one of the Python standard libraries might be more direct.

Peter


From dilara.ally at gmail.com  Mon Jun  6 12:18:44 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Mon, 06 Jun 2011 09:18:44 -0700
Subject: [Biopython] installation failure on mac OS10.6.7
Message-ID: <4DECFDE4.8040705@gmail.com>

Hi,

I was trying to install Biopython on mac OS 10.6.7.  I checked the 
archives and installed Apple's Xcode ver4.0.2.  But I got this error 
message:


building 'Bio.cpairwise2' extension
gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 
-g -O2 -DNDEBUG -g -O3 -IBio 
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c 
Bio/cpairwise2module.c -o 
build/temp.macosx-10.3-fat-2.6/Bio/cpairwise2module.o
unable to execute gcc-4.0: No such file or directory
error: command 'gcc-4.0' failed with exit status 1

Thanks so much for the help.

Cheers, Dilara

From p.j.a.cock at googlemail.com  Mon Jun  6 12:38:01 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 17:38:01 +0100
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <4DECFDE4.8040705@gmail.com>
References: <4DECFDE4.8040705@gmail.com>
Message-ID: <BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>

On Mon, Jun 6, 2011 at 5:18 PM, Dilara Ally <dilara.ally at gmail.com> wrote:
> Hi,
>
> I was trying to install Biopython on mac OS 10.6.7. ?I checked the archives
> and installed Apple's Xcode ver4.0.2. ?But I got this error message:
>
>
> building 'Bio.cpairwise2' extension
> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g
> -O2 -DNDEBUG -g -O3 -IBio
> -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
> Bio/cpairwise2module.c -o
> build/temp.macosx-10.3-fat-2.6/Bio/cpairwise2module.o
> unable to execute gcc-4.0: No such file or directory
> error: command 'gcc-4.0' failed with exit status 1
>
> Thanks so much for the help.
>
> Cheers, Dilara

That's strange - I have it under /usr/bin/gcc-4.0

When you installed X Code, did you tick the optional 10.4 SDK as recommended
here http://biopython.org/wiki/Download ?


Peter


From dilara.ally at gmail.com  Mon Jun  6 12:46:55 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Mon, 06 Jun 2011 09:46:55 -0700
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
Message-ID: <4DED047F.2090505@gmail.com>

I thought I did.  How can I find out if it has 10.4 SDK?

Thanks.

Dilara

On 6/6/11 9:38 AM, Peter Cock wrote:
> On Mon, Jun 6, 2011 at 5:18 PM, Dilara Ally<dilara.ally at gmail.com>  wrote:
>> Hi,
>>
>> I was trying to install Biopython on mac OS 10.6.7.  I checked the archives
>> and installed Apple's Xcode ver4.0.2.  But I got this error message:
>>
>>
>> building 'Bio.cpairwise2' extension
>> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g
>> -O2 -DNDEBUG -g -O3 -IBio
>> -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
>> Bio/cpairwise2module.c -o
>> build/temp.macosx-10.3-fat-2.6/Bio/cpairwise2module.o
>> unable to execute gcc-4.0: No such file or directory
>> error: command 'gcc-4.0' failed with exit status 1
>>
>> Thanks so much for the help.
>>
>> Cheers, Dilara
> That's strange - I have it under /usr/bin/gcc-4.0
>
> When you installed X Code, did you tick the optional 10.4 SDK as recommended
> here http://biopython.org/wiki/Download ?
>
>
> Peter
>

From ilancaster at gmail.com  Mon Jun  6 12:56:13 2011
From: ilancaster at gmail.com (Ian Lancaster)
Date: Mon, 6 Jun 2011 12:56:13 -0400
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
Message-ID: <5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>

The 10.4 SDK support option was removed in Xcode 4, along with gcc 4.0 support necessary for building numpy and others. Xcode 3 installs Apple's gcc 4.0, but Xcode 4 installs only 4.2. The easiest solution I've found is to start clean by removing Xcode 4, install Xcode 3 (which is free), and then upgrade back to Xcode 4. Then you will have both the required gcc 4.0 and 4.2. 

http://stackoverflow.com/questions/5333490/how-can-we-restore-ppc-ppc64-as-well-as-full-10-4-10-5-sdk-support-to-xcode-4

Ian

Sorry for duplicates, I forgot to cc the list at first.

On Jun 6, 2011, at 12:38 PM, Peter Cock wrote:

> On Mon, Jun 6, 2011 at 5:18 PM, Dilara Ally <dilara.ally at gmail.com> wrote:
>> Hi,
>> 
>> I was trying to install Biopython on mac OS 10.6.7.  I checked the archives
>> and installed Apple's Xcode ver4.0.2.  But I got this error message:
>> 
>> 
>> building 'Bio.cpairwise2' extension
>> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g
>> -O2 -DNDEBUG -g -O3 -IBio
>> -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
>> Bio/cpairwise2module.c -o
>> build/temp.macosx-10.3-fat-2.6/Bio/cpairwise2module.o
>> unable to execute gcc-4.0: No such file or directory
>> error: command 'gcc-4.0' failed with exit status 1
>> 
>> Thanks so much for the help.
>> 
>> Cheers, Dilara
> 
> That's strange - I have it under /usr/bin/gcc-4.0
> 
> When you installed X Code, did you tick the optional 10.4 SDK as recommended
> here http://biopython.org/wiki/Download ?
> 
> 
> Peter
> 
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython



From p.j.a.cock at googlemail.com  Mon Jun  6 12:59:05 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 17:59:05 +0100
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
Message-ID: <BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>

On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> The 10.4 SDK support option was removed in Xcode 4, along with gcc 4.0
> support necessary for building numpy and others. Xcode 3 installs Apple's
> gcc 4.0, but Xcode 4 installs only 4.2. The easiest solution I've found is to
> start clean by removing Xcode 4, install Xcode 3 (which is free), and then
> upgrade back to Xcode 4. Then you will have both the required gcc 4.0 and 4.2.
>
> http://stackoverflow.com/questions/5333490/how-can-we-restore-ppc-ppc64-as-well-as-full-10-4-10-5-sdk-support-to-xcode-4
>
> Ian

Hi Ian,

That's a very interesting link - do you have anything specific on what it is
that numpy (and therefore likely also Biopython) doesn't like?

Thank you,

Peter

From devaniranjan at gmail.com  Mon Jun  6 13:53:51 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Mon, 6 Jun 2011 13:53:51 -0400
Subject: [Biopython] _align in pairwise
Message-ID: <BANLkTik+mh2PCH5TFAD5aYXYnA8smcv_9w@mail.gmail.com>

I want to align one sequence to several multiple sequences using pairwise
alignment --I am trying to use _align but getting stumped by the variables I
need to specify.

Can someone give me some info on that? --Thanks a lot

From p.j.a.cock at googlemail.com  Mon Jun  6 14:01:28 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 19:01:28 +0100
Subject: [Biopython] _align in pairwise
In-Reply-To: <BANLkTik+mh2PCH5TFAD5aYXYnA8smcv_9w@mail.gmail.com>
References: <BANLkTik+mh2PCH5TFAD5aYXYnA8smcv_9w@mail.gmail.com>
Message-ID: <BANLkTinEgOZBjFuciO_2pLwYXLhOPusigA@mail.gmail.com>

On Mon, Jun 6, 2011 at 6:53 PM, George Devaniranjan
<devaniranjan at gmail.com> wrote:
> I want to align one sequence to several multiple sequences using pairwise
> alignment --I am trying to use _align but getting stumped by the variables I
> need to specify.
>
> Can someone give me some info on that? --Thanks a lot

As a general rule, anything in python starting with a single underscore
is a private method/function/variable and should not be used.

Have you looked at the help, either from within Python or here:
http://www.biopython.org/DIST/docs/api/Bio.pairwise2-module.html

Peter

From p.j.a.cock at googlemail.com  Mon Jun  6 14:23:05 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 19:23:05 +0100
Subject: [Biopython] _align in pairwise
In-Reply-To: <BANLkTim4nwoaHYcXphN1k836sUXkOmyN6w@mail.gmail.com>
References: <BANLkTik+mh2PCH5TFAD5aYXYnA8smcv_9w@mail.gmail.com>
	<BANLkTinEgOZBjFuciO_2pLwYXLhOPusigA@mail.gmail.com>
	<BANLkTim4nwoaHYcXphN1k836sUXkOmyN6w@mail.gmail.com>
Message-ID: <BANLkTinsvxAhZxZ1=-kCHVFRHnLG-ExaCQ@mail.gmail.com>

Hi George,

Please try to CC the mailing list in your replies.

On Mon, Jun 6, 2011 at 7:08 PM, George Devaniranjan
<devaniranjan at gmail.com> wrote:
> oh thanks Peter --I am a newbie to python and used to C programming so even
> in python my use of classes is very limited and tend to use simple
> functions.
>
> what I want to do is.......
> I have a file containing 10 FASTA like sequences (actually 1000s but for now
> 10) and I want to calculate the alignment score for the first 1 with the
> other 9 using FASTA like symbols and also use a blossum like matrix to look
> up penalties.
>
> _align looked like a good candidate so I tried to use that--is there another
> way?
>
> Thanks a lot,
> George

Something like this? Check if you want global or local alignments:

http://lists.open-bio.org/pipermail/biopython/2009-January/004855.html

Peter

From ilancaster at gmail.com  Mon Jun  6 15:14:10 2011
From: ilancaster at gmail.com (Ian Lancaster)
Date: Mon, 6 Jun 2011 15:14:10 -0400
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
	<BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
Message-ID: <A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>

After gcc 4.0 the Wno-long-double option was removed, among others, which was apparently used in building python. However, I don't think the problem is with gcc per se, but the version of python. 

For instance, installing numpy with Apple's python2.6 and 2.5 failed on my machine with the gcc 4.2 compiler. Then I installed python2.7 from the official package at python.org; numpy and Biopython installed and tested fine (I used pip). This might be a better solution for Snow Leopard users, particularly those who have only installed Xcode 4. 

Ian

On Jun 6, 2011, at 12:59 PM, Peter Cock wrote:

> On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> 
> Hi Ian,
> 
> That's a very interesting link - do you have anything specific on what it is
> that numpy (and therefore likely also Biopython) doesn't like?
> 
> Thank you,
> 
> Peter



From mictadlo at gmail.com  Mon Jun  6 17:52:21 2011
From: mictadlo at gmail.com (Michal)
Date: Tue, 07 Jun 2011 07:52:21 +1000
Subject: [Biopython] IUPAC code contribution
Message-ID: <4DED4C15.4010705@gmail.com>

Hello,
I would like to contribute the following IUPAC function to Biopython:

def iupac_base(alignment):
     IUPAC = {
       ord('N'): 'N',
       ord('G'): 'G',
       ord('A'): 'A',
       ord('T'): 'T',
       ord('C'): 'C',
       ord('G') + ord('A'): 'R',
       ord('T') + ord('C'): 'Y',
       ord('A') + ord('C'): 'M',
       ord('G') + ord('T'): 'K',
       ord('G') + ord('C'): 'S',
       ord('A') + ord('T'): 'W',
       ord('A') + ord('C') + ord('T'): 'H',
       ord('G') + ord('T') + ord('C'): 'B',
       ord('G') + ord('C') + ord('A'): 'V',
       ord('G') + ord('A') + ord('T'): 'D',
       ord('G') + ord('A') + ord('T') + ord('C'): 'N'}

     return IUPAC[sum(map(ord, {}.fromkeys(alignment).keys()))]


a = iupac_base(['A','A','T','T','T'])

Cheers,
Michal

From mictadlo at gmail.com  Mon Jun  6 17:59:39 2011
From: mictadlo at gmail.com (Michal)
Date: Tue, 07 Jun 2011 07:59:39 +1000
Subject: [Biopython] multiprocessing problem with pysam
In-Reply-To: <20110515155346.GD2530@kunkel>
References: <4DA1137E.1090803@gmail.com> <20110410111510.GA2634@kunkel>
	<4DA2EC9D.7040004@gmail.com> <20110412013119.GF2053@kunkel>
	<4DCF660B.30309@gmail.com> <20110515155346.GD2530@kunkel>
Message-ID: <4DED4DCB.8070605@gmail.com>

On 05/16/2011 01:53 AM, Brad Chapman wrote:
> Michal;
>
> [multiprocessing]
> multiprocessing is sensitive to passing or calling complex class
> objects. My suggestion is to use functions without associated state
> attributes and pass in your information as standard python objects
> (strings, lists, dicts). I use a little decorator to make writing
> the functions passed easier:
>
> import functools
> def map_wrap(f):
>      @functools.wraps(f)
>      def wrapper(*args, **kwargs):
>          return apply(f, *args, **kwargs)
>      return wrapper
>
> Then would write your function as:
>
> @map_wrap
> def run_test(bam_filename, cultivars, ref_name):
>      bam_fh = pysam.Samfile(bam_filename, "rb")
>      print os.getpid(), ref_name, cultivars
>      return (os.getpid(), ref_name)
>
> and call it with:
>
> cultivars = 'Ja,Ea,As'.replace(' ', '').split(',')
> bam_filename = "/media/usb/tests/test.bam"
> bamfile = pysam.Samfile(bam_filename, "rb")
> ref_names = bamfile.references
> bamfile.close()
>
> pool = Pool()
> results = dict(pool.imap(run_test, ((bam_filename, cultivars, ref)
>                                      for ref in ref_names)))
> pool.close()
>
> Hope this helps,
> Brad
Thank you Brad it works and I also found the following solution:

import os
from multiprocessing import Pool
from pprint import pprint
import functools


def calc_p(fname, start_pos, end_pos, reference_name):
     print os.getpid()
     print "fname", fname
     print "reference_name", reference_name
     print "start_pos", start_pos
     print "end_pos", end_pos
     print
     return (reference_name, [os.getpid(), 'x1', 'x2'])


if __name__ == '__main__':
     pool = Pool()

     fname = "ex1.txt"
     references = ['Test1', 'Test2', 'Test3', 'Test4']

     run_test = functools.partial(calc_p, fname, 100, 120)
     result = dict(pool.imap_unordered(run_test, references))

     pprint(result)


Michal

From p.j.a.cock at googlemail.com  Mon Jun  6 18:18:29 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 23:18:29 +0100
Subject: [Biopython] IUPAC code contribution
In-Reply-To: <4DED4C15.4010705@gmail.com>
References: <4DED4C15.4010705@gmail.com>
Message-ID: <BANLkTincLfkH+dbbPP_eWkNJTPDi7JWBQA@mail.gmail.com>

On Mon, Jun 6, 2011 at 10:52 PM, Michal <mictadlo at gmail.com> wrote:
> Hello,
> I would like to contribute the following IUPAC function to Biopython:
>
> def iupac_base(alignment):
> ? ?IUPAC = {
> ? ? ?ord('N'): 'N',
> ? ? ?ord('G'): 'G',
> ? ? ?ord('A'): 'A',
> ? ? ?ord('T'): 'T',
> ? ? ?ord('C'): 'C',
> ? ? ?ord('G') + ord('A'): 'R',
> ? ? ?ord('T') + ord('C'): 'Y',
> ? ? ?ord('A') + ord('C'): 'M',
> ? ? ?ord('G') + ord('T'): 'K',
> ? ? ?ord('G') + ord('C'): 'S',
> ? ? ?ord('A') + ord('T'): 'W',
> ? ? ?ord('A') + ord('C') + ord('T'): 'H',
> ? ? ?ord('G') + ord('T') + ord('C'): 'B',
> ? ? ?ord('G') + ord('C') + ord('A'): 'V',
> ? ? ?ord('G') + ord('A') + ord('T'): 'D',
> ? ? ?ord('G') + ord('A') + ord('T') + ord('C'): 'N'}
>
> ? ?return IUPAC[sum(map(ord, {}.fromkeys(alignment).keys()))]
>
>
> a = iupac_base(['A','A','T','T','T'])
>
> Cheers,
> Michal

Well it would need some documentation at least (e.g. a docstring).
What is is meant to do? It looks like you just want a reverse lookup
of Bio.Data.IUPACData.ambiguous_dna_values - e.g.

from Bio.Data.IUPACData import ambiguous_dna_values
rev_map = dict((frozenset(v),k) for (k,v) in ambiguous_dna_values.iteritems())
assert rev_map[frozenset('CG')] == rev_map[frozenset('GC')]

Peter


From dilara.ally at gmail.com  Mon Jun  6 18:29:15 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Mon, 6 Jun 2011 15:29:15 -0700
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
	<BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
	<A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>
Message-ID: <BANLkTimKRCXUE6aHeZi=gnFe1rWfyv=ysw@mail.gmail.com>

Hi Ian,

I've installed python2.7 and because of an earlier email  I removed Xcode4.0
and installed  Xcode3.0 +10.4 sdk then upgraded to Xcode4.0.  I also changed
the version of numpy and tested to see if I could import it.  There was no
problem importing numpy.

I tried to install biopython by directing entering the directory
biopython-1.57 and typing the command python setup.py install but got this
message:

creating build/lib.macosx-10.6-intel-2.7
error: could not create 'build/lib.macosx-10.6-intel-2.7': Permission denied

Then when I tried the easy install using this command:

sudo easy_install -f http://biopython.org/DIST/ biopython

I got the following error:  Is it still having trouble with the gcc 4.2
compiler

Searching for biopython
Reading http://biopython.org/DIST/
Best match: biopython 1.57
Downloading http://biopython.org/DIST/biopython-1.57.zip
Processing biopython-1.57.zip
Running biopython-1.57/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-8RE8Sh/biopython-1.57/egg-dist-tmp-YMF_hu
warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
warning: no previously-included files found matching 'Tests/Graphics/*.eps'
warning: no previously-included files found matching 'Tests/Graphics/*.svg'
warning: no previously-included files found matching 'Tests/Graphics/*.png'
warning: no previously-included files matching '*' found under directory
'Tests/UnitTests'
warning: no previously-included files matching '.cvsignore' found under
directory '*'
warning: no previously-included files matching '.gitignore' found under
directory '*'
warning: no previously-included files matching '*.pyc' found under directory
'*'
unable to execute gcc-4.2: No such file or directory
error: Setup script exited with error: command 'gcc-4.2' failed with exit
status 1


I'm stumped.

Thanks for the help.

Dilara



On Mon, Jun 6, 2011 at 12:14 PM, Ian Lancaster <ilancaster at gmail.com> wrote:

> After gcc 4.0 the Wno-long-double option was removed, among others, which
> was apparently used in building python. However, I don't think the problem
> is with gcc per se, but the version of python.
>
> For instance, installing numpy with Apple's python2.6 and 2.5 failed on my
> machine with the gcc 4.2 compiler. Then I installed python2.7 from the
> official package at python.org; numpy and Biopython installed and tested
> fine (I used pip). This might be a better solution for Snow Leopard users,
> particularly those who have only installed Xcode 4.
>
> Ian
>
> On Jun 6, 2011, at 12:59 PM, Peter Cock wrote:
>
> > On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster <ilancaster at gmail.com>
> wrote:
> >
> > Hi Ian,
> >
> > That's a very interesting link - do you have anything specific on what it
> is
> > that numpy (and therefore likely also Biopython) doesn't like?
> >
> > Thank you,
> >
> > Peter
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>

From ilancaster at gmail.com  Mon Jun  6 19:10:43 2011
From: ilancaster at gmail.com (Ian Lancaster)
Date: Mon, 6 Jun 2011 19:10:43 -0400
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <BANLkTimKRCXUE6aHeZi=gnFe1rWfyv=ysw@mail.gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
	<BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
	<A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>
	<BANLkTimKRCXUE6aHeZi=gnFe1rWfyv=ysw@mail.gmail.com>
Message-ID: <AD366D51-805F-4A99-B8F1-BF06A12D6B3D@gmail.com>

First of all, make sure everything is in place. Type which gcc-4.2; it should be in /usr/bin. Which easy_install and which python should points to /Library/Frameworks/Python.framework/Versions/2.7/bin if you used the python.org installer. 

You shouldn't have to use sudo to install python packages, unless you are still pointed at the system version of python. I suspect this is the case based on the permissions error. Add the correct python to your path by adding to the end of ~/.bash_profile

	PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"
	export PATH"

When you run python the shell prompt should display the GCC version in the beginning. You can explicitly set the compiler for distutils before running easy_install with the command export CC=gcc-4.2. Then easy_install biopython.

Also, if you are going to be managing more python packages (why not) pip is much better at this than easy_install, and actually supports uninstallation. Easy_install pip, then pip install biopython or whatever. Not necessary, but useful. www.pip-installer.org

Ian

On Jun 6, 2011, at 6:29 PM, Dilara Ally wrote:

> Hi Ian, 
> 
> I've installed python2.7 and because of an earlier email  I removed Xcode4.0 and installed  Xcode3.0 +10.4 sdk then upgraded to Xcode4.0.  I also changed the version of numpy and tested to see if I could import it.  There was no problem importing numpy.
> 
> I tried to install biopython by directing entering the directory biopython-1.57 and typing the command python setup.py install but got this message:
> 
> creating build/lib.macosx-10.6-intel-2.7
> error: could not create 'build/lib.macosx-10.6-intel-2.7': Permission denied
> 
> Then when I tried the easy install using this command:  
> sudo easy_install -f http://biopython.org/DIST/ biopython
> I got the following error:  Is it still having trouble with the gcc 4.2 compiler
> 
> Searching for biopython
> Reading http://biopython.org/DIST/
> Best match: biopython 1.57
> Downloading http://biopython.org/DIST/biopython-1.57.zip
> Processing biopython-1.57.zip
> Running biopython-1.57/setup.py -q bdist_egg --dist-dir /tmp/easy_install-8RE8Sh/biopython-1.57/egg-dist-tmp-YMF_hu
> warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
> warning: no previously-included files found matching 'Tests/Graphics/*.eps'
> warning: no previously-included files found matching 'Tests/Graphics/*.svg'
> warning: no previously-included files found matching 'Tests/Graphics/*.png'
> warning: no previously-included files matching '*' found under directory 'Tests/UnitTests'
> warning: no previously-included files matching '.cvsignore' found under directory '*'
> warning: no previously-included files matching '.gitignore' found under directory '*'
> warning: no previously-included files matching '*.pyc' found under directory '*'
> unable to execute gcc-4.2: No such file or directory
> error: Setup script exited with error: command 'gcc-4.2' failed with exit status 1
> 
> 
> I'm stumped.
> 
> Thanks for the help.
> 
> Dilara
> 
> 
> 
> On Mon, Jun 6, 2011 at 12:14 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> After gcc 4.0 the Wno-long-double option was removed, among others, which was apparently used in building python. However, I don't think the problem is with gcc per se, but the version of python.
> 
> For instance, installing numpy with Apple's python2.6 and 2.5 failed on my machine with the gcc 4.2 compiler. Then I installed python2.7 from the official package at python.org; numpy and Biopython installed and tested fine (I used pip). This might be a better solution for Snow Leopard users, particularly those who have only installed Xcode 4.
> 
> Ian
> 
> On Jun 6, 2011, at 12:59 PM, Peter Cock wrote:
> 
> > On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> >
> > Hi Ian,
> >
> > That's a very interesting link - do you have anything specific on what it is
> > that numpy (and therefore likely also Biopython) doesn't like?
> >
> > Thank you,
> >
> > Peter
> 
> 
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 



From mjldehoon at yahoo.com  Mon Jun  6 22:24:18 2011
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Mon, 6 Jun 2011 19:24:18 -0700 (PDT)
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTikaPRc=34QkHdB5VzHz7k0ynCk=kw@mail.gmail.com>
Message-ID: <449273.3301.qm@web161220.mail.bf1.yahoo.com>

--- On Mon, 6/6/11, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> > And, if that is correct, what is the advantage of
> > using Bio.Entrez.parse
> > over using another Python XML lib?
> 
> If you're not scared of XML, not much.
> 
That is a misconception, to say the least.
Bio.Entrez parses the DTD associated with the XML file, and is therefore able to store the information in the XML file as a Python object in a sensible way. In addition, Bio.Entrez.parse can handle multi-gigabyte XML files (such as the ones from the Entrez Gene database). I'd like to see you do that with another Python XML lib.

--Michiel.

From p.j.a.cock at googlemail.com  Tue Jun  7 03:47:27 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 7 Jun 2011 08:47:27 +0100
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <449273.3301.qm@web161220.mail.bf1.yahoo.com>
References: <BANLkTikaPRc=34QkHdB5VzHz7k0ynCk=kw@mail.gmail.com>
	<449273.3301.qm@web161220.mail.bf1.yahoo.com>
Message-ID: <BANLkTim+rf2N3-wRtrAERpKayL5sbmAppw@mail.gmail.com>

On Tue, Jun 7, 2011 at 3:24 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> --- On Mon, 6/6/11, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> > And, if that is correct, what is the advantage of
>> > using Bio.Entrez.parse
>> > over using another Python XML lib?
>>
>> If you're not scared of XML, not much.
>>
> That is a misconception, to say the least.
> Bio.Entrez parses the DTD associated with the XML file, and
> is therefore able to store the information in the XML file as a
> Python object in a sensible way. In addition, Bio.Entrez.parse
> can handle multi-gigabyte XML files (such as the ones from
> the Entrez Gene database). I'd like to see you do that with
> another Python XML lib.

I was probably being too glib. My point was if you are already
experienced with another Python XML lib, you may find it more
productive to use that. The particular case where you only want
to pull out one or two fields is an interesting one, because here
there is no need to parse all the other data into objects in
memory.

Peter

From devaniranjan at gmail.com  Tue Jun  7 09:39:17 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 7 Jun 2011 09:39:17 -0400
Subject: [Biopython] shuffle sequences
Message-ID: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>

Hello everyone,
I need to 'shuffle' a sequence so that I can calculate the statistical
alignment scores--I tried the random.shuffle opetion but it does not seem to
work

I defined the sequence as a string like the following

w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
random.shuffle(w)


also like this...
my_protein=IUPAC.protein
from Bio.Seq import Seq
myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)

random.shuffle(myseq)

Both don't seem to work--where am I going wrong?

Thanks a lot,
George

From anaryin at gmail.com  Tue Jun  7 10:46:28 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Tue, 7 Jun 2011 16:46:28 +0200
Subject: [Biopython] shuffle sequences
In-Reply-To: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
References: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
Message-ID: <BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>

Hey George,

random.shuffle works on lists or other datatypes that support item
assignment. Therefore, neither a string nor Seq will work. I would extract
the sequence out of Seq and build a new sequence object with that.

Cheers,

Jo?o [...] Rodrigues
http://nmr.chem.uu.nl/~joao



On Tue, Jun 7, 2011 at 3:39 PM, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Hello everyone,
> I need to 'shuffle' a sequence so that I can calculate the statistical
> alignment scores--I tried the random.shuffle opetion but it does not seem
> to
> work
>
> I defined the sequence as a string like the following
>
> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
> random.shuffle(w)
>
>
> also like this...
> my_protein=IUPAC.protein
> from Bio.Seq import Seq
> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>
> random.shuffle(myseq)
>
> Both don't seem to work--where am I going wrong?
>
> Thanks a lot,
> George
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From eric.talevich at gmail.com  Tue Jun  7 10:56:37 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 7 Jun 2011 10:56:37 -0400
Subject: [Biopython] IUPAC code contribution
In-Reply-To: <BANLkTincLfkH+dbbPP_eWkNJTPDi7JWBQA@mail.gmail.com>
References: <4DED4C15.4010705@gmail.com>
	<BANLkTincLfkH+dbbPP_eWkNJTPDi7JWBQA@mail.gmail.com>
Message-ID: <BANLkTinmH1+Y3fTfqKvWXJE6R68xHgh1BA@mail.gmail.com>

On Mon, Jun 6, 2011 at 6:18 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Mon, Jun 6, 2011 at 10:52 PM, Michal <mictadlo at gmail.com> wrote:
> > Hello,
> > I would like to contribute the following IUPAC function to Biopython:
> >
> > def iupac_base(alignment):
> >    IUPAC = {
> >      ord('N'): 'N',
> >      ord('G'): 'G',
> >      ord('A'): 'A',
> >      ord('T'): 'T',
> >      ord('C'): 'C',
> >      ord('G') + ord('A'): 'R',
> >      ord('T') + ord('C'): 'Y',
> >      ord('A') + ord('C'): 'M',
> >      ord('G') + ord('T'): 'K',
> >      ord('G') + ord('C'): 'S',
> >      ord('A') + ord('T'): 'W',
> >      ord('A') + ord('C') + ord('T'): 'H',
> >      ord('G') + ord('T') + ord('C'): 'B',
> >      ord('G') + ord('C') + ord('A'): 'V',
> >      ord('G') + ord('A') + ord('T'): 'D',
> >      ord('G') + ord('A') + ord('T') + ord('C'): 'N'}
> >
> >    return IUPAC[sum(map(ord, {}.fromkeys(alignment).keys()))]
> >
> >
> > a = iupac_base(['A','A','T','T','T'])
> >
> > Cheers,
> > Michal
>
> Well it would need some documentation at least (e.g. a docstring).
> What is is meant to do? It looks like you just want a reverse lookup
> of Bio.Data.IUPACData.ambiguous_dna_values - e.g.
>
> from Bio.Data.IUPACData import ambiguous_dna_values
> rev_map = dict((frozenset(v),k) for (k,v) in
> ambiguous_dna_values.iteritems())
> assert rev_map[frozenset('CG')] == rev_map[frozenset('GC')]
>
>
This is also a good candidate for a Cookbook entry on the Biopython wiki:
http://biopython.org/wiki/Category:Cookbook

Then others can easily comment on it, describe use cases and suggest
alternatives.

-Eric

From devaniranjan at gmail.com  Tue Jun  7 09:55:36 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 7 Jun 2011 09:55:36 -0400
Subject: [Biopython] correction and follow up to previous question
Message-ID: <BANLkTimrJ_em-Si7Zr8gFABu3p+_=7s+1Q@mail.gmail.com>

Sorry guys--It seems to work when I define the seqence as  a LIST

however I have another  doubt......

the top is the original seqence the bottom the shuffled seqence--while some
residues are shuffled, its not "very" shuffled
is this "normal" ?
First time I am doing this so I just wondered......

Thanks once again.
George

From anaryin at gmail.com  Tue Jun  7 11:01:16 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Tue, 7 Jun 2011 17:01:16 +0200
Subject: [Biopython] correction and follow up to previous question
In-Reply-To: <BANLkTimrJ_em-Si7Zr8gFABu3p+_=7s+1Q@mail.gmail.com>
References: <BANLkTimrJ_em-Si7Zr8gFABu3p+_=7s+1Q@mail.gmail.com>
Message-ID: <BANLkTim0Z1vF3LsLWO635rfsxOva_nUCJQ@mail.gmail.com>

Hey George,

>From the Python Docs:

random.shuffle(*x*[, *random*])
>
> Shuffle the sequence *x* in place. The optional argument *random* is a
> 0-argument function returning a random float in [0.0, 1.0); by default, this
> is the function random()<http://docs.python.org/library/random.html#random.random>
> .
>
> Note that for even rather small len(x), the total number of permutations
> of *x* is larger than the period of most random number generators; this
> implies that most permutations of a long sequence can never be generated.
>
This might be the answer to your last question. A more efficient combination
perhaps would be to use random.choice and then append to a list.. perhaps
this leads to better randomized sequences, but I'm talking out of thin air,
not based on experience..

Cheers

Jo?o [...] Rodrigues
http://nmr.chem.uu.nl/~joao



On Tue, Jun 7, 2011 at 3:55 PM, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Sorry guys--It seems to work when I define the seqence as  a LIST
>
> however I have another  doubt......
>
> the top is the original seqence the bottom the shuffled seqence--while some
> residues are shuffled, its not "very" shuffled
> is this "normal" ?
> First time I am doing this so I just wondered......
>
> Thanks once again.
> George
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From devaniranjan at gmail.com  Tue Jun  7 11:01:41 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 7 Jun 2011 11:01:41 -0400
Subject: [Biopython] shuffle sequences
In-Reply-To: <BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>
References: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
	<BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>
Message-ID: <BANLkTim+5jbv3BLsSopNwVoPcKd-u6EcqA@mail.gmail.com>

Hello Jo?o,

Thanks for the answer but I am confused--"new sequence object with that"
so I still need to create a seq object?
I tried this ...
myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)

I was thinking if it would be possible to have FOR loop and loop throught
the entire sequence then shuffle it and then write the shuffled list (going
though it one by one using another FOR loop) to a seq object.

Thank you,
George

On Tue, Jun 7, 2011 at 10:46 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hey George,
>
> random.shuffle works on lists or other datatypes that support item
> assignment. Therefore, neither a string nor Seq will work. I would extract
> the sequence out of Seq and build a new sequence object with that.
>
> Cheers,
>
> Jo?o [...] Rodrigues
> http://nmr.chem.uu.nl/~joao
>
>
>
> On Tue, Jun 7, 2011 at 3:39 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hello everyone,
>> I need to 'shuffle' a sequence so that I can calculate the statistical
>> alignment scores--I tried the random.shuffle opetion but it does not seem
>> to
>> work
>>
>> I defined the sequence as a string like the following
>>
>> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
>> random.shuffle(w)
>>
>>
>> also like this...
>> my_protein=IUPAC.protein
>> from Bio.Seq import Seq
>> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>>
>> random.shuffle(myseq)
>>
>> Both don't seem to work--where am I going wrong?
>>
>> Thanks a lot,
>> George
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>


From idoerg at gmail.com  Tue Jun  7 11:11:05 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Tue, 7 Jun 2011 11:11:05 -0400
Subject: [Biopython] shuffle sequences
In-Reply-To: <BANLkTim+5jbv3BLsSopNwVoPcKd-u6EcqA@mail.gmail.com>
References: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
	<BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>
	<BANLkTim+5jbv3BLsSopNwVoPcKd-u6EcqA@mail.gmail.com>
Message-ID: <BANLkTin5-jX8ia6CsEFC9W0rErc2nja1Cw@mail.gmail.com>

probably a good solution wouls be to convert to  a list and then back to a
string (or a Seq object).

To shuffle w:
w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
wl=list(w)
random.shuffle(wl)
w=''.join(wl)

And with a Seq object:
myseq=Seq('KVFGRCELAAAMKRHGL')
lms = list(myseq)
random.shuffle(lms)
myseq = Seq(''.join(lms))

On Tue, Jun 7, 2011 at 11:01 AM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hello Jo?o,
>
> Thanks for the answer but I am confused--"new sequence object with that"
> so I still need to create a seq object?
> I tried this ...
> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>
> I was thinking if it would be possible to have FOR loop and loop throught
> the entire sequence then shuffle it and then write the shuffled list (going
> though it one by one using another FOR loop) to a seq object.
>
> Thank you,
> George
>
> On Tue, Jun 7, 2011 at 10:46 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:
>
> > Hey George,
> >
> > random.shuffle works on lists or other datatypes that support item
> > assignment. Therefore, neither a string nor Seq will work. I would
> extract
> > the sequence out of Seq and build a new sequence object with that.
> >
> > Cheers,
> >
> > Jo?o [...] Rodrigues
> > http://nmr.chem.uu.nl/~joao
> >
> >
> >
> > On Tue, Jun 7, 2011 at 3:39 PM, George Devaniranjan <
> > devaniranjan at gmail.com> wrote:
> >
> >> Hello everyone,
> >> I need to 'shuffle' a sequence so that I can calculate the statistical
> >> alignment scores--I tried the random.shuffle opetion but it does not
> seem
> >> to
> >> work
> >>
> >> I defined the sequence as a string like the following
> >>
> >> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
> >> random.shuffle(w)
> >>
> >>
> >> also like this...
> >> my_protein=IUPAC.protein
> >> from Bio.Seq import Seq
> >> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
> >>
> >> random.shuffle(myseq)
> >>
> >> Both don't seem to work--where am I going wrong?
> >>
> >> Thanks a lot,
> >> George
> >> _______________________________________________
> >> Biopython mailing list  -  Biopython at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biopython
> >>
> >
> >
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html


From devaniranjan at gmail.com  Tue Jun  7 11:24:43 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 7 Jun 2011 11:24:43 -0400
Subject: [Biopython] shuffle sequences
In-Reply-To: <BANLkTin5-jX8ia6CsEFC9W0rErc2nja1Cw@mail.gmail.com>
References: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
	<BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>
	<BANLkTim+5jbv3BLsSopNwVoPcKd-u6EcqA@mail.gmail.com>
	<BANLkTin5-jX8ia6CsEFC9W0rErc2nja1Cw@mail.gmail.com>
Message-ID: <BANLkTim9T+LSUm4d=m8=Yv2nVmZ69a4ojw@mail.gmail.com>

Thanks Iddo and Jo?o,
I think this works and it seems to shuffle the sequence well to
differentiate between the original and shuffled (very diff scores for
alignment.)

George

On Tue, Jun 7, 2011 at 11:11 AM, Iddo Friedberg <idoerg at gmail.com> wrote:

> probably a good solution wouls be to convert to  a list and then back to a
> string (or a Seq object).
>
> To shuffle w:
> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
> wl=list(w)
> random.shuffle(wl)
> w=''.join(wl)
>
> And with a Seq object:
> myseq=Seq('KVFGRCELAAAMKRHGL')
> lms = list(myseq)
> random.shuffle(lms)
> myseq = Seq(''.join(lms))
>
>
> On Tue, Jun 7, 2011 at 11:01 AM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hello Jo?o,
>>
>> Thanks for the answer but I am confused--"new sequence object with that"
>> so I still need to create a seq object?
>> I tried this ...
>> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>>
>> I was thinking if it would be possible to have FOR loop and loop throught
>> the entire sequence then shuffle it and then write the shuffled list
>> (going
>> though it one by one using another FOR loop) to a seq object.
>>
>> Thank you,
>> George
>>
>> On Tue, Jun 7, 2011 at 10:46 AM, Jo?o Rodrigues <anaryin at gmail.com>
>> wrote:
>>
>> > Hey George,
>> >
>> > random.shuffle works on lists or other datatypes that support item
>> > assignment. Therefore, neither a string nor Seq will work. I would
>> extract
>> > the sequence out of Seq and build a new sequence object with that.
>> >
>> > Cheers,
>> >
>> > Jo?o [...] Rodrigues
>> > http://nmr.chem.uu.nl/~joao
>> >
>> >
>> >
>> > On Tue, Jun 7, 2011 at 3:39 PM, George Devaniranjan <
>> > devaniranjan at gmail.com> wrote:
>> >
>> >> Hello everyone,
>> >> I need to 'shuffle' a sequence so that I can calculate the statistical
>> >> alignment scores--I tried the random.shuffle opetion but it does not
>> seem
>> >> to
>> >> work
>> >>
>> >> I defined the sequence as a string like the following
>> >>
>> >> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
>> >> random.shuffle(w)
>> >>
>> >>
>> >> also like this...
>> >> my_protein=IUPAC.protein
>> >> from Bio.Seq import Seq
>> >> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>> >>
>> >> random.shuffle(myseq)
>> >>
>> >> Both don't seem to work--where am I going wrong?
>> >>
>> >> Thanks a lot,
>> >> George
>> >> _______________________________________________
>> >> Biopython mailing list  -  Biopython at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/biopython
>> >>
>> >
>> >
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>


From eric.talevich at gmail.com  Tue Jun  7 11:25:55 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 7 Jun 2011 11:25:55 -0400
Subject: [Biopython] correction and follow up to previous question
In-Reply-To: <BANLkTim0Z1vF3LsLWO635rfsxOva_nUCJQ@mail.gmail.com>
References: <BANLkTimrJ_em-Si7Zr8gFABu3p+_=7s+1Q@mail.gmail.com>
	<BANLkTim0Z1vF3LsLWO635rfsxOva_nUCJQ@mail.gmail.com>
Message-ID: <BANLkTinS_VakXd_YB=0W=TQd=Yi2PgTd_A@mail.gmail.com>

 On Tue, Jun 7, 2011 at 3:55 PM, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Sorry guys--It seems to work when I define the seqence as  a LIST
>
> however I have another  doubt......
>
> the top is the original seqence the bottom the shuffled seqence--while
some
> residues are shuffled, its not "very" shuffled
> is this "normal" ?

With random.shuffle, all sequence combinations are supposed to be equally
probable. This means a sequence that's similar to the input is possible, as
is a sequence that's very different.

>>> stuff = list('ASDFSDFG')
>>> random.shuffle(stuff)
>>> ''.join(stuff)
'GFSFADDS'
>>> random.shuffle(stuff)
>>> ''.join(stuff)
'FADDSGSF'

In theory, anything is possible.
http://dilbert.com/strips/comic/2001-10-25/


On Tue, Jun 7, 2011 at 11:01 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hey George,
>
> From the Python Docs:
>
> random.shuffle(*x*[, *random*])
> >
> > Shuffle the sequence *x* in place. The optional argument *random* is a
> > 0-argument function returning a random float in [0.0, 1.0); by default,
> this
> > is the function random()<
> http://docs.python.org/library/random.html#random.random>
> > .
> >
> > Note that for even rather small len(x), the total number of permutations
> > of *x* is larger than the period of most random number generators; this
> > implies that most permutations of a long sequence can never be generated.
> >
> This might be the answer to your last question. A more efficient
> combination
> perhaps would be to use random.choice and then append to a list.. perhaps
> this leads to better randomized sequences, but I'm talking out of thin air,
> not based on experience..
>
>
According to the docs, the pseudo-RNG implementation has a cycle of
 2**19937-1. If I'm understanding random.shuffle correctly, a string of
length k has k! permutations. So:

>>> 2**19937-1 < math.factorial(2081)
True
>>> 2**19937-1 < math.factorial(2080)
False

It should work as expected for lists of up to 2080 elements, and after that,
gradually become less purely "random" (but still behave fairly well for most
use cases in biology). So random.shufffle is an acceptable choice for
protein sequences, but not for whole genomes. But for whole genomes you'd
probably want to use a more clever HMM-based model for generating random
sequences, anyway.

Cheers,
Eric


From dilara.ally at gmail.com  Wed Jun  8 13:37:48 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Wed, 08 Jun 2011 10:37:48 -0700
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <AD366D51-805F-4A99-B8F1-BF06A12D6B3D@gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
	<BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
	<A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>
	<BANLkTimKRCXUE6aHeZi=gnFe1rWfyv=ysw@mail.gmail.com>
	<AD366D51-805F-4A99-B8F1-BF06A12D6B3D@gmail.com>
Message-ID: <4DEFB36C.9080002@gmail.com>

thanks a bunch!

On 6/6/11 4:10 PM, Ian Lancaster wrote:
> First of all, make sure everything is in place. Type which gcc-4.2; it should be in /usr/bin. Which easy_install and which python should points to /Library/Frameworks/Python.framework/Versions/2.7/bin if you used the python.org installer.
>
> You shouldn't have to use sudo to install python packages, unless you are still pointed at the system version of python. I suspect this is the case based on the permissions error. Add the correct python to your path by adding to the end of ~/.bash_profile
>
> 	PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"
> 	export PATH"
>
> When you run python the shell prompt should display the GCC version in the beginning. You can explicitly set the compiler for distutils before running easy_install with the command export CC=gcc-4.2. Then easy_install biopython.
>
> Also, if you are going to be managing more python packages (why not) pip is much better at this than easy_install, and actually supports uninstallation. Easy_install pip, then pip install biopython or whatever. Not necessary, but useful. www.pip-installer.org
>
> Ian
>
> On Jun 6, 2011, at 6:29 PM, Dilara Ally wrote:
>
>> Hi Ian,
>>
>> I've installed python2.7 and because of an earlier email  I removed Xcode4.0 and installed  Xcode3.0 +10.4 sdk then upgraded to Xcode4.0.  I also changed the version of numpy and tested to see if I could import it.  There was no problem importing numpy.
>>
>> I tried to install biopython by directing entering the directory biopython-1.57 and typing the command python setup.py install but got this message:
>>
>> creating build/lib.macosx-10.6-intel-2.7
>> error: could not create 'build/lib.macosx-10.6-intel-2.7': Permission denied
>>
>> Then when I tried the easy install using this command:
>> sudo easy_install -f http://biopython.org/DIST/ biopython
>> I got the following error:  Is it still having trouble with the gcc 4.2 compiler
>>
>> Searching for biopython
>> Reading http://biopython.org/DIST/
>> Best match: biopython 1.57
>> Downloading http://biopython.org/DIST/biopython-1.57.zip
>> Processing biopython-1.57.zip
>> Running biopython-1.57/setup.py -q bdist_egg --dist-dir /tmp/easy_install-8RE8Sh/biopython-1.57/egg-dist-tmp-YMF_hu
>> warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
>> warning: no previously-included files found matching 'Tests/Graphics/*.eps'
>> warning: no previously-included files found matching 'Tests/Graphics/*.svg'
>> warning: no previously-included files found matching 'Tests/Graphics/*.png'
>> warning: no previously-included files matching '*' found under directory 'Tests/UnitTests'
>> warning: no previously-included files matching '.cvsignore' found under directory '*'
>> warning: no previously-included files matching '.gitignore' found under directory '*'
>> warning: no previously-included files matching '*.pyc' found under directory '*'
>> unable to execute gcc-4.2: No such file or directory
>> error: Setup script exited with error: command 'gcc-4.2' failed with exit status 1
>>
>>
>> I'm stumped.
>>
>> Thanks for the help.
>>
>> Dilara
>>
>>
>>
>> On Mon, Jun 6, 2011 at 12:14 PM, Ian Lancaster<ilancaster at gmail.com>  wrote:
>> After gcc 4.0 the Wno-long-double option was removed, among others, which was apparently used in building python. However, I don't think the problem is with gcc per se, but the version of python.
>>
>> For instance, installing numpy with Apple's python2.6 and 2.5 failed on my machine with the gcc 4.2 compiler. Then I installed python2.7 from the official package at python.org; numpy and Biopython installed and tested fine (I used pip). This might be a better solution for Snow Leopard users, particularly those who have only installed Xcode 4.
>>
>> Ian
>>
>> On Jun 6, 2011, at 12:59 PM, Peter Cock wrote:
>>
>>> On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster<ilancaster at gmail.com>  wrote:
>>>
>>> Hi Ian,
>>>
>>> That's a very interesting link - do you have anything specific on what it is
>>> that numpy (and therefore likely also Biopython) doesn't like?
>>>
>>> Thank you,
>>>
>>> Peter
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>

From eric.talevich at gmail.com  Fri Jun 10 12:33:00 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Fri, 10 Jun 2011 12:33:00 -0400
Subject: [Biopython] Deprecating and renaming some keyword args in
	Phylo/NewickIO
Message-ID: <BANLkTikD1nbj1GCvTWhbtx3sOQ26uMOYuA@mail.gmail.com>

Folks,

I'd like to rename several optional arguments used for the Newick parser and
writer in Bio.Phylo. The old argument names will be supported in Biopython
1.58, but trigger a deprecation warning, and then be removed in version
1.59.

The changed functions are in Bio.Phylo.NewickIO.

Parser.parse:
  values_are_support  =>  values_are_confidence
(This isn't currently accessible through Phylo.read/parse or
NewickIO.read/parse, but I will enable that in the next release.)

Writer.write:
  support_as_branchlengths  =>  confidence_as_branch_length
  max_support  =>  max_confidence
  branchlengths_only  =>  branch_length_only


Example:

tree = Phylo.read(infile, 'newick', values_are_support=True)
Phylo.write(tree, outfile, 'newick', support_as_branchlengths=True,
max_support=100)

becomes:

tree = Phylo.read(infile, 'newick', values_are_confidence=True)
Phylo.write(tree, outfile, 'newick', confidence_as_branch_length=True,
max_confidence=100)


Why? NewickIO was originally ported from Bio.Nexus.Trees, where tree node
objects have an attribute called 'support', equivalent to clade.confidence.
Since this attribute is called 'confidence' in Bio.Phylo, these original
argument names no longer make sense. Oops. Also, branch_length grew an
underscore in Bio.Phylo.

So, does anyone have a problem with deprecating these arguments in the next
release, and removing them after that?

Thanks,
Eric

From matsen at fhcrc.org  Mon Jun 13 23:08:01 2011
From: matsen at fhcrc.org (Erick Matsen)
Date: Mon, 13 Jun 2011 20:08:01 -0700
Subject: [Biopython] programmer position open in our group (Seattle, WA)
Message-ID: <BANLkTimpGoEZMv8csAqxOEZttsfSVmG5+A@mail.gmail.com>

Hello there Biopython community--


We are looking for another top programmer to join our group. The full
text of the ad is below, or see the online version at
http://matsen.fhcrc.org/programmer-ad.html


Thanks!

Erick

----

Advance biology with the tools you love

Our group at the Fred Hutchinson Cancer Research Center in Seattle is
looking for an experienced programmer to write code and analyze data.
We develop methods for the evolutionary analysis of next-generation
DNA sequence data for HIV research and the study of the human
microbiome (bacteria that live on and inside of us). And we love
coding, especially in OCaml and Python.

Your job will be to develop, deploy, and apply a computational
pipeline for metagenomics annotation using phylogenetics. This will
include:

    A framework to automatically select collections of sequences for
evolutionary comparison using phylogenetic and taxonomic criteria
    Implementation of high performance phylogenetic models
    Implementation of methods to infer gene function and taxonomic
identity from phylogenetic trees
    Application of machine learning techniques to phylogenetic placement data

You will be joining a core group of one group leader and two
programmers, as well as a larger community of programmers and many
biologists. There is a lot of knowledge here, and you will have
support while you are learning the ropes. On the other hand, in order
to succeed at this job you will need to be able to read scientific
papers and work through references to find the necessary background.
Scientific curiosity strictly required.

You will also need some serious coding chops. Your code should be DRY,
well documented, and robust. Long-time linux hacker a big plus.

If you are not already aware, biology is a tremendously exciting area
right now, and this is an opportunity to work at the forefront. The
work environment will be dynamic, and we are always looking for better
ways to do our work. On the other hand we?re serious about helping
biologists with their data and sometimes that just means turning the
crank on data analysis. All finalized code will be open source, and
you will be required to feed as much code as possible into Biopython
or other relevant projects.

Fred Hutchinson Cancer Research Center, home of about 190 faculty
including three Nobel laureates, is an independent, nonprofit research
institution dedicated to the development and advancement of biomedical
research. The environment is lively yet casual, with a strong emphasis
on collaborative work. The center has great benefits and a lovely
campus next to Lake Union within walking distance from downtown.
Powerful computing resources and a helpful IT staff await you.

Although the FHCRC is a large facility, this will be much more like an
informal startup-style job. You?ll be expected to come into work for
design discussions, but other than that your schedule will be your
own, as long as those commits keep coming. Competitive salary, which
will scale according to your level of experience.

You can find out more about our work by visiting:

    http://matsen.fhcrc.org/
    http://github.com/matsen
    http://github.com/fhcrc

Requirements

    BS in a relevant field or at least four years relevant work experience
    a high level of linux proficiency (at least three years)
    top-notch programming skills, with at least a year of Python experience
    experience using a VCS, preferably git
    SQL experience a plus
    the ability to work independently with a long-range goal in mind
    interest in bioinformatics

How to apply

Please send a CV and significant code sample, preferably in Python, to
Nerreda Chavez at nchavez at fhcrc.org. The code should be DRY, well
documented, and show that you can use some non-trivial features of
your chosen language.

-- 
Frederick "Erick" Matsen, Assistant Member
Fred Hutchinson Cancer Research Center
http://matsen.fhcrc.org/


From b.invergo at gmail.com  Tue Jun 14 09:15:52 2011
From: b.invergo at gmail.com (Brandon Invergo)
Date: Tue, 14 Jun 2011 15:15:52 +0200
Subject: [Biopython] introducing PAML for Biopython
Message-ID: <BANLkTi=nVuwk87yAsmGs2T+z=DU64O17qA@mail.gmail.com>

Hi everyone,

I have written a Python interface to the PAML (Phylogenetic Analysis
by Maximum Likelihood) package of programs by Ziheng Yang which is in
the process of being added to Biopython. In advance of adding it, it
would be great if some people would be willing to take it for a
test-drive to make sure things are working the way you would like them
to, that it's useful, that it's not buggy, etc. For the moment, it can
be had as a branch of Biopython here:
https://github.com/brandoninvergo/biopython/tree/paml-branch
(If you click Downloads you can download the source code as a .tar.gz file)

The PAML interface is located in Bio.Phylo.PAML and includes the
following modules: codeml, baseml, yn00 and chi2. I have not written
implementations of the evolver or mcmctree programs from the package.
Evolver requires menu interaction from the user, so it can't be
scripted easily. As for mcmctree, I will profess complete ignorance in
how people use the program, so I was not sure of the best way to
implement it (particularly in parsing the results). If you use
mcmctree and you would like me to implement an interface to it, feel
free to contact me and we can discuss it.


If you're interested in using the library, I have not yet written
documentation, however usage would be something like this (codeml,
baseml, and yn00 all function similarly):

> from Bio.Phylo.PAML import codeml
> cml = codeml.Codeml()
> cml.alignment = "path/to/alignment"  #can use either relative or absolute paths; they all get converted to relative paths to avoid the path-length limits imposed in PAML
> cml.tree = "path/to/tree"
> cml.working_dir = "path/to/working_directory"
> cml.out_file = "path/to/output_file"
#or, alternatively:
> cml = codeml.Codeml(alignment="path/to/alignment", tree="path/to/tree", working_dir="path/to/working_dir", out_file="path/to/out_file")

# view all options
> cml.print_options()

# read in an existing control file
> cml.read_ctl_file("path/to/control_file")

# set an option
> cml.set_option("clock", 1)
> cml.set_option("NSsites", [0,1,2])
> cml.set_option("aaRatefile", None)

# get an option value
> cml.get_option("clock")

# write all options to a control file (this is done automatically when
you do the run() method, so you probably won't have to do this)
> cml.ctl_file = "path/to/ctl_file"
> cml.write_ctl_file()


# run the program, which returns the results in dict format
> results = cml.run()

# or, to see all of codeml's output to the screen
> results = cml.run(verbose=True)

# or, to specify the location of the executable (ie if it's not in
your path or if you use multiple versions of it)
> results = cml.run(command = "path/to/codeml")

# or, to skip parsing the results
> cml.run(parse = False)

# parse an existing results file
> results = codeml.read("path/to/results_file")



The results are stored in a giant dictionary. I will have to describe
all the contents in the documentation but for now I would recommend
just exploring it to see what's there. For each program, I tried to
parse out as much as possible, on the assumption that I don't know
what *you* need to know from the output file. So, the results dict
probably contains far more than anyone needs. Still, if you find that
you need something that has not been parsed, please let me know and
I'll try to implement it  (I have not parsed Naive Emperical Bayes or
Bayes Empirical Bayes results, for example, or the various codon usage
statistics in the beginning of the file).
nssites = results.get("NSsites")
m0 = nssites.get(0)
m0_maxlnl = m0.get("max lnL")
etc...

I do recommend using the results.get(key) method rather than
results[key] because if codeml encounters an error, the keys won't be
added to the results dictionary and results[key] will raise an
exception.

At the moment, the chi2 program in PAML doesn't properly take
command-line arguments so it's not easily scriptable. Since using PAML
programs calls for a lot of likelihood ratio testing, I went ahead and
reimplemented it in pure Python from the original C code (with
permission). In most cases, it works fine however I have found that if
you have many degrees of freedom, such as in the case of the FMutSel
model testing (41 df), it takes an unacceptably long time to compute.
I've been told that the next version of PAML will include a chi2 which
takes both the test statistic and the d.f. as command line arguments,
so I'll be able to just write an interface to it.

Ok, I think that sums it up for now. I hope that you find this to be
useful! Please let me know if you have any problems, suggestions,
bugs, etc., especially in the parsing!

Thanks!
Brandon Invergo

From from.d.putto at gmail.com  Thu Jun 16 07:43:06 2011
From: from.d.putto at gmail.com (Sheila the angel)
Date: Thu, 16 Jun 2011 13:43:06 +0200
Subject: [Biopython] processing genbank file
Message-ID: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>

Hi to all,
>From a genbank file I want to extract certain information. Here is my code

#---------------------------------------------------------------------------------------------------------
from Bio import SeqIO
handle = open('NP_954888.1.gb', "rU")
for gb_record in SeqIO.parse(handle, 'gb'):
 for gb_feature in gb_record.features:
if gb_feature.type == 'CDS':
 gene=gb_feature.qualifiers['gene'][0]
                 db_xref=gb_feature.qualifiers['db_xref']
                                print gene, db_xref

print gb_record.annotations['organism']

#====================================================

Is there any simple way to print information like gene name, GeneID etc. or
I have to use this loop method :( for an example to print organism name I
need to do only gb_record.annotations['organism'] while to print 'gene' id I
need the for loop !!!!
Another problem is the db_xref=gb_feature.qualifiers['db_xref'] gives me
all /db_xref entries in CDS field while I want only /db_xref="GeneID:309165"
(or only the GeneID)...how to do that

Thanks in Advance

--
Cheers
Sheila

From p.j.a.cock at googlemail.com  Thu Jun 16 07:52:02 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 Jun 2011 12:52:02 +0100
Subject: [Biopython] processing genbank file
In-Reply-To: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>
References: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>
Message-ID: <BANLkTinQe8+_PW6bC37Qgt-tLRGCe5bS+Q@mail.gmail.com>

On Thu, Jun 16, 2011 at 12:43 PM, Sheila the angel
<from.d.putto at gmail.com> wrote:
> Hi to all,
> >From a genbank file I want to extract certain information. Here is my code
>
> #---------------------------------------------------------------------------------------------------------
> from Bio import SeqIO
> handle = open('NP_954888.1.gb', "rU")
> for gb_record in SeqIO.parse(handle, 'gb'):

If you've only got one record in the file, you can get rid of one loop:

gb_record = SeqIO.read('NP_954888.1.gb', 'gb')

Since there will in generally be many features in a GenBank file,
you do need this loop to look at each potential gene:

> ?for gb_feature in gb_record.features:
> if gb_feature.type == 'CDS':
> ?gene=gb_feature.qualifiers['gene'][0]
> ? ? ? ? ? ? ? ? db_xref=gb_feature.qualifiers['db_xref']

Note in the above not all CDS features will have a gene or db_xref
qualifier - you may get a KeyError exception with some files.

> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?print gene, db_xref
>
> print gb_record.annotations['organism']
>
> #====================================================
>
> Is there any simple way to print information like gene name, GeneID etc. or
> I have to use this loop method :( for an example to print organism name I
> need to do only gb_record.annotations['organism'] while to print 'gene' id I
> need the for loop !!!!

You will need some loops in general: One single GenBank file can hold
multiple records, each of which can hold multiple features, each of which
can have multiple names and database cross-references.

> Another problem is the db_xref=gb_feature.qualifiers['db_xref'] gives me
> all /db_xref entries in CDS field while I want only /db_xref="GeneID:309165"
> (or only the GeneID)...how to do that
>
> Thanks in Advance

Since you can get multiple /db_xref (or other qualifiers), when the parser
was designed a list was used for the values. You could filter on what the
entries start with, e.g. db_xref.startswith("GeneID:")

Peter


From from.d.putto at gmail.com  Thu Jun 16 08:28:34 2011
From: from.d.putto at gmail.com (Sheila the angel)
Date: Thu, 16 Jun 2011 14:28:34 +0200
Subject: [Biopython] processing genbank file
In-Reply-To: <BANLkTinQe8+_PW6bC37Qgt-tLRGCe5bS+Q@mail.gmail.com>
References: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>
	<BANLkTinQe8+_PW6bC37Qgt-tLRGCe5bS+Q@mail.gmail.com>
Message-ID: <BANLkTikozeKazjZJdFJi-bFizMijt-cLyA@mail.gmail.com>

So if I have only one file which contains only 1 record (say 'NP_954888.1.gb'
) and I want to extract information like  'gene' name I can't do it in one
line e.g.
#------------------------------------------------------------------------------
gene=gb_record.features['CDS'].qualifiers['gene'][0]     #or
something similar to this will not work
#-----------------------------------------------------------------------------

But I have to use loop as
#-----------------------------------------------------------------------------
gb_record = SeqIO.read('NP_954888.1.gb', 'gb')
for gb_feature in gb_record.features:
      if gb_feature.type == 'CDS':
      gene=gb_feature.qualifiers['gene'][0]
      print gene
#-----------------------------------------------------------------------------

?????


On Thu, Jun 16, 2011 at 1:52 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Jun 16, 2011 at 12:43 PM, Sheila the angel
> <from.d.putto at gmail.com> wrote:
> > Hi to all,
> > >From a genbank file I want to extract certain information. Here is my
> code
> >
> >
> #---------------------------------------------------------------------------------------------------------
> > from Bio import SeqIO
> > handle = open('NP_954888.1.gb', "rU")
> > for gb_record in SeqIO.parse(handle, 'gb'):
>
> If you've only got one record in the file, you can get rid of one loop:
>
> gb_record = SeqIO.read('NP_954888.1.gb', 'gb')
>
> Since there will in generally be many features in a GenBank file,
> you do need this loop to look at each potential gene:
>
> >  for gb_feature in gb_record.features:
> > if gb_feature.type == 'CDS':
> >  gene=gb_feature.qualifiers['gene'][0]
> >                 db_xref=gb_feature.qualifiers['db_xref']
>
> Note in the above not all CDS features will have a gene or db_xref
> qualifier - you may get a KeyError exception with some files.
>
> >                                print gene, db_xref
> >
> > print gb_record.annotations['organism']
> >
> > #====================================================
> >
> > Is there any simple way to print information like gene name, GeneID etc.
> or
> > I have to use this loop method :( for an example to print organism name I
> > need to do only gb_record.annotations['organism'] while to print 'gene'
> id I
> > need the for loop !!!!
>
> You will need some loops in general: One single GenBank file can hold
> multiple records, each of which can hold multiple features, each of which
> can have multiple names and database cross-references.
>
> > Another problem is the db_xref=gb_feature.qualifiers['db_xref'] gives me
> > all /db_xref entries in CDS field while I want only
> /db_xref="GeneID:309165"
> > (or only the GeneID)...how to do that
> >
> > Thanks in Advance
>
> Since you can get multiple /db_xref (or other qualifiers), when the parser
> was designed a list was used for the values. You could filter on what the
> entries start with, e.g. db_xref.startswith("GeneID:")
>
> Peter
>

From p.j.a.cock at googlemail.com  Thu Jun 16 09:24:02 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 Jun 2011 14:24:02 +0100
Subject: [Biopython] processing genbank file
In-Reply-To: <BANLkTikozeKazjZJdFJi-bFizMijt-cLyA@mail.gmail.com>
References: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>
	<BANLkTinQe8+_PW6bC37Qgt-tLRGCe5bS+Q@mail.gmail.com>
	<BANLkTikozeKazjZJdFJi-bFizMijt-cLyA@mail.gmail.com>
Message-ID: <BANLkTinHhokSZOF3c+L80MfBr7S+egEUQg@mail.gmail.com>

On Thu, Jun 16, 2011 at 1:28 PM, Sheila the angel
<from.d.putto at gmail.com> wrote:
> So if I have only one file which contains only 1 record (say
> 'NP_954888.1.gb' ) and I want to extract?information like
>??'gene' name I can't do it in one line e.g.
> #------------------------------------------------------------------------------
> gene=gb_record.features['CDS'].qualifiers['gene'][0] ? ? #or
> something?similar?to this will not work

Supposing there was a neat built in way to filter the features by type,
in general there would still be multiple CDS features - often 1000s,
so you'd need to choose from them.

> #-----------------------------------------------------------------------------
> But I have to use loop as
> #-----------------------------------------------------------------------------
> gb_record = SeqIO.read('NP_954888.1.gb', 'gb')
> for gb_feature in gb_record.features:
> ? ? ? if gb_feature.type == 'CDS':
> ? ? ? gene=gb_feature.qualifiers['gene'][0]
> ? ? ? print gene
> #-----------------------------------------------------------------------------
> ?????

I've checked your example NP_954888 and it is actually a GenPept
file (a protein GenBank file), and it does have just one CDS feature.

Do you prefer this syntax?

gb_record = SeqIO.read('NP_954888.1.gb', 'gb')
cds_features = [f for f in gb_record.features if f.type=="CDS"]
assert len(cds_features)==1
print cds_features[0].qualifiers['gene'][0]

Peter


From bjorn_johansson at bio.uminho.pt  Mon Jun 20 02:36:14 2011
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Mon, 20 Jun 2011 07:36:14 +0100
Subject: [Biopython] common substrings
Message-ID: <BANLkTi=Np0bXa-qPVpNwJcnF196Sycb36Q@mail.gmail.com>

Hi,

I am interested in finding perfect substrings between two sequences that are
longer than a certain specified cut off value. I would like to return the
positions in each sequence and the substring.

The code below is a working implementation that is based on dynamic
programming. I would like to have a faster implementation if possible. I
wonder if someone has a comment on the implementation, if there are better
ways to do it or shortcuts that can be made. In the code below, every
character is compared in both strings. I don't think there is anything like
this in biopython? The pairwise2 comes close, but seems overkill for this
purpose?

Most code and examples I find by google is about the longest common
substring problem, which is slightly different from this.

Thanks for any feedback,
Bjorn


def CommonSubstrings(S1, S2, limit=30):

    M = [[0]*(len(S2)) for i in xrange(len(S1))]

    matches=[]

    for x in xrange(1,len(S1)):
        for y in xrange(1,len(S2)):

            upperleftcell = M[x-1][y-1]

            if S1[x-1] == S2[y-1]:
                M[x][y] = upperleftcell + 1
            else:
                M[x][y] = 0
                if upperleftcell>limit:
                    matches.append((x-1-upperleftcell,y-1-upperleftcell,
upperleftcell))

    for x in xrange(1,len(S1)):
        if M[x][len(S2)-1]>limit:

matches.append(((x-M[x][len(S2)-1]),len(S2)-1-M[x][len(S2)-1],M[x][len(S2)-1]))
            #print M[x][len(S2)-1]

    for y in xrange(1,len(S2)):
        if M[len(S1)-1][y]>limit:

matches.append((len(S1)-1-M[len(S1)-1][y],y-M[len(S1)-1][y]-1,M[len(S1)-1][y]))
            #print M[len(S1)-1][y]

    return matches

x='''TTCTAGAACTAGTGGATCCCCCGGGCTGCAGATGAGTGAAGGCCCCGTCAAATTCGAAAAAAATACCGTCATATCTGTCTTTGGTGCGTCAGGTGATCTGGCAAAGAAGAAGACTTTTCCCGCCTTATTTGGGCTTTTCAGAGAAGGTTACCTTGATCCATCTACCAAGATCTTCGGTTATGCCCGGTCCAAATTGTCCATGGAGGAGGACCTGAAGTCCCGTGTCCTACCCCACTTGAAAAAACCTCACGGTGAAGCCGATGACTCTAAGGTCGAACAGTTCTTCAAGATGGTCAGCTACATTTCGGGAAATTACGACACAGATGAAGGCTTCGACGAATTAAGAACGCAGATCGAGAAATTCGAGAAAAGTGCCAACGTCGATGTCCCACACCGTCTCTTCTATCTGGCCTTGCCGCCAAGCGTTTTTTTGACGGTGGCCAAGCAGATCAAGAGTCGTGTGTACGCAGAGAATGGCATCACCCGTGTAATCGTAGAGAAACCTTTCGGCCACGACCTGGCCTCTGCCAGGGAGCTGCAAAAAAACCTGGGGCCCCTCTTTAAAGAAGAAGAGTTGTACAGAATTGACCATTACTTGGGTAAAGAGTTGGTCAAGAATCTTTTAGTCTTGAGGTTCGGTAACCAGTTTTTGAATGCCTCGTGGAATAGAGACAACATTCAAAGCGTTCAGATTTCGTTTAAAGAGAGGTTCGGCACCGAAGGCCGTGGCGGCTATTTCGACTCTATAGGCATAATCAGAGACGTGATGCAGAACCATCTGTTACAAATCATGACTCTCTTGACTATGGAAAGACCGGTGTCTTTTGACCCGGAATCTATTCGTGACGAAAAGGTTAAGGTTCTAAAGGCCGTGGCCCCCATCGACACGGACGACGTCCTCTTGGGCCAGTACGGTAAATCTGAGGACGGGTCTAAGCCCGCCTACGTGGATGATGACACTGTAGACAAGGACTCTAAATGTGTCACTTTTGCAGCAATGACTTTCAACATCGAAAACGAGCGTTGGGAGGGCGTCCCCATCATGATGCGTGCCGGTAAGGCTTTGAATGAGTCCAAGGTGGAGATCAGACTGCAGTACAAAGCGGTCGCATCGGGTGTCTTCAAAGACATTCCAAATAACGAACTGGTCATCAGAGTGCAGCCCGATGCCGCTGTGTACCTAAAGTTTAATGCTAAGACCCCTGGTCTGTCAAATGCTACCCAAGTCACAGATCTGAATCTAACTTACGCAAGCAGGTACCAAGACTTTTGGATTCCAGAGGCTTACGAGGTGTTGATAAGAGACGCCCTACTGGGTGACCATTCCAACTTTGTCAGAGATGACGAATTGGATATCAGTTGGGGCATATTCACCCCATTACTGAAGCACATAGAGCGTCCGGACGGTCCAACACCGGAAATTTACCCCTACGGATCAAGAGGTCCAAAGGGATTGAAGGAATATATGCAAAAACACAAGTATGTTATGCCCGAAAAGCACCCTTACGCTTGGCCCGTGACTAAGCCAGAAGATACGAAGGATAATTAGCTGCAGGAATTCGATATCAAGCTTATCGATA'''

y='''GACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGTATGATCCAATATCAAAGGAAATGATAGCATTGAAGGATGAGACTAATCCAATTGAGGAGTGGCAGCATATAGAACAGCTAAAGGGTAGTGCTGAAGGAAGCATACGATACCCCGCATGGAATGGGATAATATCACAGGAGGTACTAGACTACCTTTCATCCTACATAAATAGACGCATATAAGTACGCATTTAAGCATAAACACGCACTATGCCGTTCTTCTCATGTATATATATATACAGGCAACACGCAGATATAGGTGCGACGTGAACAGTGAGCTGTATGTGCGCAGCTCGCGTTGCATTTTCGGAAGCGCTCGTTTTCGGAAACGCTTTGAAGTTCCTATTCCGAAGTTCCTATTCTCTAGAAAGTATAGGAACTTCAGAGCGCTTTTGAAAACCAAAAGCGCTCTGAAGACGCACTTTCAAAAAACCAAAAACGCACCGGACTGTAACGAGCTACTAAAATATTGCGAATACCGCTTCCACAAACATTGCTCAAAAGTATCTCTTTGCTATATATCTCTGTGCTATATCCCTATATAACCTACCCATCCACCTTTCGCTCCTTGAACTTGCATCTAAACTCGACCTCTACATTTTTTATGTTTATCTCTAGTATTACTCTTTAGACAAAAAAATTGTAGTAAGAACTATTCATAGAGTGAATCGAAAACAATACGAAAATGTAAACATTTCCTATACGTAGTATATAGAGACAAAATAGAAGAAACCGTTCATAATTTTCTGACCAATGAAGAATCATCAACGCTATCACTTTCTGTTCACAAAGTATGCGCAATCCACATCGGTATAGAATATAATCGGGGATGCCTTTATCTTGAAAAAATGCACCCGCAGCTTCGCTAGTAATCAGTAAACGCGGGAAGTGGAGTCAGGCTTTTTTTATGGAAGAGAAAATAGACACCAAAGTAGCCTTCTTCTAACCTTAACGGACCTACAGTGCAAAAAGTTATCAAGAGACTGCATTATAGAGCGCACAAAGGAGAAAAAAAGTAATCTAAGATGCTTTGTTAGAAAAATAGCGCTCTCGGGATGCATTTTTGTAGAACAAAAAAGAAGTATAGATTCTTTGTTGGTAAAATAGCGCTCTCGCGTTGCATTTCTGTTCTGTAAAAATGCAGCTCAGATTCTTTGTTTGAAAAATTAGCGCTCTCGCGTTGCATTTTTGTTTTACAAAAATGAAGCACAGATTCTTCGTTGGTAAAATAGCGCTTTCGCGTTGCATTTCTGTTCTGTAAAAATGCAGCTCAGATTCTTTGTTTGAAAAATTAGCGCTCTCGCGTTGCATTTTTGTTCTACAAAATGAAGCACAGATGCTTCGTTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTACCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCCTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGAGCTCAGTTTATCATTATCAATACTCGCCATTTCAAAGAATACGTAAATAATTAATAGTAGTGATTTTCCTAACTTTATTTAGTCAAAAAATTAGCCTTTTAATTCTGCTGTAACCCGTACATGCCCAAAATAGGGGGCGGGTTACACAGAATATATAACATCGTAGGTGTCTGGGTGAACAGTTTATTCCTGGCATCCACTAAATATAATGGAGCCCGCTTTTTAAGCTGGCATCCAGAAAAAAAAAGAATCCCAGCACCAAAATATTGTTTTCTTCACCAACCATCAGTTCATAGGTCCATTCTCTTAGCGCAACTACAGAGAACAGGGGCACAAACAGGCAAAAAACGGGCACAACCTCAATGGAGTGATGCAACCTGCCTGGAGTAAATGATGACACAAGGCAATTGACCCACGCATGTATCTATCTCATTTTCTTACACCTTCTATTACCTTCTGCTCTCTCTGATTTGGAAAAAGCTGAAAAAAAAGGTTGAAACCAGTTCCCTGAAATTATTCCCCTACTTGACTAATAAGTATATAAAGACGGTAGGTATTGATTGTAATTCTGTAAATCTATTTCTTAAACTTCTTAAATTCTACTTTTATAGTTAGTCTTTTTTTTAGTTTTAAAACACCAGAACTTAGTTTCGACGGATTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGATATCAAGCTTATCGATACCGTCGACCTCGAGTCATGTAATTAGTTATGTCACGCTTACATTCACGCCCTCCCCCCACATCCGCTCTAACCGAAAAGGAAGGAGTTAGACAACCTGAAGTCTAGGTCCCTATTTATTTTTTTATAGTTATGTTAGTATTAAGAACGTTATTTATATTTCAAATTTTTCTTTTTTTTCTGTACAGACGCGTGTACGCATGTAACATTATACTGAAAACCTTGCTTGAGAAGGTTTTGGGACGCTCGAAGGCTTTAATTTGCGGCCGGTACCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCGACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAACGCGAATTTTAACAAAATATTAACGTTTACAATTTCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATCGACGGTCGAGGAGAACTTCTAGTATATCCACATACCTAATATTATTGCCTTATTAAAAATGGAATCCCAACAATTACATCAAAATCCACATTCTCTTCAAAATCAATTGTCCTGTACTTCCTTGTTCATGTGTGTTCAAAAACGTTATATTTATAGGATAATTATACTCTATTTCTCAACAAGTAATTGGTTGTTTGGCCGAGCGGTCTAAGGCGCCTGATTCAAGAAATATCTTGACCGCAGTTAACTGTGGGAATACTCAGGTATCGTAAGATGCAAGAGTTCGAATCTCTTAGCAACCATTATTTTTTTCCTCAACATAACGAGAACACACAGGGGCGCTATCGCACAGAATCAAATTCGATGACTGGAAATTTTTTGTTAATTTCAGAGGTCGCCTGACGCATATACCTTTTTCAACTGAAAAATTGGGAGAAAAAGGAAAGGTGAGAGGCCGGAACCGGCTTTTCATATAGAATAGAGAAGCGTTCATGACTAAATGCTTGCATCACAATACTTGAAGTTGACAATATTATTTAAGGACCTATTGTTTTTTCCAATAGGTGGTTAGCAATCGTCTTACTTTCTAACTTTTCTTACCTTTTACATTTCAGCAATATATATATATATTTCAAGGATATACCATTCTAATGTCTGCCCCTATGTCTGCCCCTAAGAAGATCGTCGTTTTGCCAGGTGACCACGTTGGTCAAGAAATCACAGCCGAAGCCATTAAGGTTCTTAAAGCTATTTCTGATGTTCGTTCCAATGTCAAGTTCGATTTCGAAAATCATTTAATTGGTGGTGCTGCTATCGATGCTACAGGTGTCCCACTTCCAGATGAGGCGCTGGAAGCCTCCAAGAAGGTTGATGCCGTTTTGTTAGGTGCTGTGGCTGGTCCTAAATGGGGTACCGGTAGTGTTAGACCTGAACAAGGTTTACTAAAAATCCGTAAAGAACTTCAATTGTACGCCAACTTAAGACCATGTAACTTTGCATCCGACTCTCTTTTAGACTTATCTCCAATCAAGCCACAATTTGCTAAAGGTACTGACTTCGTTGTTGTCAGAGAATTAGTGGGAGGTATTTACTTTGGTAAGAGAAAGGAAGACGATGGTGATGGTGTCGCTTGGGATAGTGAACAATACACCGTTCCAGAAGTGCAAAGAATCACAAGAATGGCCGCTTTCATGGCCCTACAACATGAGCCACCATTGCCTATTTGGTCCTTGGATAAAGCTAATCTTTTGGCCTCTTCAAGATTATGGAGAAAAACTGTGGAGGAAACCATCAAGAACGAATTCCCTACATTGAAGGTTCAACATCAATTGATTGATTCTGCCGCCATGATCCTAGTTAAGAACCCAACCCACCTAAATGGTATTATAATCACCAGCAACATGTTTGGTGATATCATCTCCGATGAAGCCTCCGTTATCCCAGGTTCCTTGGGTTTGTTGCCATCTGCGTCCTTGGCCTCTTTGCCAGACAAGAACACCGCATTTGGTTTGTACGAACCATGCCACGGTTCTGCTCCAGATTTGCCAAAGAATAAGGTTGACCCTATCGCCACTATCTTGTCTGCTGCAATGATGTTGAAATTGTCATTGAACTTGCCTGAAGAAGGTAAGGCCATTGAAGATGCAGTTAAAAAGGTTTTGGATGCAGGTATCAGAACTGGTGATTTAGGTGGTTCCAACAGTACCACCGAAGTCGGTGATGCTGTCGCCGAAGAAGTTAAGAAAATCCTTGCTTAAAAAGATTCTCTTTTTTTATGATATTTGTACATAAACTTTATAAATGAAATTCATAATAGAAACGACACGAAATTACAAAATGGAATATGTTCATAGGGTAGACGAAACTATATACGCAATCTACATACATTTATCAAGAAGGAGAAAAAGGAGGATAGTAAAGGAATACAGGTAAGCAAATTGATACTAATGGCTCAACGTGATAAGGAAAAAGAATTGCACTTTAACATTAATATTGACAAGGAGGAGGGCACCACACAAAAAGTTAGGTGTAACAGAAAATCATGAAACTACGATTCCTAATTTGATATTGGAGGATTTTCTCTAAAAAAAAAAAAATACAACAAATAAAAAACACTCAATGACCTGACCATTTGATGGAGTTTAAGTCAATACCTTCTTGAAGCATTTCCCATAATGGTGAAAGTTCCCTCAAGAATTTTACTCTGTCAGAAACGGCCTTACGACGTAGTCGATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGTTAAGCCAGCCCCGACACCCGCCAACACCCGCTGACGCGCCCTGACGGGCTTGTCTGCTCCCGGCATCCGCTTACAGACAAGCTGTGACCGTCTCCGGGAGCTGCATGTGTCAGAGGTTTTCACCGTCATCACCGAAACGCGCGA'''

c = CommonSubstrings(x,y)

"def CommonSubstrings(S1, S2, limit=30):

    M = [[0]*(len(S2)) for i in xrange(len(S1))]

    matches=[]

    for x in xrange(1,len(S1)):
        for y in xrange(1,len(S2)):

            upperleftcell = M[x-1][y-1]

            if S1[x-1] == S2[y-1]:
                M[x][y] = upperleftcell + 1
            else:
                M[x][y] = 0
                if upperleftcell>limit:
                    matches.append((x-1-upperleftcell,y-1-upperleftcell,
upperleftcell))

    for x in xrange(1,len(S1)):
        if M[x][len(S2)-1]>limit:

matches.append(((x-M[x][len(S2)-1]),len(S2)-1-M[x][len(S2)-1],M[x][len(S2)-1]))
            #print M[x][len(S2)-1]

    for y in xrange(1,len(S2)):
        if M[len(S1)-1][y]>limit:

matches.append((len(S1)-1-M[len(S1)-1][y],y-M[len(S1)-1][y]-1,M[len(S1)-1][y]))
            #print M[len(S1)-1][y]

    return matches

x='''TTCTAGAACTAGTGGATCCCCCGGGCTGCAGATGAGTGAAGGCCCCGTCAAATTCGAAAAAAATACCGTCATATCTGTCTTTGGTGCGTCAGGTGATCTGGCAAAGAAGAAGACTTTTCCCGCCTTATTTGGGCTTTTCAGAGAAGGTTACCTTGATCCATCTACCAAGATCTTCGGTTATGCCCGGTCCAAATTGTCCATGGAGGAGGACCTGAAGTCCCGTGTCCTACCCCACTTGAAAAAACCTCACGGTGAAGCCGATGACTCTAAGGTCGAACAGTTCTTCAAGATGGTCAGCTACATTTCGGGAAATTACGACACAGATGAAGGCTTCGACGAATTAAGAACGCAGATCGAGAAATTCGAGAAAAGTGCCAACGTCGATGTCCCACACCGTCTCTTCTATCTGGCCTTGCCGCCAAGCGTTTTTTTGACGGTGGCCAAGCAGATCAAGAGTCGTGTGTACGCAGAGAATGGCATCACCCGTGTAATCGTAGAGAAACCTTTCGGCCACGACCTGGCCTCTGCCAGGGAGCTGCAAAAAAACCTGGGGCCCCTCTTTAAAGAAGAAGAGTTGTACAGAATTGACCATTACTTGGGTAAAGAGTTGGTCAAGAATCTTTTAGTCTTGAGGTTCGGTAACCAGTTTTTGAATGCCTCGTGGAATAGAGACAACATTCAAAGCGTTCAGATTTCGTTTAAAGAGAGGTTCGGCACCGAAGGCCGTGGCGGCTATTTCGACTCTATAGGCATAATCAGAGACGTGATGCAGAACCATCTGTTACAAATCATGACTCTCTTGACTATGGAAAGACCGGTGTCTTTTGACCCGGAATCTATTCGTGACGAAAAGGTTAAGGTTCTAAAGGCCGTGGCCCCCATCGACACGGACGACGTCCTCTTGGGCCAGTACGGTAAATCTGAGGACGGGTCTAAGCCCGCCTACGTGGATGATGACACTGTAGACAAGGACTCTAAATGTGTCACTTTTGCAGCAATGACTTTCAACATCGAAAACGAGCGTTGGGAGGGCGTCCCCATCATGATGCGTGCCGGTAAGGCTTTGAATGAGTCCAAGGTGGAGATCAGACTGCAGTACAAAGCGGTCGCATCGGGTGTCTTCAAAGACATTCCAAATAACGAACTGGTCATCAGAGTGCAGCCCGATGCCGCTGTGTACCTAAAGTTTAATGCTAAGACCCCTGGTCTGTCAAATGCTACCCAAGTCACAGATCTGAATCTAACTTACGCAAGCAGGTACCAAGACTTTTGGATTCCAGAGGCTTACGAGGTGTTGATAAGAGACGCCCTACTGGGTGACCATTCCAACTTTGTCAGAGATGACGAATTGGATATCAGTTGGGGCATATTCACCCCATTACTGAAGCACATAGAGCGTCCGGACGGTCCAACACCGGAAATTTACCCCTACGGATCAAGAGGTCCAAAGGGATTGAAGGAATATATGCAAAAACACAAGTATGTTATGCCCGAAAAGCACCCTTACGCTTGGCCCGTGACTAAGCCAGAAGATACGAAGGATAATTAGCTGCAGGAATTCGATATCAAGCTTATCGATA'''

y='''GACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGTATGATCCAATATCAAAGGAAATGATAGCATTGAAGGATGAGACTAATCCAATTGAGGAGTGGCAGCATATAGAACAGCTAAAGGGTAGTGCTGAAGGAAGCATACGATACCCCGCATGGAATGGGATAATATCACAGGAGGTACTAGACTACCTTTCATCCTACATAAATAGACGCATATAAGTACGCATTTAAGCATAAACACGCACTATGCCGTTCTTCTCATGTATATATATATACAGGCAACACGCAGATATAGGTGCGACGTGAACAGTGAGCTGTATGTGCGCAGCTCGCGTTGCATTTTCGGAAGCGCTCGTTTTCGGAAACGCTTTGAAGTTCCTATTCCGAAGTTCCTATTCTCTAGAAAGTATAGGAACTTCAGAGCGCTTTTGAAAACCAAAAGCGCTCTGAAGACGCACTTTCAAAAAACCAAAAACGCACCGGACTGTAACGAGCTACTAAAATATTGCGAATACCGCTTCCACAAACATTGCTCAAAAGTATCTCTTTGCTATATATCTCTGTGCTATATCCCTATATAACCTACCCATCCACCTTTCGCTCCTTGAACTTGCATCTAAACTCGACCTCTACATTTTTTATGTTTATCTCTAGTATTACTCTTTAGACAAAAAAATTGTAGTAAGAACTATTCATAGAGTGAATCGAAAACAATACGAAAATGTAAACATTTCCTATACGTAGTATATAGAGACAAAATAGAAGAAACCGTTCATAATTTTCTGACCAATGAAGAATCATCAACGCTATCACTTTCTGTTCACAAAGTATGCGCAATCCACATCGGTATAGAATATAATCGGGGATGCCTTTATCTTGAAAAAATGCACCCGCAGCTTCGCTAGTAATCAGTAAACGCGGGAAGTGGAGTCAGGCTTTTTTTATGGAAGAGAAAATAGACACCAAAGTAGCCTTCTTCTAACCTTAACGGACCTACAGTGCAAAAAGTTATCAAGAGACTGCATTATAGAGCGCACAAAGGAGAAAAAAAGTAATCTAAGATGCTTTGTTAGAAAAATAGCGCTCTCGGGATGCATTTTTGTAGAACAAAAAAGAAGTATAGATTCTTTGTTGGTAAAATAGCGCTCTCGCGTTGCATTTCTGTTCTGTAAAAATGCAGCTCAGATTCTTTGTTTGAAAAATTAGCGCTCTCGCGTTGCATTTTTGTTTTACAAAAATGAAGCACAGATTCTTCGTTGGTAAAATAGCGCTTTCGCGTTGCATTTCTGTTCTGTAAAAATGCAGCTCAGATTCTTTGTTTGAAAAATTAGCGCTCTCGCGTTGCATTTTTGTTCTACAAAATGAAGCACAGATGCTTCGTTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTACCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCCTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGAGCTCAGTTTATCATTATCAATACTCGCCATTTCAAAGAATACGTAAATAATTAATAGTAGTGATTTTCCTAACTTTATTTAGTCAAAAAATTAGCCTTTTAATTCTGCTGTAACCCGTACATGCCCAAAATAGGGGGCGGGTTACACAGAATATATAACATCGTAGGTGTCTGGGTGAACAGTTTATTCCTGGCATCCACTAAATATAATGGAGCCCGCTTTTTAAGCTGGCATCCAGAAAAAAAAAGAATCCCAGCACCAAAATATTGTTTTCTTCACCAACCATCAGTTCATAGGTCCATTCTCTTAGCGCAACTACAGAGAACAGGGGCACAAACAGGCAAAAAACGGGCACAACCTCAATGGAGTGATGCAACCTGCCTGGAGTAAATGATGACACAAGGCAATTGACCCACGCATGTATCTATCTCATTTTCTTACACCTTCTATTACCTTCTGCTCTCTCTGATTTGGAAAAAGCTGAAAAAAAAGGTTGAAACCAGTTCCCTGAAATTATTCCCCTACTTGACTAATAAGTATATAAAGACGGTAGGTATTGATTGTAATTCTGTAAATCTATTTCTTAAACTTCTTAAATTCTACTTTTATAGTTAGTCTTTTTTTTAGTTTTAAAACACCAGAACTTAGTTTCGACGGATTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGATATCAAGCTTATCGATACCGTCGACCTCGAGTCATGTAATTAGTTATGTCACGCTTACATTCACGCCCTCCCCCCACATCCGCTCTAACCGAAAAGGAAGGAGTTAGACAACCTGAAGTCTAGGTCCCTATTTATTTTTTTATAGTTATGTTAGTATTAAGAACGTTATTTATATTTCAAATTTTTCTTTTTTTTCTGTACAGACGCGTGTACGCATGTAACATTATACTGAAAACCTTGCTTGAGAAGGTTTTGGGACGCTCGAAGGCTTTAATTTGCGGCCGGTACCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCGACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAACGCGAATTTTAACAAAATATTAACGTTTACAATTTCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATCGACGGTCGAGGAGAACTTCTAGTATATCCACATACCTAATATTATTGCCTTATTAAAAATGGAATCCCAACAATTACATCAAAATCCACATTCTCTTCAAAATCAATTGTCCTGTACTTCCTTGTTCATGTGTGTTCAAAAACGTTATATTTATAGGATAATTATACTCTATTTCTCAACAAGTAATTGGTTGTTTGGCCGAGCGGTCTAAGGCGCCTGATTCAAGAAATATCTTGACCGCAGTTAACTGTGGGAATACTCAGGTATCGTAAGATGCAAGAGTTCGAATCTCTTAGCAACCATTATTTTTTTCCTCAACATAACGAGAACACACAGGGGCGCTATCGCACAGAATCAAATTCGATGACTGGAAATTTTTTGTTAATTTCAGAGGTCGCCTGACGCATATACCTTTTTCAACTGAAAAATTGGGAGAAAAAGGAAAGGTGAGAGGCCGGAACCGGCTTTTCATATAGAATAGAGAAGCGTTCATGACTAAATGCTTGCATCACAATACTTGAAGTTGACAATATTATTTAAGGACCTATTGTTTTTTCCAATAGGTGGTTAGCAATCGTCTTACTTTCTAACTTTTCTTACCTTTTACATTTCAGCAATATATATATATATTTCAAGGATATACCATTCTAATGTCTGCCCCTATGTCTGCCCCTAAGAAGATCGTCGTTTTGCCAGGTGACCACGTTGGTCAAGAAATCACAGCCGAAGCCATTAAGGTTCTTAAAGCTATTTCTGATGTTCGTTCCAATGTCAAGTTCGATTTCGAAAATCATTTAATTGGTGGTGCTGCTATCGATGCTACAGGTGTCCCACTTCCAGATGAGGCGCTGGAAGCCTCCAAGAAGGTTGATGCCGTTTTGTTAGGTGCTGTGGCTGGTCCTAAATGGGGTACCGGTAGTGTTAGACCTGAACAAGGTTTACTAAAAATCCGTAAAGAACTTCAATTGTACGCCAACTTAAGACCATGTAACTTTGCATCCGACTCTCTTTTAGACTTATCTCCAATCAAGCCACAATTTGCTAAAGGTACTGACTTCGTTGTTGTCAGAGAATTAGTGGGAGGTATTTACTTTGGTAAGAGAAAGGAAGACGATGGTGATGGTGTCGCTTGGGATAGTGAACAATACACCGTTCCAGAAGTGCAAAGAATCACAAGAATGGCCGCTTTCATGGCCCTACAACATGAGCCACCATTGCCTATTTGGTCCTTGGATAAAGCTAATCTTTTGGCCTCTTCAAGATTATGGAGAAAAACTGTGGAGGAAACCATCAAGAACGAATTCCCTACATTGAAGGTTCAACATCAATTGATTGATTCTGCCGCCATGATCCTAGTTAAGAACCCAACCCACCTAAATGGTATTATAATCACCAGCAACATGTTTGGTGATATCATCTCCGATGAAGCCTCCGTTATCCCAGGTTCCTTGGGTTTGTTGCCATCTGCGTCCTTGGCCTCTTTGCCAGACAAGAACACCGCATTTGGTTTGTACGAACCATGCCACGGTTCTGCTCCAGATTTGCCAAAGAATAAGGTTGACCCTATCGCCACTATCTTGTCTGCTGCAATGATGTTGAAATTGTCATTGAACTTGCCTGAAGAAGGTAAGGCCATTGAAGATGCAGTTAAAAAGGTTTTGGATGCAGGTATCAGAACTGGTGATTTAGGTGGTTCCAACAGTACCACCGAAGTCGGTGATGCTGTCGCCGAAGAAGTTAAGAAAATCCTTGCTTAAAAAGATTCTCTTTTTTTATGATATTTGTACATAAACTTTATAAATGAAATTCATAATAGAAACGACACGAAATTACAAAATGGAATATGTTCATAGGGTAGACGAAACTATATACGCAATCTACATACATTTATCAAGAAGGAGAAAAAGGAGGATAGTAAAGGAATACAGGTAAGCAAATTGATACTAATGGCTCAACGTGATAAGGAAAAAGAATTGCACTTTAACATTAATATTGACAAGGAGGAGGGCACCACACAAAAAGTTAGGTGTAACAGAAAATCATGAAACTACGATTCCTAATTTGATATTGGAGGATTTTCTCTAAAAAAAAAAAAATACAACAAATAAAAAACACTCAATGACCTGACCATTTGATGGAGTTTAAGTCAATACCTTCTTGAAGCATTTCCCATAATGGTGAAAGTTCCCTCAAGAATTTTACTCTGTCAGAAACGGCCTTACGACGTAGTCGATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGTTAAGCCAGCCCCGACACCCGCCAACACCCGCTGACGCGCCCTGACGGGCTTGTCTGCTCCCGGCATCCGCTTACAGACAAGCTGTGACCGTCTCCGGGAGCTGCATGTGTCAGAGGTTTTCACCGTCATCACCGAAACGCGCGA'''

c = CommonSubstrings(x,y)

#print x
#print y

for a in c:
    print a[0],a[0]+a[2],x[a[0]:a[0]+a[2]]
    print a[1],a[1]+a[2],y[a[1]:a[1]+a[2]]print x
print y

for a in c:
    print a[0],a[0]+a[2],x[a[0]:a[0]+a[2]]
    print a[1],a[1]+a[2],y[a[1]:a[1]+a[2]]


From devaniranjan at gmail.com  Mon Jun 20 16:35:24 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Mon, 20 Jun 2011 16:35:24 -0400
Subject: [Biopython] ClastalW and creating own log odd table
Message-ID: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>

I want to try set up a log-odds matrix for my own and was experimenting with
the BIOPYTHON TUTURIOL


import os
from Bio import Clustalw
from Bio.Clustalw import MultipleAlignCL
cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
cline.set_output('test.aln')

alignment =Clustalw.do_alignment(cline)


The output was as follows..........

sh: clustalw: command not found
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
line 134, in do_alignment
    raise IOError("Output .aln file %s not produced, commandline: %s"
IOError: Output .aln file test.aln not produced, commandline: clustalw
./sequence.fasta -OUTFILE=test.aln


I am not sure where I am going wrong.
Thank you,
George

From idoerg at gmail.com  Mon Jun 20 16:43:56 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Mon, 20 Jun 2011 16:43:56 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
Message-ID: <BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>

George,

It seems like wither you do no have clustalw installed, or it is not
installed in your normal path. Clustalw is a 3rd party program,
unaffiliated with biopython. To download and install, go here:
http://www.clustal.org/

Iddo



On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> I want to try set up a log-odds matrix for my own and was experimenting
> with
> the BIOPYTHON TUTURIOL
>
>
> import os
> from Bio import Clustalw
> from Bio.Clustalw import MultipleAlignCL
> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
> cline.set_output('test.aln')
>
> alignment =Clustalw.do_alignment(cline)
>
>
> The output was as follows..........
>
> sh: clustalw: command not found
> Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
> line 134, in do_alignment
>    raise IOError("Output .aln file %s not produced, commandline: %s"
> IOError: Output .aln file test.aln not produced, commandline: clustalw
> ./sequence.fasta -OUTFILE=test.aln
>
>
> I am not sure where I am going wrong.
> Thank you,
> George
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html

From devaniranjan at gmail.com  Mon Jun 20 16:49:37 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Mon, 20 Jun 2011 16:49:37 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
	<BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
Message-ID: <BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>

Hi Iddo,

Thank you but when I do

from Bio import Clustalw

It does not raise an error, and under
Python2.4/Site-Packages/Bio/
There is a folder called ClustalW

So does it mean there is something extra to be installed than the above
which already exist?

Thank you,
George


On Mon, Jun 20, 2011 at 4:43 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> George,
>
> It seems like wither you do no have clustalw installed, or it is not
> installed in your normal path. Clustalw is a 3rd party program,
> unaffiliated with biopython. To download and install, go here:
> http://www.clustal.org/
>
> Iddo
>
>
>
> On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> I want to try set up a log-odds matrix for my own and was experimenting
>> with
>> the BIOPYTHON TUTURIOL
>>
>>
>> import os
>> from Bio import Clustalw
>> from Bio.Clustalw import MultipleAlignCL
>> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
>> cline.set_output('test.aln')
>>
>> alignment =Clustalw.do_alignment(cline)
>>
>>
>> The output was as follows..........
>>
>> sh: clustalw: command not found
>> Traceback (most recent call last):
>>  File "<stdin>", line 1, in ?
>>  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
>> line 134, in do_alignment
>>    raise IOError("Output .aln file %s not produced, commandline: %s"
>> IOError: Output .aln file test.aln not produced, commandline: clustalw
>> ./sequence.fasta -OUTFILE=test.aln
>>
>>
>> I am not sure where I am going wrong.
>> Thank you,
>> George
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>

From idoerg at gmail.com  Mon Jun 20 17:05:13 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Mon, 20 Jun 2011 17:05:13 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
	<BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
	<BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>
Message-ID: <BANLkTikV_Lce0zPYJCiXh=5kHQn0oEuvFA@mail.gmail.com>

Clustalw is a 3rd party package, it is not part of Biopython.

What you are importing via Python is not clustalw, but rather the Biopython
interface to clustalw.

./I


On Mon, Jun 20, 2011 at 4:49 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi Iddo,
>
> Thank you but when I do
>
> from Bio import Clustalw
>
> It does not raise an error, and under
> Python2.4/Site-Packages/Bio/
> There is a folder called ClustalW
>
> So does it mean there is something extra to be installed than the above
> which already exist?
>
> Thank you,
> George
>
>
>
> On Mon, Jun 20, 2011 at 4:43 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>
>> George,
>>
>> It seems like wither you do no have clustalw installed, or it is not
>> installed in your normal path. Clustalw is a 3rd party program,
>> unaffiliated with biopython. To download and install, go here:
>> http://www.clustal.org/
>>
>> Iddo
>>
>>
>>
>> On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <
>> devaniranjan at gmail.com> wrote:
>>
>>> I want to try set up a log-odds matrix for my own and was experimenting
>>> with
>>> the BIOPYTHON TUTURIOL
>>>
>>>
>>> import os
>>> from Bio import Clustalw
>>> from Bio.Clustalw import MultipleAlignCL
>>> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
>>> cline.set_output('test.aln')
>>>
>>> alignment =Clustalw.do_alignment(cline)
>>>
>>>
>>> The output was as follows..........
>>>
>>> sh: clustalw: command not found
>>> Traceback (most recent call last):
>>>  File "<stdin>", line 1, in ?
>>>  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
>>> line 134, in do_alignment
>>>    raise IOError("Output .aln file %s not produced, commandline: %s"
>>> IOError: Output .aln file test.aln not produced, commandline: clustalw
>>> ./sequence.fasta -OUTFILE=test.aln
>>>
>>>
>>> I am not sure where I am going wrong.
>>> Thank you,
>>> George
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>
>>
>>
>>
>> --
>> Iddo Friedberg
>> http://iddo-friedberg.net/contact.html
>>
>
>


-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html

From devaniranjan at gmail.com  Mon Jun 20 17:14:18 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Mon, 20 Jun 2011 17:14:18 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTikV_Lce0zPYJCiXh=5kHQn0oEuvFA@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
	<BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
	<BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>
	<BANLkTikV_Lce0zPYJCiXh=5kHQn0oEuvFA@mail.gmail.com>
Message-ID: <BANLkTinyNMzx8arv9vwqav19doy1KCL7kA@mail.gmail.com>

Thank you Iddo,
Could I also ask if I should install ClustalW within the
python2.4/site-packages
or somewhere else?
Thank you for your answers,
George


On Mon, Jun 20, 2011 at 5:05 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> Clustalw is a 3rd party package, it is not part of Biopython.
>
> What you are importing via Python is not clustalw, but rather the Biopython
> interface to clustalw.
>
> ./I
>
>
> On Mon, Jun 20, 2011 at 4:49 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hi Iddo,
>>
>> Thank you but when I do
>>
>> from Bio import Clustalw
>>
>> It does not raise an error, and under
>> Python2.4/Site-Packages/Bio/
>> There is a folder called ClustalW
>>
>> So does it mean there is something extra to be installed than the above
>> which already exist?
>>
>> Thank you,
>> George
>>
>>
>>
>> On Mon, Jun 20, 2011 at 4:43 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>>
>>> George,
>>>
>>> It seems like wither you do no have clustalw installed, or it is not
>>> installed in your normal path. Clustalw is a 3rd party program,
>>> unaffiliated with biopython. To download and install, go here:
>>> http://www.clustal.org/
>>>
>>> Iddo
>>>
>>>
>>>
>>> On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <
>>> devaniranjan at gmail.com> wrote:
>>>
>>>> I want to try set up a log-odds matrix for my own and was experimenting
>>>> with
>>>> the BIOPYTHON TUTURIOL
>>>>
>>>>
>>>> import os
>>>> from Bio import Clustalw
>>>> from Bio.Clustalw import MultipleAlignCL
>>>> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
>>>> cline.set_output('test.aln')
>>>>
>>>> alignment =Clustalw.do_alignment(cline)
>>>>
>>>>
>>>> The output was as follows..........
>>>>
>>>> sh: clustalw: command not found
>>>> Traceback (most recent call last):
>>>>  File "<stdin>", line 1, in ?
>>>>  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
>>>> line 134, in do_alignment
>>>>    raise IOError("Output .aln file %s not produced, commandline: %s"
>>>> IOError: Output .aln file test.aln not produced, commandline: clustalw
>>>> ./sequence.fasta -OUTFILE=test.aln
>>>>
>>>>
>>>> I am not sure where I am going wrong.
>>>> Thank you,
>>>> George
>>>> _______________________________________________
>>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>>
>>>
>>>
>>>
>>> --
>>> Iddo Friedberg
>>> http://iddo-friedberg.net/contact.html
>>>
>>
>>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>

From idoerg at gmail.com  Mon Jun 20 17:29:34 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Mon, 20 Jun 2011 17:29:34 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTinyNMzx8arv9vwqav19doy1KCL7kA@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
	<BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
	<BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>
	<BANLkTikV_Lce0zPYJCiXh=5kHQn0oEuvFA@mail.gmail.com>
	<BANLkTinyNMzx8arv9vwqav19doy1KCL7kA@mail.gmail.com>
Message-ID: <BANLkTikN+AGytu=Ke0TE6mrVSf6XUXaVnA@mail.gmail.com>

For installation instrucitons go here:

http://www.clustal.org/

This varies with your operating system.

On Mon, Jun 20, 2011 at 5:14 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Thank you Iddo,
> Could I also ask if I should install ClustalW within the
> python2.4/site-packages
> or somewhere else?
> Thank you for your answers,
> George
>
>
>
> On Mon, Jun 20, 2011 at 5:05 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>
>> Clustalw is a 3rd party package, it is not part of Biopython.
>>
>> What you are importing via Python is not clustalw, but rather the
>> Biopython interface to clustalw.
>>
>> ./I
>>
>>
>> On Mon, Jun 20, 2011 at 4:49 PM, George Devaniranjan <
>> devaniranjan at gmail.com> wrote:
>>
>>> Hi Iddo,
>>>
>>> Thank you but when I do
>>>
>>> from Bio import Clustalw
>>>
>>> It does not raise an error, and under
>>> Python2.4/Site-Packages/Bio/
>>> There is a folder called ClustalW
>>>
>>> So does it mean there is something extra to be installed than the above
>>> which already exist?
>>>
>>> Thank you,
>>> George
>>>
>>>
>>>
>>> On Mon, Jun 20, 2011 at 4:43 PM, Iddo Friedberg <idoerg at gmail.com>wrote:
>>>
>>>> George,
>>>>
>>>> It seems like wither you do no have clustalw installed, or it is not
>>>> installed in your normal path. Clustalw is a 3rd party program,
>>>> unaffiliated with biopython. To download and install, go here:
>>>> http://www.clustal.org/
>>>>
>>>> Iddo
>>>>
>>>>
>>>>
>>>> On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <
>>>> devaniranjan at gmail.com> wrote:
>>>>
>>>>> I want to try set up a log-odds matrix for my own and was experimenting
>>>>> with
>>>>> the BIOPYTHON TUTURIOL
>>>>>
>>>>>
>>>>> import os
>>>>> from Bio import Clustalw
>>>>> from Bio.Clustalw import MultipleAlignCL
>>>>> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
>>>>> cline.set_output('test.aln')
>>>>>
>>>>> alignment =Clustalw.do_alignment(cline)
>>>>>
>>>>>
>>>>> The output was as follows..........
>>>>>
>>>>> sh: clustalw: command not found
>>>>> Traceback (most recent call last):
>>>>>  File "<stdin>", line 1, in ?
>>>>>  File
>>>>> "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
>>>>> line 134, in do_alignment
>>>>>    raise IOError("Output .aln file %s not produced, commandline: %s"
>>>>> IOError: Output .aln file test.aln not produced, commandline: clustalw
>>>>> ./sequence.fasta -OUTFILE=test.aln
>>>>>
>>>>>
>>>>> I am not sure where I am going wrong.
>>>>> Thank you,
>>>>> George
>>>>> _______________________________________________
>>>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Iddo Friedberg
>>>> http://iddo-friedberg.net/contact.html
>>>>
>>>
>>>
>>
>>
>> --
>> Iddo Friedberg
>> http://iddo-friedberg.net/contact.html
>>
>
>


-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html

From ssphatak at mdanderson.org  Mon Jun 20 18:25:15 2011
From: ssphatak at mdanderson.org (Sharangdhar Phatak)
Date: Mon, 20 Jun 2011 17:25:15 -0500
Subject: [Biopython] pubmed import
Message-ID: <1308608715.29480.34.camel@KVJ>

Hi, 
 I would like to download pubmed abstracts by using limits based on
publication dates. Can someone please provide a couple of pointers on
how to do so?

Regards,
Sharang


From devaniranjan at gmail.com  Tue Jun 21 14:01:31 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 21 Jun 2011 14:01:31 -0400
Subject: [Biopython] BLOCKS BLOSUM
Message-ID: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>

Hi,
This might not be the correct place to ask this question-but some of you may
have experience in this.
I went to the BLOCKS database and downloaded a text file that contains many
BLOCKS but I would like to see the structure of these blocks either in
VMD/Pymol
Is there a way to find the PDB ID of these blocks?

What I want is to use the same BLOCKS info and develop my own BLOSUM like
matrix using biopyhton.
Thank you and my apologies is this is not directly related to biopython.
(example of a block from the downloaded text file is given below)
George

NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN

From idoerg at gmail.com  Tue Jun 21 14:36:46 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Tue, 21 Jun 2011 14:36:46 -0400
Subject: [Biopython] BLOCKS BLOSUM
In-Reply-To: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
References: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
Message-ID: <BANLkTi=hu7FzXhZzxPwsHC1D7yG7i_J9rg@mail.gmail.com>

Go here:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc232

On Tue, Jun 21, 2011 at 2:01 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi,
> This might not be the correct place to ask this question-but some of you
> may
> have experience in this.
> I went to the BLOCKS database and downloaded a text file that contains many
> BLOCKS but I would like to see the structure of these blocks either in
> VMD/Pymol
> Is there a way to find the PDB ID of these blocks?
>
> What I want is to use the same BLOCKS info and develop my own BLOSUM like
> matrix using biopyhton.
> Thank you and my apologies is this is not directly related to biopython.
> (example of a block from the downloaded text file is given below)
> George
>
> NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
> NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
> NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
> NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
> NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
> NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html

From devaniranjan at gmail.com  Tue Jun 21 14:45:34 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 21 Jun 2011 14:45:34 -0400
Subject: [Biopython] BLOCKS BLOSUM
In-Reply-To: <BANLkTi=hu7FzXhZzxPwsHC1D7yG7i_J9rg@mail.gmail.com>
References: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
	<BANLkTi=hu7FzXhZzxPwsHC1D7yG7i_J9rg@mail.gmail.com>
Message-ID: <BANLkTinrbnEcZEZfKF9RgD9MaZ1P_fX11g@mail.gmail.com>

Hi Iddo,
I actaully want to see the fragments being used for the BLOCK in pymol or
VMD but as you can see below
(Is it a alpha helix or a beta sheet..etc)
NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN

I cant find the PDB ID these fragments came from.
The actual calcualtion of the matrix I think I can do.
Thank you,
George






On Tue, Jun 21, 2011 at 2:36 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> Go here:
>
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc232
>
> On Tue, Jun 21, 2011 at 2:01 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hi,
>> This might not be the correct place to ask this question-but some of you
>> may
>> have experience in this.
>> I went to the BLOCKS database and downloaded a text file that contains
>> many
>> BLOCKS but I would like to see the structure of these blocks either in
>> VMD/Pymol
>> Is there a way to find the PDB ID of these blocks?
>>
>> What I want is to use the same BLOCKS info and develop my own BLOSUM like
>> matrix using biopyhton.
>> Thank you and my apologies is this is not directly related to biopython.
>> (example of a block from the downloaded text file is given below)
>> George
>>
>> NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
>> NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
>> NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
>> NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
>> NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
>> NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
>> NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
>> NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
>> NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
>> NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
>> NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
>> NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
>> NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
>> NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>

From Aisling.ODriscoll at cit.ie  Tue Jun 21 16:07:07 2011
From: Aisling.ODriscoll at cit.ie (Aisling ODriscoll)
Date: Tue, 21 Jun 2011 21:07:07 +0100
Subject: [Biopython] Teaching BioPython
Message-ID: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>

Hi everyone,
 
I have been asked to deliver BioPython classes to biologists. Having a
computer science background myself (Python), I am not finding it easy to
tie python back to concepts that the biology students will relate to.
This will be very important as I'm not there to teach them to be expert
Python computer programmers - they're programming skills must relate to
their discipline. Has anyone delivered such a course? Even better would
someone have any lesson plans available which I could use as a starting
point?
 
I came across this post but the it's a bit old and the information
provided in the link no longer seems to be hosted.
http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
 
Any help appreciated. Thanks in advance. 
 
Aisling.
 


From idoerg at gmail.com  Tue Jun 21 16:28:02 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Tue, 21 Jun 2011 16:28:02 -0400
Subject: [Biopython] Teaching BioPython
In-Reply-To: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
Message-ID: <BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com>

Not exactly what you are looking for, but you may be able to grab some
examples from teh course at the Institut Pasteur, which is a programming
course for biologists using Python:

http://www.pasteur.fr/formation/infobio/python/

The same people used to have a biopython course, but it seems not to be
available online anymore. Maybe you can email them directly.

Iddo

On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll <Aisling.ODriscoll at cit.ie
> wrote:

> Hi everyone,
>
> I have been asked to deliver BioPython classes to biologists. Having a
> computer science background myself (Python), I am not finding it easy to
> tie python back to concepts that the biology students will relate to.
> This will be very important as I'm not there to teach them to be expert
> Python computer programmers - they're programming skills must relate to
> their discipline. Has anyone delivered such a course? Even better would
> someone have any lesson plans available which I could use as a starting
> point?
>
> I came across this post but the it's a bit old and the information
> provided in the link no longer seems to be hosted.
> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
>
> Any help appreciated. Thanks in advance.
>
> Aisling.
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html

From p.j.a.cock at googlemail.com  Tue Jun 21 16:33:08 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 21 Jun 2011 21:33:08 +0100
Subject: [Biopython] Teaching BioPython
In-Reply-To: <BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
	<BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com>
Message-ID: <C2B83F16-7FE2-4884-A9B4-4C1BC7D018E9@googlemail.com>



On 21 Jun 2011, at 21:28, Iddo Friedberg <idoerg at gmail.com> wrote:

> Not exactly what you are looking for, but you may be able to grab some
> examples from teh course at the Institut Pasteur, which is a programming
> course for biologists using Python:
> 
> http://www.pasteur.fr/formation/infobio/python/
> 
> The same people used to have a biopython course, but it seems not to be
> available online anymore. Maybe you can email them directly.

Unfortunately large parts of their Biopython material had become out of date.

> 
> On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll wrote:
> 
>> Hi everyone,
>> 
>> I have been asked to deliver BioPython classes to biologists. Having a
>> computer science background myself (Python), I am not finding it easy to
>> tie python back to concepts that the biology students will relate to.
>> This will be very important as I'm not there to teach them to be expert
>> Python computer programmers - they're programming skills must relate to
>> their discipline. Has anyone delivered such a course? Even better would
>> someone have any lesson plans available which I could use as a starting
>> point?
>> 
>> I came across this post but the it's a bit old and the information
>> provided in the link no longer seems to be hosted.
>> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
>> 
>> Any help appreciated. Thanks in advance.
>> 
>> Aisling.
>> 
>> 

I've not tried to do anything quite that ambitious. Have you got an idea of the amount of contact time you have to work with? That would make a big difference.

Peter

From idoerg at gmail.com  Tue Jun 21 16:34:08 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Tue, 21 Jun 2011 16:34:08 -0400
Subject: [Biopython] Teaching BioPython
In-Reply-To: <C2B83F16-7FE2-4884-A9B4-4C1BC7D018E9@googlemail.com>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
	<BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com>
	<C2B83F16-7FE2-4884-A9B4-4C1BC7D018E9@googlemail.com>
Message-ID: <BANLkTikC+50irwx1jnLrgq-_SwctEVV_AA@mail.gmail.com>

There is also Sebastian Bassi's book...
http://www.amazon.com/Bioinformatics-Chapman-Mathematical-Computational-Biology/dp/1584889292/ref=sr_1_1?ie=UTF8&s=books&qid=1308688427&sr=8-1

On Tue, Jun 21, 2011 at 4:33 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

>
>
> On 21 Jun 2011, at 21:28, Iddo Friedberg <idoerg at gmail.com> wrote:
>
> > Not exactly what you are looking for, but you may be able to grab some
> > examples from teh course at the Institut Pasteur, which is a programming
> > course for biologists using Python:
> >
> > http://www.pasteur.fr/formation/infobio/python/
> >
> > The same people used to have a biopython course, but it seems not to be
> > available online anymore. Maybe you can email them directly.
>
> Unfortunately large parts of their Biopython material had become out of
> date.
>
> >
> > On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll wrote:
> >
> >> Hi everyone,
> >>
> >> I have been asked to deliver BioPython classes to biologists. Having a
> >> computer science background myself (Python), I am not finding it easy to
> >> tie python back to concepts that the biology students will relate to.
> >> This will be very important as I'm not there to teach them to be expert
> >> Python computer programmers - they're programming skills must relate to
> >> their discipline. Has anyone delivered such a course? Even better would
> >> someone have any lesson plans available which I could use as a starting
> >> point?
> >>
> >> I came across this post but the it's a bit old and the information
> >> provided in the link no longer seems to be hosted.
> >> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
> >>
> >> Any help appreciated. Thanks in advance.
> >>
> >> Aisling.
> >>
> >>
>
> I've not tried to do anything quite that ambitious. Have you got an idea of
> the amount of contact time you have to work with? That would make a big
> difference.
>
> Peter




-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html

From Aisling.ODriscoll at cit.ie  Tue Jun 21 16:41:50 2011
From: Aisling.ODriscoll at cit.ie (Aisling ODriscoll)
Date: Tue, 21 Jun 2011 21:41:50 +0100
Subject: [Biopython] Teaching BioPython
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie><BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com><C2B83F16-7FE2-4884-A9B4-4C1BC7D018E9@googlemail.com>
	<BANLkTikC+50irwx1jnLrgq-_SwctEVV_AA@mail.gmail.com>
Message-ID: <DA2A8F990E1A4745BBE58A7F7952347802E95F97@CITMAIL.cit.ie>


Thanks Iddo for providing links.

Peter, the contact time is 1 hour lecture and 2 hours lab. 

Thanks again. 

-----Original Message-----
From: Iddo Friedberg [mailto:idoerg at gmail.com]
Sent: Tue 21/06/2011 21:34
To: Peter Cock
Cc: Aisling ODriscoll; biopython at lists.open-bio.org
Subject: Re: [Biopython] Teaching BioPython
 
There is also Sebastian Bassi's book...
http://www.amazon.com/Bioinformatics-Chapman-Mathematical-Computational-Biology/dp/1584889292/ref=sr_1_1?ie=UTF8&s=books&qid=1308688427&sr=8-1

On Tue, Jun 21, 2011 at 4:33 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

>
>
> On 21 Jun 2011, at 21:28, Iddo Friedberg <idoerg at gmail.com> wrote:
>
> > Not exactly what you are looking for, but you may be able to grab some
> > examples from teh course at the Institut Pasteur, which is a programming
> > course for biologists using Python:
> >
> > http://www.pasteur.fr/formation/infobio/python/
> >
> > The same people used to have a biopython course, but it seems not to be
> > available online anymore. Maybe you can email them directly.
>
> Unfortunately large parts of their Biopython material had become out of
> date.
>
> >
> > On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll wrote:
> >
> >> Hi everyone,
> >>
> >> I have been asked to deliver BioPython classes to biologists. Having a
> >> computer science background myself (Python), I am not finding it easy to
> >> tie python back to concepts that the biology students will relate to.
> >> This will be very important as I'm not there to teach them to be expert
> >> Python computer programmers - they're programming skills must relate to
> >> their discipline. Has anyone delivered such a course? Even better would
> >> someone have any lesson plans available which I could use as a starting
> >> point?
> >>
> >> I came across this post but the it's a bit old and the information
> >> provided in the link no longer seems to be hosted.
> >> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
> >>
> >> Any help appreciated. Thanks in advance.
> >>
> >> Aisling.
> >>
> >>
>
> I've not tried to do anything quite that ambitious. Have you got an idea of
> the amount of contact time you have to work with? That would make a big
> difference.
>
> Peter




-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html



From eric.talevich at gmail.com  Tue Jun 21 20:29:55 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 21 Jun 2011 20:29:55 -0400
Subject: [Biopython] Teaching BioPython
In-Reply-To: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
Message-ID: <BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>

On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll <Aisling.ODriscoll at cit.ie
> wrote:

> Hi everyone,
>
> I have been asked to deliver BioPython classes to biologists. Having a
> computer science background myself (Python), I am not finding it easy to
> tie python back to concepts that the biology students will relate to.
> This will be very important as I'm not there to teach them to be expert
> Python computer programmers - they're programming skills must relate to
> their discipline. Has anyone delivered such a course? Even better would
> someone have any lesson plans available which I could use as a starting
> point?
>
> I came across this post but the it's a bit old and the information
> provided in the link no longer seems to be hosted.
> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
>
>
Hi Aisling,

I've run a few 2-hour workshops on Python and Biopython at the University of
Georgia using these slide sets:
http://www.slideshare.net/etalevich/biopython-programming-workshop-at-uga
http://www.slideshare.net/etalevich/python-workshop-1-uga-bioinformatics

I'm due to update the Biopython set soon with a section on Bio.Phylo, and I
can send that to you when it's done if you'd like (or post it here).

The second chapter of the official tutorial, Quick Start, is a good starting
point for designing your own lecture and lab, pulling in more detailed
material from the other chapters as needed.
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc6

Also: It's much easier to run a workshop if the participants have set up the
same environment on their own laptops, or the computers on site all have the
same software installed. Specifically, make sure everyone has IDLE and
Python 2.7 installed. Earlier I let students choose between ipython and
IDLE, and during the workshops I typed my examples into ipython -- this was
highly confusing for 100% of the students, including those who did have
ipython installed but weren't familiar with it. In IDLE, everyone has the
same environment and GUI, and the distinction between interpreter and script
is clear.

Cheers,
Eric

From eric.talevich at gmail.com  Tue Jun 21 20:47:45 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 21 Jun 2011 20:47:45 -0400
Subject: [Biopython] BLOCKS BLOSUM
In-Reply-To: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
References: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
Message-ID: <BANLkTinhfOXRfQ3E2s91jC=u_M+ud2ybUA@mail.gmail.com>

HI George,

If the PDB ID isn't listed with the blocks, then I don't know of an
immediate way to look up the source structure PDBID, but since the blocks
are highly conserved (by definition) you should be able to get a reliable
hit by BLASTing with any of the sequences in the block against NCBI's PDBAA
database. If you'd like to be more rigorous you can construct an HMM profile
from the BLOCKS alignment and use HMMer to search PDBAA. And, if secondary
structure is all you're worried about, you can also try a secondary
structure prediction program like JPred with any of the source sequences as
the query.

Best,
Eric

On Tue, Jun 21, 2011 at 2:01 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi,
> This might not be the correct place to ask this question-but some of you
> may
> have experience in this.
> I went to the BLOCKS database and downloaded a text file that contains many
> BLOCKS but I would like to see the structure of these blocks either in
> VMD/Pymol
> Is there a way to find the PDB ID of these blocks?
>
> What I want is to use the same BLOCKS info and develop my own BLOSUM like
> matrix using biopyhton.
> Thank you and my apologies is this is not directly related to biopython.
> (example of a block from the downloaded text file is given below)
> George
>
> NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
> NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
> NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
> NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
> NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
> NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>

From p.j.a.cock at googlemail.com  Wed Jun 22 03:46:53 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 22 Jun 2011 08:46:53 +0100
Subject: [Biopython] Teaching BioPython
In-Reply-To: <BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
	<BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>
Message-ID: <BANLkTimJgv7zcVmnED+oFz-wCbGZWpC1mg@mail.gmail.com>

On Wed, Jun 22, 2011 at 1:29 AM, Eric Talevich wrote:
> Hi Aisling,
>
> I've run a few 2-hour workshops on Python and Biopython at the University
> of Georgia using these slide sets:
> http://www.slideshare.net/etalevich/biopython-programming-workshop-at-uga
> http://www.slideshare.net/etalevich/python-workshop-1-uga-bioinformatics
>
> I'm due to update the Biopython set soon with a section on Bio.Phylo, and I
> can send that to you when it's done if you'd like (or post it here).
>
> The second chapter of the official tutorial, Quick Start, is a good starting
> point for designing your own lecture and lab, pulling in more detailed
> material from the other chapters as needed.
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc6

Certainly that could be a good basis - but you're going to have to
be selective given the limited contact time. Realistically you can
expect the students to type in and run some short examples, and
get a flavour of Python (and Biopython). For most of them that
will be all the take away - but a few could be tempted to learn more
(of Python or programming in general).

> Also: It's much easier to run a workshop if the participants have set up the
> same environment on their own laptops, or the computers on site all have
> the same software installed.

For a short course like yours, this is essential - otherwise you (Aisling)
could easily spend the first hour troubleshooting several different setups
and making sure everyone can start the examples.

> Specifically, make sure everyone has IDLE and
> Python 2.7 installed. Earlier I let students choose between ipython and
> IDLE, and during the workshops I typed my examples into ipython -- this
> was highly confusing for 100% of the students, including those who did
> have ipython installed but weren't familiar with it. In IDLE, everyone has
> the same environment and GUI, and the distinction between interpreter
> and script is clear.

Assuming your class are not using the Mac, I'd also use IDLE in a class.
Apple doesn't include it by default on the Mac for some reason.

It is likely your group be using a set of Windows machines, so the
installation of Python 2.7, NumPy and Biopython via the installers
should be easy. You might also look at the Enthought Python Distribution,
which I think comes with them all bundled (but not necessarily the latest
versions).

Peter

From Aisling.ODriscoll at cit.ie  Wed Jun 22 06:51:38 2011
From: Aisling.ODriscoll at cit.ie (Aisling ODriscoll)
Date: Wed, 22 Jun 2011 11:51:38 +0100
Subject: [Biopython] Teaching BioPython
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie><BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>
	<BANLkTimJgv7zcVmnED+oFz-wCbGZWpC1mg@mail.gmail.com>
Message-ID: <DA2A8F990E1A4745BBE58A7F7952347802E95F9A@CITMAIL.cit.ie>

Many thanks to all who have taken the time to reply and to provide links and advice. Apologies, I should have been more explicit about the course duration.
It will be a 1 hour lecture and 2 hours lab delivered over 11 weeks (excluding assessments). I will probably introduce them to a little Perl as well (but not too much because otherwide it will just become confusing for them I think) so I would imagine at least 8-9 weeks will be dedicated to Python/Biopython.
 
So I need to devise 8/9 weeks of lecture notes and 8/9 weeks 2 hour lab exercises and problems - While the first week or so might be dedicated to just getting to grips with Python (they have 4 non contact hours too per week so they can use them for this), I want to introduce them to BioPython and applying programming to biology-related problems as quickly as possible so that they can see the relevance of what they're doing. 
 
Kind Regards,
Aisling.

________________________________

From: Peter Cock [mailto:p.j.a.cock at googlemail.com]
Sent: Wed 22/06/2011 08:46
To: Eric Talevich
Cc: Aisling ODriscoll; biopython at lists.open-bio.org
Subject: Re: [Biopython] Teaching BioPython



On Wed, Jun 22, 2011 at 1:29 AM, Eric Talevich wrote:
> Hi Aisling,
>
> I've run a few 2-hour workshops on Python and Biopython at the University
> of Georgia using these slide sets:
> http://www.slideshare.net/etalevich/biopython-programming-workshop-at-uga
> http://www.slideshare.net/etalevich/python-workshop-1-uga-bioinformatics
>
> I'm due to update the Biopython set soon with a section on Bio.Phylo, and I
> can send that to you when it's done if you'd like (or post it here).
>
> The second chapter of the official tutorial, Quick Start, is a good starting
> point for designing your own lecture and lab, pulling in more detailed
> material from the other chapters as needed.
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc6

Certainly that could be a good basis - but you're going to have to
be selective given the limited contact time. Realistically you can
expect the students to type in and run some short examples, and
get a flavour of Python (and Biopython). For most of them that
will be all the take away - but a few could be tempted to learn more
(of Python or programming in general).

> Also: It's much easier to run a workshop if the participants have set up the
> same environment on their own laptops, or the computers on site all have
> the same software installed.

For a short course like yours, this is essential - otherwise you (Aisling)
could easily spend the first hour troubleshooting several different setups
and making sure everyone can start the examples.

> Specifically, make sure everyone has IDLE and
> Python 2.7 installed. Earlier I let students choose between ipython and
> IDLE, and during the workshops I typed my examples into ipython -- this
> was highly confusing for 100% of the students, including those who did
> have ipython installed but weren't familiar with it. In IDLE, everyone has
> the same environment and GUI, and the distinction between interpreter
> and script is clear.

Assuming your class are not using the Mac, I'd also use IDLE in a class.
Apple doesn't include it by default on the Mac for some reason.

It is likely your group be using a set of Windows machines, so the
installation of Python 2.7, NumPy and Biopython via the installers
should be easy. You might also look at the Enthought Python Distribution,
which I think comes with them all bundled (but not necessarily the latest
versions).

Peter




From p.j.a.cock at googlemail.com  Wed Jun 22 07:27:05 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 22 Jun 2011 12:27:05 +0100
Subject: [Biopython] Teaching BioPython
In-Reply-To: <DA2A8F990E1A4745BBE58A7F7952347802E95F9A@CITMAIL.cit.ie>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
	<BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>
	<BANLkTimJgv7zcVmnED+oFz-wCbGZWpC1mg@mail.gmail.com>
	<DA2A8F990E1A4745BBE58A7F7952347802E95F9A@CITMAIL.cit.ie>
Message-ID: <BANLkTin15bWC+jD9HKmcEuWPPG-kxDmX9w@mail.gmail.com>

On Wed, Jun 22, 2011 at 11:51 AM, Aisling ODriscoll
<Aisling.ODriscoll at cit.ie> wrote:
> Many thanks to all who have taken the time to reply and to provide links and
> advice. Apologies, I should have been more explicit about the course
> duration.
> It will be a 1 hour lecture and 2 hours lab delivered over 11 weeks
> (excluding assessments). I will probably introduce them to a little Perl as
> well (but not?too much because otherwide it will just become?confusing for
> them?I think) so I would imagine at least 8-9 weeks will be dedicated to
> Python/Biopython.

Oh right - so a total of about 11 hours lectures and 22 hours in the lab.
That does make things much more interesting (and more work).

> So I need to devise 8/9 weeks of lecture notes and 8/9 weeks 2 hour lab
> exercises and problems - While the first week or so might be dedicated to
> just getting to grips with Python (they have 4 non contact hours too per
> week?so they can use them for this), I want to introduce them to BioPython
> and applying programming to biology-related problems as quickly as possible
> so that they can see the relevance of what they're doing.

I would start by looking at existing introductory Python materials, and probably
put a little more emphasis on string manipulation with biological sequence
examples. Maybe get them to write their own FASTA parser as an exercise,
before then bringing in Biopython.

I've never tried to teach (Bio)python on that scale - but if you find any errors
or omissions in our documentation (especially the Tutorial), we would
welcome feedback.

Peter


From mnemonico at posthocergopropterhoc.net  Mon Jun 27 03:00:37 2011
From: mnemonico at posthocergopropterhoc.net (A M Torres, Hugo)
Date: Mon, 27 Jun 2011 04:00:37 -0300
Subject: [Biopython] biopython cookbook error
Message-ID: <BANLkTim__OXzYwa5FXnaj8b_h0vrnOQTBG3STfdpvAUM_+o=TQ@mail.gmail.com>

Hi, I am new to this list excuse me if this is not the appropriate place to
report this:

I am just trying to teach myself some biopython and at section "2.4.1  Simple
FASTA parsing example" of the biopython tutorial it suggests us to run this
code:

from Bio import SeqIO
> for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
>     print seq_record.id
>     print repr(seq_record.seq)
>     print len(seq_record)
>
>
Which outputs the error:

Traceback (most recent call last):
> File "simple_parser_2_4_1.py", line 4, in <module>
> for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"): #this seems
> wrong in the tutorial
> File "/usr/lib/pymodules/python2.6/Bio/SeqIO/__init__.py", line 424, in
> parse
> raise TypeError("Need a file handle, not a string (i.e. not a filename)")
> TypeError: Need a file handle, not a string (i.e. not a filename)
>

Python novices like me might have a problem understanding what a "file
handle" is. I tryed this and it seems to work:

from Bio import SeqIO
>
> with open("ls_orchid.fasta", 'rU') as data:
>     for seq_record in SeqIO.parse(data, "fasta"):
>         print seq_record.id
>         print repr(seq_record.seq)
>         print len(seq_record)
>

Maybe someone here can help me notify whoever maintains the tutorial.

Thanks,

Hugo Torres

From chapmanb at 50mail.com  Mon Jun 27 06:38:34 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 27 Jun 2011 06:38:34 -0400
Subject: [Biopython] biopython cookbook error
In-Reply-To: <BANLkTim__OXzYwa5FXnaj8b_h0vrnOQTBG3STfdpvAUM_+o=TQ@mail.gmail.com>
References: <BANLkTim__OXzYwa5FXnaj8b_h0vrnOQTBG3STfdpvAUM_+o=TQ@mail.gmail.com>
Message-ID: <20110627103834.GA22214@sobchak>

Hugo;
Thanks for the e-mail and reporting the problem you were running
into.

> Hi, I am new to this list excuse me if this is not the appropriate place to
> report this:
> 
> I am just trying to teach myself some biopython and at section "2.4.1  Simple
> FASTA parsing example" of the biopython tutorial it suggests us to run this
> code:
[...]
> Which outputs the error:
[...]
> > TypeError: Need a file handle, not a string (i.e. not a filename)

It sounds like you have an old version of Biopython. SeqIO was
changed a few releases ago to support string filenames instead of
handles for the reason you mention: to make it easier for new Python
developers. See FAQ #14 for more information, and #3 for information
about checking your version of Biopython:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc5

If you have easy_install available, you can update with:

sudo easy_install -U biopython

Hope this helps,
Brad

From pjthorpe at gmail.com  Mon Jun 27 12:06:06 2011
From: pjthorpe at gmail.com (Peter Thorpe)
Date: Mon, 27 Jun 2011 17:06:06 +0100
Subject: [Biopython] Biopython Digest, Vol 102, Issue 16
In-Reply-To: <mailman.1.1309190402.19877.biopython@lists.open-bio.org>
References: <mailman.1.1309190402.19877.biopython@lists.open-bio.org>
Message-ID: <BANLkTik1CMoMX1CtBT6zzdXwLKu276UYoQ@mail.gmail.com>

On 27 June 2011 17:00, <biopython-request at lists.open-bio.org> wrote:

> Send Biopython mailing list submissions to
>        biopython at lists.open-bio.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.open-bio.org/mailman/listinfo/biopython
> or, via email, send a message with subject or body 'help' to
>        biopython-request at lists.open-bio.org
>
> You can reach the person managing the list at
>        biopython-owner at lists.open-bio.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biopython digest..."
>
>
> Today's Topics:
>
>   1. biopython cookbook error (A M Torres, Hugo)
>   2. Re: biopython cookbook error (Brad Chapman)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 27 Jun 2011 04:00:37 -0300
> From: "A M Torres, Hugo" <mnemonico at posthocergopropterhoc.net>
> Subject: [Biopython] biopython cookbook error
> To: biopython at lists.open-bio.org
> Message-ID:
>        <BANLkTim__OXzYwa5FXnaj8b_h0vrnOQTBG3STfdpvAUM_+o=TQ at mail.gmail.com
> >
> Content-Type: text/plain; charset=UTF-8
>
> Hi, I am new to this list excuse me if this is not the appropriate place to
> report this:
>
> I am just trying to teach myself some biopython and at section "2.4.1
>  Simple
> FASTA parsing example" of the biopython tutorial it suggests us to run this
> code:
>
> from Bio import SeqIO
> > for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
> >     print seq_record.id
> >     print repr(seq_record.seq)
> >     print len(seq_record)
> >
> >
> Which outputs the error:
>
> Traceback (most recent call last):
> > File "simple_parser_2_4_1.py", line 4, in <module>
> > for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"): #this seems
> > wrong in the tutorial
> > File "/usr/lib/pymodules/python2.6/Bio/SeqIO/__init__.py", line 424, in
> > parse
> > raise TypeError("Need a file handle, not a string (i.e. not a filename)")
> > TypeError: Need a file handle, not a string (i.e. not a filename)
> >
>
> Python novices like me might have a problem understanding what a "file
> handle" is. I tryed this and it seems to work:
>
> from Bio import SeqIO
> >
> > with open("ls_orchid.fasta", 'rU') as data:
> >     for seq_record in SeqIO.parse(data, "fasta"):
> >         print seq_record.id
> >         print repr(seq_record.seq)
> >         print len(seq_record)
> >
>
> Maybe someone here can help me notify whoever maintains the tutorial.
>
> Thanks,
>
> Hugo Torres
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 27 Jun 2011 06:38:34 -0400
> From: Brad Chapman <chapmanb at 50mail.com>
> Subject: Re: [Biopython] biopython cookbook error
> To: biopython at lists.open-bio.org
> Message-ID: <20110627103834.GA22214 at sobchak>
> Content-Type: text/plain; charset=us-ascii
>
> Hugo;
> Thanks for the e-mail and reporting the problem you were running
> into.
>
> > Hi, I am new to this list excuse me if this is not the appropriate place
> to
> > report this:
> >
> > I am just trying to teach myself some biopython and at section "2.4.1
>  Simple
> > FASTA parsing example" of the biopython tutorial it suggests us to run
> this
> > code:
> [...]
> > Which outputs the error:
> [...]
> > > TypeError: Need a file handle, not a string (i.e. not a filename)
>
> It sounds like you have an old version of Biopython. SeqIO was
> changed a few releases ago to support string filenames instead of
> handles for the reason you mention: to make it easier for new Python
> developers. See FAQ #14 for more information, and #3 for information
> about checking your version of Biopython:
>
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc5
>
> If you have easy_install available, you can update with:
>
> sudo easy_install -U biopython
>
> Hope this helps,
> Brad
>
>
> Subject: Re: [Biopython] biopython cookbook error

Hi All,

This is my first post too... The current version of biopython and current
cookbook example does work fine. So, as Brad says, you may be using an old
version.

Pete Thorpe

> ------------------------------
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>
> End of Biopython Digest, Vol 102, Issue 16
> ******************************************
>

From ajingnk at gmail.com  Mon Jun 27 17:53:30 2011
From: ajingnk at gmail.com (Jing Lu)
Date: Mon, 27 Jun 2011 14:53:30 -0700
Subject: [Biopython]  How to pull out the coordinates for het groups?
Message-ID: <BANLkTin3FZk4jybQVFnMhoVLOq6w0OvXXA@mail.gmail.com>

Hi,

I want to pull out ligand from pdb file, then for each ligand(or het group)
save it as pdb, and keep the header. I have try the following code, but it
didn't return the result I want. Could you please give me some suggestion?

''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
for filename in os.listdir(workdir):
        print filename
        if '.bio' in filename:
            parser = PDBParser(PERMISSIVE=1)
            structure = parser.get_structure(filename[:4], filename)
            structure_copy = copy.deepcopy(structure) # for each ligand
renew the structure

            het_id_all = get_het_id(structure_copy) # only return the
ligands of structure

            for het_id in het_id_all:
                for model in structure_copy:
                    for chain in model:
                        for residue in chain:
                            id = residue.id
                            if id[0] is not het_id:
                                chain.detach_child(id)
                        if len(chain) == 0:
                            model.detach_child(chain.id)

                name = './ligand/' + filename[:9] + '_' + het_id[2:] + '_' +
str(id[1]).zfill(4) + chain.id + '.pdb'
                save_structure(structure_copy, name)
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''

From dilara.ally at gmail.com  Mon Jun 27 18:33:42 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Mon, 27 Jun 2011 15:33:42 -0700
Subject: [Biopython] using a function on a batch of files
Message-ID: <4E090546.7080002@gmail.com>

Hi All

I'm a newbie to python and I'm interested in using a function on a batch 
of files.

I know that in R, you can set the working directory to the directory of 
interest.  Is there a way to do this in Python?  This would allow me to 
access files that were in a different location than where the script 
file is.  The reason I would be interested to do this is that I have a 
function that I want to apply to 400 different files.  If I were 
scripting in R (which I am familiar with) I could use the fn list.files 
that would list the files in the directory.  Then I could read them in 
one by one with a loop.  Apply the function and then write the files to 
a different directory.

What is the best way to do this in python?

Thanks for the help.

Cheers, Dilara

From idoerg at gmail.com  Mon Jun 27 19:09:17 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Mon, 27 Jun 2011 19:09:17 -0400
Subject: [Biopython] using a function on a batch of files
In-Reply-To: <4E090546.7080002@gmail.com>
References: <4E090546.7080002@gmail.com>
Message-ID: <BANLkTikvT38XyREuFahv3XLriBKjN9o3hw@mail.gmail.com>

Hi Dilara,

Read up on the glob module. http://docs.python.org/library/glob.html

That being said, this kind of question is probably better directed to one of
the Python community resources: http://python.org/community/

This list is primarily for Biopython inquiries.

Cheers,

Iddo

On Mon, Jun 27, 2011 at 6:33 PM, Dilara Ally <dilara.ally at gmail.com> wrote:

> Hi All
>
> I'm a newbie to python and I'm interested in using a function on a batch of
> files.
>
> I know that in R, you can set the working directory to the directory of
> interest.  Is there a way to do this in Python?  This would allow me to
> access files that were in a different location than where the script file
> is.  The reason I would be interested to do this is that I have a function
> that I want to apply to 400 different files.  If I were scripting in R
> (which I am familiar with) I could use the fn list.files that would list the
> files in the directory.  Then I could read them in one by one with a loop.
>  Apply the function and then write the files to a different directory.
>
> What is the best way to do this in python?
>
> Thanks for the help.
>
> Cheers, Dilara
> ______________________________**_________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/**mailman/listinfo/biopython<http://lists.open-bio.org/mailman/listinfo/biopython>
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html

From eric.talevich at gmail.com  Mon Jun 27 19:18:10 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Mon, 27 Jun 2011 19:18:10 -0400
Subject: [Biopython] using a function on a batch of files
In-Reply-To: <4E090546.7080002@gmail.com>
References: <4E090546.7080002@gmail.com>
Message-ID: <BANLkTi=KPMyTCjrTt2mL79xerMmt_cP9dg@mail.gmail.com>

Hi Dilara,

If the glob module doesn't do what you want, then os.listdir might be it:
http://docs.python.org/library/os.html#os.listdir

Usage:
for fname in os.listdir("path/to/files/"):     print fname

Cheers,
Eric

On Mon, Jun 27, 2011 at 6:33 PM, Dilara Ally <dilara.ally at gmail.com> wrote:

> Hi All
>
> I'm a newbie to python and I'm interested in using a function on a batch of
> files.
>
> I know that in R, you can set the working directory to the directory of
> interest.  Is there a way to do this in Python?  This would allow me to
> access files that were in a different location than where the script file
> is.  The reason I would be interested to do this is that I have a function
> that I want to apply to 400 different files.  If I were scripting in R
> (which I am familiar with) I could use the fn list.files that would list the
> files in the directory.  Then I could read them in one by one with a loop.
>  Apply the function and then write the files to a different directory.
>
> What is the best way to do this in python?
>
> Thanks for the help.
>
> Cheers, Dilara
> ______________________________**_________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/**mailman/listinfo/biopython<http://lists.open-bio.org/mailman/listinfo/biopython>
>

From laserson at mit.edu  Tue Jun 28 00:26:50 2011
From: laserson at mit.edu (Uri Laserson)
Date: Tue, 28 Jun 2011 00:26:50 -0400
Subject: [Biopython] Serialize SeqRecord to JSON?
In-Reply-To: <BANLkTiktqaj=7V_y-ajvfA+etqpKi1_SOA@mail.gmail.com>
References: <BANLkTinGvFuT8NCmO8-VkvMjwEWd7qzC-g@mail.gmail.com>
	<BANLkTiktqaj=7V_y-ajvfA+etqpKi1_SOA@mail.gmail.com>
Message-ID: <BANLkTinf1JpK9XVALja48=eEUgR83bgaPw@mail.gmail.com>

I am interested in easily loading SeqRecords into MongoDB, including all
annotations/features.

I made a hack where I convert everything to python dict and list types, and
back.  If anyone is interested, they can find it on my github page:

http://goo.gl/b3bts

It's worked well for me thus far.

Uri

...................................................................................
Uri Laserson
Graduate Student, Biomedical Engineering
Harvard-MIT Division of Health Sciences and Technology
M +1 917 742 8019
laserson at mit.edu

From devaniranjan at gmail.com  Wed Jun 29 12:15:17 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Wed, 29 Jun 2011 12:15:17 -0400
Subject: [Biopython] identify triplet sequences
Message-ID: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>

Hi,

Not sure if this is a python or  bio-python question -but suggestions are
most welcome.

I have some FASTA sequences....like
AAAAWWWHHHHH
TTTYYYYYHGGGG
NNNNNGGGGFFFF

I extract from each sequence triplets moving from 1st residue and extracting
the 2nd, 3rd as one triplet then 2/3/4 as another triplet then 3/4/5 as
another triplet ...ect
So for the 1st sequence given above.....
AAA
AAA
AAW
AWW
.
.
.
so on.....

Now my question for 20amino acids there will be 8000 possible unique
combinations (20^3)

How can I classify them using python/biopython and write them out to 8000
unique text files .....is there a way to classify them without writing 8000
IF/ELSIF statements?
I want to see which sets of triplets has the hightest occourence.

Thank you.

From w.arindrarto at gmail.com  Wed Jun 29 13:18:49 2011
From: w.arindrarto at gmail.com (Wibowo Arindrarto)
Date: Wed, 29 Jun 2011 19:18:49 +0200
Subject: [Biopython] identify triplet sequences
In-Reply-To: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>
References: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>
Message-ID: <BANLkTi=ySvjYgOo4mWmcAAVDHN2qRpbYVg@mail.gmail.com>

Hi George,

This is my first post, so greetings to everyone else as well. For your
question, do you need to name all 8000 combinations? If not, then you can
use a dictionary to enumerate the occurence of each amino acid triplet. You
don't have to take into account all possibilities, just the one you find in
your sequences.

I've made a somewhat short & dirty script to do the analysis you want. It
also generates a fasta file containing random amino acid sequences of a
certain length as a source for a demo analysis. Here it is:

#!/usr/bin/env python

import random

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC

# function to generate random protein sequence
def random_prot(length):
    seq = ''
    for i in xrange(length):
        seq += random.choice(IUPAC.protein.letters)
    return seq

# function to generate list of SeqRecord objects
def seqrecord_gen(num, length):
    seqs = []
    for i in xrange(num):
        seqs.append(SeqRecord(Seq(random_prot(length)),
                    id='fasta'+str(i+1),
                    name='',
                    description=''))
    SeqIO.write(seqs, 'random_proteins.fa', 'fasta')

# function to read fasta file and count triplets
def count_triplet(source):
    triplets = {}
    seqs = SeqIO.parse(source, 'fasta')

    for rec in seqs:
        step = 0
        while step + 3 <= len(rec.seq.tostring()):
            tri = rec.seq.tostring()[0+step:3+step]
            if tri not in triplets:
                triplets[tri] = 1
            else:
                triplets[tri] += 1
            step += 1

    with open('results', 'w') as output:
        for key in sorted(triplets, key=triplets.get, reverse=True):
            output.writelines("{0}: {1}\n".format(key, triplets[key]))

# generate mock file
seqrecord_gen(100, 30)
# count the triplet
count_triplet('random_proteins.fa')


You can also see the script here: https://gist.github.com/1054348 (in case
there are formatting problems with the mail's display). Just remove the
seqrecord_gen() call and replace run count_triplet() with your fasta file
name as the argument. You can see the output in 'results'

Hope that helps!
Wibowo Arindrarto (Bow)


On Wed, Jun 29, 2011 at 18:15, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Hi,
>
> Not sure if this is a python or  bio-python question -but suggestions are
> most welcome.
>
> I have some FASTA sequences....like
> AAAAWWWHHHHH
> TTTYYYYYHGGGG
> NNNNNGGGGFFFF
>
> I extract from each sequence triplets moving from 1st residue and
> extracting
> the 2nd, 3rd as one triplet then 2/3/4 as another triplet then 3/4/5 as
> another triplet ...ect
> So for the 1st sequence given above.....
> AAA
> AAA
> AAW
> AWW
> .
> .
> .
> so on.....
>
> Now my question for 20amino acids there will be 8000 possible unique
> combinations (20^3)
>
> How can I classify them using python/biopython and write them out to 8000
> unique text files .....is there a way to classify them without writing 8000
> IF/ELSIF statements?
> I want to see which sets of triplets has the hightest occourence.
>
> Thank you.
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>

From devaniranjan at gmail.com  Wed Jun 29 13:54:56 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Wed, 29 Jun 2011 13:54:56 -0400
Subject: [Biopython] identify triplet sequences
In-Reply-To: <BANLkTi=ySvjYgOo4mWmcAAVDHN2qRpbYVg@mail.gmail.com>
References: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>
	<BANLkTi=ySvjYgOo4mWmcAAVDHN2qRpbYVg@mail.gmail.com>
Message-ID: <BANLkTinO9m-7hzi6nCxjDuv5BUSDpobhPw@mail.gmail.com>

Hi Wibowo,
Thank you for your answer,
If I want to classify only based on 1st and 3rd charecters of the triplets
while allowing the central charecter to be anything/vary can I do that?
so  any of the following should be under one list..instead of being counted
as unique.
ACA
ARA
AEA
AGA
...etc
You are right I don't need all 8000 combinations, just the one's that occur
in the list.
Thank you,
George

On Wed, Jun 29, 2011 at 1:18 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com>wrote:

> Hi George,
>
> This is my first post, so greetings to everyone else as well. For your
> question, do you need to name all 8000 combinations? If not, then you can
> use a dictionary to enumerate the occurence of each amino acid triplet. You
> don't have to take into account all possibilities, just the one you find in
> your sequences.
>
> I've made a somewhat short & dirty script to do the analysis you want. It
> also generates a fasta file containing random amino acid sequences of a
> certain length as a source for a demo analysis. Here it is:
>
> #!/usr/bin/env python
>
> import random
>
> from Bio import SeqIO
> from Bio.Seq import Seq
> from Bio.SeqRecord import SeqRecord
> from Bio.Alphabet import IUPAC
>
> # function to generate random protein sequence
> def random_prot(length):
>     seq = ''
>     for i in xrange(length):
>         seq += random.choice(IUPAC.protein.letters)
>     return seq
>
> # function to generate list of SeqRecord objects
> def seqrecord_gen(num, length):
>     seqs = []
>     for i in xrange(num):
>         seqs.append(SeqRecord(Seq(random_prot(length)),
>                     id='fasta'+str(i+1),
>                     name='',
>                     description=''))
>     SeqIO.write(seqs, 'random_proteins.fa', 'fasta')
>
> # function to read fasta file and count triplets
> def count_triplet(source):
>     triplets = {}
>     seqs = SeqIO.parse(source, 'fasta')
>
>     for rec in seqs:
>         step = 0
>         while step + 3 <= len(rec.seq.tostring()):
>             tri = rec.seq.tostring()[0+step:3+step]
>             if tri not in triplets:
>                 triplets[tri] = 1
>             else:
>                 triplets[tri] += 1
>             step += 1
>
>     with open('results', 'w') as output:
>         for key in sorted(triplets, key=triplets.get, reverse=True):
>             output.writelines("{0}: {1}\n".format(key, triplets[key]))
>
> # generate mock file
> seqrecord_gen(100, 30)
> # count the triplet
> count_triplet('random_proteins.fa')
>
>
> You can also see the script here: https://gist.github.com/1054348 (in case
> there are formatting problems with the mail's display). Just remove the
> seqrecord_gen() call and replace run count_triplet() with your fasta file
> name as the argument. You can see the output in 'results'
>
> Hope that helps!
> Wibowo Arindrarto (Bow)
>
>
> On Wed, Jun 29, 2011 at 18:15, George Devaniranjan <devaniranjan at gmail.com
> > wrote:
>
>> Hi,
>>
>> Not sure if this is a python or  bio-python question -but suggestions are
>> most welcome.
>>
>> I have some FASTA sequences....like
>> AAAAWWWHHHHH
>> TTTYYYYYHGGGG
>> NNNNNGGGGFFFF
>>
>> I extract from each sequence triplets moving from 1st residue and
>> extracting
>> the 2nd, 3rd as one triplet then 2/3/4 as another triplet then 3/4/5 as
>> another triplet ...ect
>> So for the 1st sequence given above.....
>> AAA
>> AAA
>> AAW
>> AWW
>> .
>> .
>> .
>> so on.....
>>
>> Now my question for 20amino acids there will be 8000 possible unique
>> combinations (20^3)
>>
>> How can I classify them using python/biopython and write them out to 8000
>> unique text files .....is there a way to classify them without writing
>> 8000
>> IF/ELSIF statements?
>> I want to see which sets of triplets has the hightest occourence.
>>
>> Thank you.
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>

From w.arindrarto at gmail.com  Wed Jun 29 14:12:28 2011
From: w.arindrarto at gmail.com (Wibowo Arindrarto)
Date: Wed, 29 Jun 2011 20:12:28 +0200
Subject: [Biopython] identify triplet sequences
In-Reply-To: <BANLkTinO9m-7hzi6nCxjDuv5BUSDpobhPw@mail.gmail.com>
References: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>
	<BANLkTi=ySvjYgOo4mWmcAAVDHN2qRpbYVg@mail.gmail.com>
	<BANLkTinO9m-7hzi6nCxjDuv5BUSDpobhPw@mail.gmail.com>
Message-ID: <BANLkTi=aS+ADjdY6eWtCkPN5C=F80qB6mA@mail.gmail.com>

Hi George,

That can be done by modifying this line:

tri = rec.seq.tostring()[0+step:3+step]

into this:

tri = rec.seq.tostring()[0+step:3+step:2]

Alternatively, if you want a prettier output ('A*A' instead of 'AA' for all
triplets starting and ending with 'A') you can replace it with these
instead:

tri = rec.seq.tostring()[0+step]
tri += '*'
tri += rec.seq.tostring()[2+step]

Hope that helps!
Bow


On Wed, Jun 29, 2011 at 19:54, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Hi Wibowo,
> Thank you for your answer,
> If I want to classify only based on 1st and 3rd charecters of the triplets
> while allowing the central charecter to be anything/vary can I do that?
> so  any of the following should be under one list..instead of being counted
> as unique.
> ACA
> ARA
> AEA
> AGA
> ...etc
> You are right I don't need all 8000 combinations, just the one's that occur
> in the list.
> Thank you,
> George
>
>
> On Wed, Jun 29, 2011 at 1:18 PM, Wibowo Arindrarto <w.arindrarto at gmail.com
> > wrote:
>
>> Hi George,
>>
>> This is my first post, so greetings to everyone else as well. For your
>> question, do you need to name all 8000 combinations? If not, then you can
>> use a dictionary to enumerate the occurence of each amino acid triplet. You
>> don't have to take into account all possibilities, just the one you find in
>> your sequences.
>>
>> I've made a somewhat short & dirty script to do the analysis you want. It
>> also generates a fasta file containing random amino acid sequences of a
>> certain length as a source for a demo analysis. Here it is:
>>
>> #!/usr/bin/env python
>>
>> import random
>>
>> from Bio import SeqIO
>> from Bio.Seq import Seq
>> from Bio.SeqRecord import SeqRecord
>> from Bio.Alphabet import IUPAC
>>
>> # function to generate random protein sequence
>> def random_prot(length):
>>     seq = ''
>>     for i in xrange(length):
>>         seq += random.choice(IUPAC.protein.letters)
>>     return seq
>>
>> # function to generate list of SeqRecord objects
>> def seqrecord_gen(num, length):
>>     seqs = []
>>     for i in xrange(num):
>>         seqs.append(SeqRecord(Seq(random_prot(length)),
>>                     id='fasta'+str(i+1),
>>                     name='',
>>                     description=''))
>>     SeqIO.write(seqs, 'random_proteins.fa', 'fasta')
>>
>> # function to read fasta file and count triplets
>> def count_triplet(source):
>>     triplets = {}
>>     seqs = SeqIO.parse(source, 'fasta')
>>
>>     for rec in seqs:
>>         step = 0
>>         while step + 3 <= len(rec.seq.tostring()):
>>             tri = rec.seq.tostring()[0+step:3+step]
>>             if tri not in triplets:
>>                 triplets[tri] = 1
>>             else:
>>                 triplets[tri] += 1
>>             step += 1
>>
>>     with open('results', 'w') as output:
>>         for key in sorted(triplets, key=triplets.get, reverse=True):
>>             output.writelines("{0}: {1}\n".format(key, triplets[key]))
>>
>> # generate mock file
>> seqrecord_gen(100, 30)
>> # count the triplet
>> count_triplet('random_proteins.fa')
>>
>>
>> You can also see the script here: https://gist.github.com/1054348 (in
>> case there are formatting problems with the mail's display). Just remove the
>> seqrecord_gen() call and replace run count_triplet() with your fasta file
>> name as the argument. You can see the output in 'results'
>>
>> Hope that helps!
>> Wibowo Arindrarto (Bow)
>>
>>
>> On Wed, Jun 29, 2011 at 18:15, George Devaniranjan <
>> devaniranjan at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> Not sure if this is a python or  bio-python question -but suggestions are
>>> most welcome.
>>>
>>> I have some FASTA sequences....like
>>> AAAAWWWHHHHH
>>> TTTYYYYYHGGGG
>>> NNNNNGGGGFFFF
>>>
>>> I extract from each sequence triplets moving from 1st residue and
>>> extracting
>>> the 2nd, 3rd as one triplet then 2/3/4 as another triplet then 3/4/5 as
>>> another triplet ...ect
>>> So for the 1st sequence given above.....
>>> AAA
>>> AAA
>>> AAW
>>> AWW
>>> .
>>> .
>>> .
>>> so on.....
>>>
>>> Now my question for 20amino acids there will be 8000 possible unique
>>> combinations (20^3)
>>>
>>> How can I classify them using python/biopython and write them out to 8000
>>> unique text files .....is there a way to classify them without writing
>>> 8000
>>> IF/ELSIF statements?
>>> I want to see which sets of triplets has the hightest occourence.
>>>
>>> Thank you.
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>
>>
>>
>

From babbanmia at gmail.com  Wed Jun 29 14:54:38 2011
From: babbanmia at gmail.com (Babban Mia)
Date: Wed, 29 Jun 2011 14:54:38 -0400
Subject: [Biopython] DIHEDRAL ANGLES from PDB
Message-ID: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>

Hello Everyone


I am looking for a tool that can calculate dihedral angle with in a python
script between four atoms in PDB file.

I hope Biopython has something to offer.

Please advise.


Best

From babbanmia at gmail.com  Wed Jun 29 14:54:38 2011
From: babbanmia at gmail.com (Babban Mia)
Date: Wed, 29 Jun 2011 14:54:38 -0400
Subject: [Biopython] DIHEDRAL ANGLES from PDB
Message-ID: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>

Hello Everyone


I am looking for a tool that can calculate dihedral angle with in a python
script between four atoms in PDB file.

I hope Biopython has something to offer.

Please advise.


Best

From p.j.a.cock at googlemail.com  Wed Jun 29 17:10:02 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jun 2011 22:10:02 +0100
Subject: [Biopython] DIHEDRAL ANGLES from PDB
In-Reply-To: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>
References: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>
Message-ID: <BANLkTikpw94xJaU68FZBTwZMoX2u8=4c+w@mail.gmail.com>

On Wed, Jun 29, 2011 at 7:54 PM, Babban Mia <babbanmia at gmail.com> wrote:
> Hello Everyone
>
>
> I am looking for a tool that can calculate dihedral angle with in a python
> script between four atoms in PDB file.
>
> I hope Biopython has something to offer.
>
> Please advise.
>
> Best

Yes, try this:
http://www.warwick.ac.uk/go/peter_cock/python/ramachandran/

Peter

From p.j.a.cock at googlemail.com  Wed Jun 29 17:10:02 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jun 2011 22:10:02 +0100
Subject: [Biopython] DIHEDRAL ANGLES from PDB
In-Reply-To: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>
References: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>
Message-ID: <BANLkTikpw94xJaU68FZBTwZMoX2u8=4c+w@mail.gmail.com>

On Wed, Jun 29, 2011 at 7:54 PM, Babban Mia <babbanmia at gmail.com> wrote:
> Hello Everyone
>
>
> I am looking for a tool that can calculate dihedral angle with in a python
> script between four atoms in PDB file.
>
> I hope Biopython has something to offer.
>
> Please advise.
>
> Best

Yes, try this:
http://www.warwick.ac.uk/go/peter_cock/python/ramachandran/

Peter

From dilara.ally at gmail.com  Wed Jun 29 18:55:35 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Wed, 29 Jun 2011 15:55:35 -0700
Subject: [Biopython] multiple sequence blast
Message-ID: <4E0BAD67.70305@gmail.com>

Hi All

I'm new to biopython and python.  I have 1000 files each with 100 
contigs and I'm interested in blasting each one of those contigs.  I can 
get a single file with multiple sequences to blast each file and then 
write the output.  But the problem comes with reading the file from a 
loop in the first place.  Thanks in advance for the help.  If I don't 
use the loop but instead assign fname=allfiles[1] then it will work.  
Does it have something to do with lists vs seq records??
Cheers, Dilara

Here is the code:

from Bio import SeqIO
from Bio.Blast import NCBIWWW
import time
import os

allfiles=os.listdir("/Users/dally/Desktop/NextGenData/Python_Scripts/pract_input/")
for fname in allfiles:
     print fname
     handle = open(fname, "rU") <==it doesn't recognize the file just 
the name?
     contigs =list(SeqIO.parse(handle,"fasta"))
     handle.close()
     i = 0
     start=time.time()
     for seq_record in contigs:
         print seq_record.id
         print seq_record.seq
         result_handle=NCBIWWW.qblast("blastn", "nr", 
seq_record.format("fasta"),hitlist_size=10)
         filename = "contig_%i.xml" % (i+1)
         print filename
         save_file = open(filename, "w")
         save_file.write(result_handle.read())
         save_file.close()
         result_handle.close()
         end=time.clock()
         elapsed=end-start
         min=elapsed/60 #CONVERT TO MINUTE
         print "Your stuff took", elapsed, "seconds to run, which is the 
same as ",min, "minutes"

From chapmanb at 50mail.com  Thu Jun 30 06:42:27 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Thu, 30 Jun 2011 06:42:27 -0400
Subject: [Biopython] multiple sequence blast
In-Reply-To: <4E0BAD67.70305@gmail.com>
References: <4E0BAD67.70305@gmail.com>
Message-ID: <20110630104227.GA2883@sobchak>

Dilara;
Thanks for the message. It would be helpful if you'd include the
error message traceback that you got stuck on; this will help
pinpoint the problem.

>From reading your code, my guess is that you are getting and IOError
about files not existing. When you do os.listdir, it only includes
the name of the files, not the full path to where they are located.

> allfiles=os.listdir("/Users/dally/Desktop/NextGenData/Python_Scripts/pract_input/")
> for fname in allfiles:
>     print fname
>     handle = open(fname, "rU") <==it doesn't recognize the file just the name?

You can fix this by using os.path.join with the directory name and
fname. For instance:

>>> dirname = "biopython"
>>> allfiles = os.listdir(dirname)
>>> print allfiles
['CONTRIB', 'Scripts', 'Doc', '.git', 'MANIFEST.in', 'Bio', 'BioSQL', 'README', 
'DEPRECATED', 'Tests', 'NEWS', 'setup.py', '.gitignore', 'do2to3.py', 'LICENSE']
>>> print [os.path.join(dirname, f) for f in allfiles]
['biopython/CONTRIB', 'biopython/Scripts', 'biopython/Doc', 'biopython/.git', 'biopython/MANIFEST.in', 
'biopython/Bio', 'biopython/BioSQL', 'biopython/README', 'biopython/DEPRECATED', 'biopython/Tests', 
'biopython/NEWS', 'biopython/setup.py', 'biopython/.gitignore', 'biopython/do2to3.py', 'biopython/LICENSE']

Hope this helps,
Brad

From dilara.ally at gmail.com  Thu Jun 30 21:21:47 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Thu, 30 Jun 2011 18:21:47 -0700
Subject: [Biopython] Having a hard time getting a handle on handles
Message-ID: <4E0D212B.4040206@gmail.com>

Hi All

I have ~700,000 contigs that I would like to blast search and then from 
the blast record parse out particular pieces of information from the 
BLAST report.  I can get my code to pull in files and then loop over 
seq_records, blast, and then write a BLAST report.  But since I don't 
want to have 700,000 BLAST reports, I'd like to parse particular pieces 
of information from the report and store it in a table.  This is the 
error I get from the code I have pasted below:

/Users/dally/Desktop/NextGenData/Python_Scripts/batchedfastafiles/group_1.fasta
1
0
GTCTTCGGCGTTGCACCGGCGATGAAGAACCAGTACGAGGCGTCTGGCGAGAGTAACAACGCTG
Traceback (most recent call last):
   File "<stdin>", line 13, in <module>
NameError: name 'NCBIXML' is not defined

Do i have to close the result_handle and then reopen it?  If so why?  
Thanks in advance for your help.
>
> from Bio import SeqIO
> from Bio.Blast import NCBIWWW
> import time
> import os
> import os.path
>
> dirname1="/Users/dally/Desktop/NextGenData/Python_Scripts/batchedfastafiles/"
> allfiles=os.listdir(dirname1)
> fanddir=[os.path.join(dirname1,fname) for fname in allfiles]
> i = 0
> for f in fanddir:
>     print f
>     handle = open(f, "rU")
>     contigs =list(SeqIO.parse(handle,"fasta"))
>     handle.close()
>     start=time.time()
>     for seq_record in contigs:
>         i=i+1
>         print seq_record.id
>         print seq_record.seq
>         result_handle=NCBIWWW.qblast("blastn", "nr", 
> seq_record.format("fasta"),hitlist_size=10)
>         blast_record=list(NCBIXML.read(result_handle)) <== HERE IS THE 
> PROBLEM
>         E_VALUE_THRESH = 0.000004
>         countr=0
>         for alignment in blast_record.alignments:
>             countr=countr+1
>             for hsp in alignment.hsps:
>                 if hsp.expect < E_VALUE_THRESH:
>                     print '****Alignment****'
>                     print 'sequence:', alignment.title
>                     print 'length:', alignment.length
>                     print 'e value:', hsp.expect
>                     print hsp.query[0:75] + '...'
>                     print hsp.match[0:75] + '...'
>                     print hsp.sbjct[0:75] + '...'


From eric.talevich at gmail.com  Thu Jun 30 23:24:04 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Thu, 30 Jun 2011 23:24:04 -0400
Subject: [Biopython] Having a hard time getting a handle on handles
In-Reply-To: <4E0D212B.4040206@gmail.com>
References: <4E0D212B.4040206@gmail.com>
Message-ID: <BANLkTinF=T-0OMHJNmbg9bM2E2ZP61xrCw@mail.gmail.com>

On Thu, Jun 30, 2011 at 9:21 PM, Dilara Ally <dilara.ally at gmail.com> wrote:

> Hi All
>
> I have ~700,000 contigs that I would like to blast search and then from the
> blast record parse out particular pieces of information from the BLAST
> report.  I can get my code to pull in files and then loop over seq_records,
> blast, and then write a BLAST report.  But since I don't want to have
> 700,000 BLAST reports, I'd like to parse particular pieces of information
> from the report and store it in a table.  This is the error I get from the
> code I have pasted below:
>
> /Users/dally/Desktop/**NextGenData/Python_Scripts/**
> batchedfastafiles/group_1.**fasta
> 1
> 0
> GTCTTCGGCGTTGCACCGGCGATGAAGAAC**CAGTACGAGGCGTCTGGCGAGAGTAACAAC**GCTG
> Traceback (most recent call last):
>  File "<stdin>", line 13, in <module>
> NameError: name 'NCBIXML' is not defined
>
> Do i have to close the result_handle and then reopen it?  If so why?
>  Thanks in advance for your help.
>

Try adding this import to the top of your script:

from Bio.Blast import NCBIXML

Does it work now?

In general, whenever you see a NameError you should check for (a) missing
imports and (b) mis-typed variable names. The problem is usually one of
those.

Cheers,
Eric

From dilara.ally at gmail.com  Thu Jun 30 23:50:52 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Thu, 30 Jun 2011 20:50:52 -0700
Subject: [Biopython] Having a hard time getting a handle on handles
In-Reply-To: <BANLkTinF=T-0OMHJNmbg9bM2E2ZP61xrCw@mail.gmail.com>
References: <4E0D212B.4040206@gmail.com>
	<BANLkTinF=T-0OMHJNmbg9bM2E2ZP61xrCw@mail.gmail.com>
Message-ID: <4E0D441C.5020600@gmail.com>

Thanks, I tried that and now the error is

Traceback (most recent call last):
   File "<stdin>", line 12, in <module>
TypeError: iteration over non-sequence

Dilara

On 6/30/11 8:24 PM, Eric Talevich wrote:
> from Bio.Blast import NCBIXML

From p.j.a.cock at googlemail.com  Wed Jun  1 07:43:43 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 1 Jun 2011 08:43:43 +0100
Subject: [Biopython] missing dtd in Bio.Entrez
In-Reply-To: <BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
References: <mailman.16532.1306902457.2958.biopython-dev@lists.open-bio.org>
	<BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
Message-ID: <BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>

Hi Guy,

You have to have subscribed to the mailing list in order
to post to it - sadly this became necessary due to spam.

Thank you for your email, but could you give a little more
detail. Which version of Biopython do you have? Use:

import Bio
print Bio.__version__

The DTD file pubmed_110101.dtd was added to our
repository in September 2010, so should have been in
Biopython 1.56 and 1.57:-

https://github.com/biopython/biopython/commit/9ea066c5de4e8d64d16f2774bed78e0b69777b8a#Bio/Entrez/DTDs/pubmed_110101.dtd

Regards,

Peter

On Wed, Jun 1, 2011 at 5:32 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> ---------- Forwarded message ----------
> From:?Guy Eakin <guyeakin at gmail.com>
> To:?biopython-dev at biopython.org
> Date:?Wed, 1 Jun 2011 00:27:15 -0400
> Subject:?missing dtd in Bio.Entrez
> http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_110101.dtd
>
> The above is missing from the current biopython distribution. The
> error message requests that this email address be notified.
>
> Thanks,
> Guy Eakin
>
>



From guyeakin at gmail.com  Wed Jun  1 08:33:55 2011
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 1 Jun 2011 04:33:55 -0400
Subject: [Biopython] missing dtd in Bio.Entrez
In-Reply-To: <BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>
References: <mailman.16532.1306902457.2958.biopython-dev@lists.open-bio.org>
	<BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
	<BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>
Message-ID: <BANLkTik92b=dHN76mjb9dP6juLsGm4pLBw@mail.gmail.com>

Well, I suppose that explains it.  version 1.54 is what I am using.  I
downloaded it from the Ubuntu software center earlier tonight. I had
just assumed that was most recent. Sorry for the red herring.

guy

On Wed, Jun 1, 2011 at 3:43 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi Guy,
>
> You have to have subscribed to the mailing list in order
> to post to it - sadly this became necessary due to spam.
>
> Thank you for your email, but could you give a little more
> detail. Which version of Biopython do you have? Use:
>
> import Bio
> print Bio.__version__
>
> The DTD file pubmed_110101.dtd was added to our
> repository in September 2010, so should have been in
> Biopython 1.56 and 1.57:-
>
> https://github.com/biopython/biopython/commit/9ea066c5de4e8d64d16f2774bed78e0b69777b8a#Bio/Entrez/DTDs/pubmed_110101.dtd
>
> Regards,
>
> Peter
>
> On Wed, Jun 1, 2011 at 5:32 AM, Guy Eakin <guyeakin at gmail.com> wrote:
>> ---------- Forwarded message ----------
>> From:?Guy Eakin <guyeakin at gmail.com>
>> To:?biopython-dev at biopython.org
>> Date:?Wed, 1 Jun 2011 00:27:15 -0400
>> Subject:?missing dtd in Bio.Entrez
>> http://eutils.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_110101.dtd
>>
>> The above is missing from the current biopython distribution. The
>> error message requests that this email address be notified.
>>
>> Thanks,
>> Guy Eakin
>>
>>
>



From p.j.a.cock at googlemail.com  Wed Jun  1 08:42:47 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 1 Jun 2011 09:42:47 +0100
Subject: [Biopython] missing dtd in Bio.Entrez
In-Reply-To: <BANLkTik92b=dHN76mjb9dP6juLsGm4pLBw@mail.gmail.com>
References: <mailman.16532.1306902457.2958.biopython-dev@lists.open-bio.org>
	<BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
	<BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>
	<BANLkTik92b=dHN76mjb9dP6juLsGm4pLBw@mail.gmail.com>
Message-ID: <BANLkTi=xKZEgdaLogkcT4aV0cCpF7WPc5A@mail.gmail.com>

On Wed, Jun 1, 2011 at 9:33 AM, Guy Eakin <guyeakin at gmail.com> wrote:
> Well, I suppose that explains it. ?version 1.54 is what I am using. ?I
> downloaded it from the Ubuntu software center earlier tonight. I had
> just assumed that was most recent. Sorry for the red herring.
>
> guy

Yes, that makes sense.

If you want a more recent version, uou can probably ask for the latest
version to be offered on an Ubuntu backport repository - otherwise natty
has Biopython 1.56 and oneiric has 1.57 according to this:

http://packages.ubuntu.com/search?suite=all&searchon=names&keywords=python-biopython

Alternatively, try:

sudo apt-get remove python-biopython python-biopython-doc python-biopython-sql
sudo apt-get build-dep python-biopython python-biopython-doc
python-biopython-sql

and then install from source.

Peter



From guyeakin at gmail.com  Wed Jun  1 08:51:13 2011
From: guyeakin at gmail.com (Guy Eakin)
Date: Wed, 1 Jun 2011 04:51:13 -0400
Subject: [Biopython] missing dtd in Bio.Entrez
In-Reply-To: <BANLkTi=xKZEgdaLogkcT4aV0cCpF7WPc5A@mail.gmail.com>
References: <mailman.16532.1306902457.2958.biopython-dev@lists.open-bio.org>
	<BANLkTi=rhZ_fPob4UScF=Gz-jJyGiSz0bw@mail.gmail.com>
	<BANLkTimpYa6t3_8G74o=w42A5Cw2s9JL8w@mail.gmail.com>
	<BANLkTik92b=dHN76mjb9dP6juLsGm4pLBw@mail.gmail.com>
	<BANLkTi=xKZEgdaLogkcT4aV0cCpF7WPc5A@mail.gmail.com>
Message-ID: <BANLkTimSXquetU1LEnghhL959UjnH0dhcA@mail.gmail.com>

Thanks for the help.  I'll upgrade soon. Bio as well as the OS. I am
an infrequent user of linux and biopython so have been doubly lazy.
Guy

On Wed, Jun 1, 2011 at 4:42 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Wed, Jun 1, 2011 at 9:33 AM, Guy Eakin <guyeakin at gmail.com> wrote:
>> Well, I suppose that explains it. ?version 1.54 is what I am using. ?I
>> downloaded it from the Ubuntu software center earlier tonight. I had
>> just assumed that was most recent. Sorry for the red herring.
>>
>> guy
>
> Yes, that makes sense.
>
> If you want a more recent version, uou can probably ask for the latest
> version to be offered on an Ubuntu backport repository - otherwise natty
> has Biopython 1.56 and oneiric has 1.57 according to this:
>
> http://packages.ubuntu.com/search?suite=all&searchon=names&keywords=python-biopython
>
> Alternatively, try:
>
> sudo apt-get remove python-biopython python-biopython-doc python-biopython-sql
> sudo apt-get build-dep python-biopython python-biopython-doc
> python-biopython-sql
>
> and then install from source.
>
> Peter
>



From chaouki.amir at gmail.com  Wed Jun  1 13:46:43 2011
From: chaouki.amir at gmail.com (amir chaouki)
Date: Wed, 1 Jun 2011 14:46:43 +0100
Subject: [Biopython] (no subject)
Message-ID: <BANLkTinJ0YK0ePF_LTDtGFBE7JfYfMGw0w@mail.gmail.com>

biopython does the alignement or only reads alignement files formats????

-- 
*Amir Chaouki*


From p.j.a.cock at googlemail.com  Thu Jun  2 13:17:57 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 2 Jun 2011 14:17:57 +0100
Subject: [Biopython] (no subject)
In-Reply-To: <BANLkTinJ0YK0ePF_LTDtGFBE7JfYfMGw0w@mail.gmail.com>
References: <BANLkTinJ0YK0ePF_LTDtGFBE7JfYfMGw0w@mail.gmail.com>
Message-ID: <BANLkTikoE=Kn8zJMVtmzxEp+c1nLw2C1ZQ@mail.gmail.com>

On Wed, Jun 1, 2011 at 2:46 PM, amir chaouki <chaouki.amir at gmail.com> wrote:
> biopython does the alignement or only reads alignement files formats????
>
> --
> *Amir Chaouki*

Hi Amir,

Biopython's Bio.AlignIO module reads alignment files, and there
are wrappers to help call some command line alignment tools in
Bio.Align.Applications as well. Unless you are doing research on
alignment algorithms, there doesn't seem to be much need for
actually implementing this kind of thing in Python directly.

Also, there is a pairwise alignment module, Bio.pairwise2, which
might be of interest.

Peter

P.S. Please give your emails a subject


From from.d.putto at gmail.com  Mon Jun  6 13:29:24 2011
From: from.d.putto at gmail.com (Sheila the angel)
Date: Mon, 6 Jun 2011 15:29:24 +0200
Subject: [Biopython] processing XML files in Biopython
Message-ID: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>

Hi All,

I am new to BioPython. I have simple question 'How can I process XML files
in Biopython?'
For example I have NCBI Reference Sequence ID 'NP_997807.1'
I want to download the 'xml' file and want to extract certain information
(e.g. GeneID, amino acid length etc.).
To download the file I did

from Bio import Entrez
handle = Entrez.efetch(db="protein", id= "NP_997807.1", retmode="xml")
record = Entrez.read(handle)
handle.close()

Now I have no clue how to extract certain information (like GeneID) :(
plz help

--
Cheers

Sheila d. Angela


From p.j.a.cock at googlemail.com  Mon Jun  6 13:35:15 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 14:35:15 +0100
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
Message-ID: <BANLkTikys4hhxviVq3WUd_Toon_6uHU8cw@mail.gmail.com>

On Mon, Jun 6, 2011 at 2:29 PM, Sheila the angel <from.d.putto at gmail.com> wrote:
> Hi All,
>
> I am new to BioPython. I have simple question 'How can I process XML files
> in Biopython?'
> For example I have NCBI Reference Sequence ID 'NP_997807.1'

Personally I still download the plain text GenBank format file, and
use Biopython's Bio.SeqIO module to parse that.

> I want to download the 'xml' file and want to extract certain information
> (e.g. GeneID, amino acid length etc.).
> To download the file I did
>
> from Bio import Entrez
> handle = Entrez.efetch(db="protein", id= "NP_997807.1", retmode="xml")
> record = Entrez.read(handle)
> handle.close()
>
> Now I have no clue how to extract certain information (like GeneID) :(
> plz help

If you want to use the XML, then the Bio.Entrez.parse() function should
turn it into a nested structure of Python objects (dicts and lists). Or,
there are several built in XML parsers that come with Python, such
as ElementTree. That could be more efficient if you just wanted to
get one or two bits of information like a GeneID.

Peter


From reece at harts.net  Mon Jun  6 14:30:57 2011
From: reece at harts.net (Reece Hart)
Date: Mon, 6 Jun 2011 07:30:57 -0700
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTikys4hhxviVq3WUd_Toon_6uHU8cw@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
	<BANLkTikys4hhxviVq3WUd_Toon_6uHU8cw@mail.gmail.com>
Message-ID: <BANLkTimoFeXDjd5LEfszx5hA3HeQbKE8KQ@mail.gmail.com>

On Mon, Jun 6, 2011 at 6:35 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> If you want to use the XML, then the Bio.Entrez.parse() function should
> turn it into a nested structure of Python objects (dicts and lists). Or,
> there are several built in XML parsers that come with Python, such
> as ElementTree. That could be more efficient if you just wanted to
> get one or two bits of information like a GeneID.
>

In addition, the Bio.Entrez parser is not namespace-aware and therefore
won't parse some NCBI XML at all (e.g., downloaded dbSNP files). Can someone
with more experience here please corroborate?

And, if that is correct, what is the advantage of using Bio.Entrez.parse
over using another Python XML lib?

Thanks,
Reece


From p.j.a.cock at googlemail.com  Mon Jun  6 14:37:53 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 15:37:53 +0100
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTimoFeXDjd5LEfszx5hA3HeQbKE8KQ@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
	<BANLkTikys4hhxviVq3WUd_Toon_6uHU8cw@mail.gmail.com>
	<BANLkTimoFeXDjd5LEfszx5hA3HeQbKE8KQ@mail.gmail.com>
Message-ID: <BANLkTikaPRc=34QkHdB5VzHz7k0ynCk=kw@mail.gmail.com>

On Mon, Jun 6, 2011 at 3:30 PM, Reece Hart <reece at harts.net> wrote:
> On Mon, Jun 6, 2011 at 6:35 AM, Peter Cock wrote:
>>
>> If you want to use the XML, then the Bio.Entrez.parse() function should
>> turn it into a nested structure of Python objects (dicts and lists). Or,
>> there are several built in XML parsers that come with Python, such
>> as ElementTree. That could be more efficient if you just wanted to
>> get one or two bits of information like a GeneID.
>
> In addition, the?Bio.Entrez parser is not namespace-aware and therefore
> won't parse some NCBI XML at all (e.g., downloaded dbSNP files). Can
> someone with more experience here please corroborate?

See http://bugzilla.open-bio.org/show_bug.cgi?id=2771 for dbSNP.
Do you have any other problem databases with Entrez XML?

> And, if that is correct, what is the advantage of using Bio.Entrez.parse
> over using another Python XML lib?

If you're not scared of XML, not much.

Peter



From david.suarez at yahoo.com  Mon Jun  6 14:37:43 2011
From: david.suarez at yahoo.com (=?ISO-8859-1?Q?David_Su=E1rez_Pascal?=)
Date: Mon, 6 Jun 2011 09:37:43 -0500
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
Message-ID: <BANLkTi=p0WEJ_DTk_o-5LmrY=5tJk-u9Vg@mail.gmail.com>

Sheila,
I don't think you have to deal with XML files. Indeed I tried your code and
what I detected was that Entrez.read already parsed the data.
What I get when I try your code is a list:
>>> type(record)
<class 'Bio.Entrez.Parser.ListElement'>

which contains a dict with the following keys:
>>> record[0].keys()
[u'GBSeq_moltype',
 u'GBSeq_source',
 u'GBSeq_sequence',
 u'GBSeq_primary-accession',
 u'GBSeq_definition',
 u'GBSeq_accession-version',
 u'GBSeq_topology',
 u'GBSeq_length',
 u'GBSeq_feature-table',
 u'GBSeq_create-date',
 u'GBSeq_other-seqids',
 u'GBSeq_division',
 u'GBSeq_taxonomy',
 u'GBSeq_comment',
 u'GBSeq_source-db',
 u'GBSeq_references',
 u'GBSeq_update-date',
 u'GBSeq_organism',
 u'GBSeq_locus']

If you got the same response, then you can just do:
>>> record[0]['GBSeq_locus']
'NP_997807'

I hope this helps.

David

2011/6/6 Sheila the angel <from.d.putto at gmail.com>

> Hi All,
>
> I am new to BioPython. I have simple question 'How can I process XML files
> in Biopython?'
> For example I have NCBI Reference Sequence ID 'NP_997807.1'
> I want to download the 'xml' file and want to extract certain information
> (e.g. GeneID, amino acid length etc.).
> To download the file I did
>
> from Bio import Entrez
> handle = Entrez.efetch(db="protein", id= "NP_997807.1", retmode="xml")
> record = Entrez.read(handle)
> handle.close()
>
> Now I have no clue how to extract certain information (like GeneID) :(
> plz help
>
> --
> Cheers
>
> Sheila d. Angela
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From from.d.putto at gmail.com  Mon Jun  6 15:10:04 2011
From: from.d.putto at gmail.com (Sheila the angel)
Date: Mon, 6 Jun 2011 17:10:04 +0200
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTi=p0WEJ_DTk_o-5LmrY=5tJk-u9Vg@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
	<BANLkTi=p0WEJ_DTk_o-5LmrY=5tJk-u9Vg@mail.gmail.com>
Message-ID: <BANLkTi=xNcQKa0MuKAdfK2dOyjLmCBcYcg@mail.gmail.com>

@David- Yes it works but few small question
1. how to extract the information not sored in directly in record[0].keys()
for an example
record[0]['GBSeq_feature-table']
gives output which seems parsed in XML. From this how can I extract the
'GBQualifier_name' ?

2. just out of curiosity  'why we use record[0] to extract information e.g.
record[0]['GBSeq_definition']  '



On Mon, Jun 6, 2011 at 4:37 PM, David Su?rez Pascal
<david.suarez at yahoo.com>wrote:

> Sheila,
> I don't think you have to deal with XML files. Indeed I tried your code and
> what I detected was that Entrez.read already parsed the data.
> What I get when I try your code is a list:
> >>> type(record)
> <class 'Bio.Entrez.Parser.ListElement'>
>
> which contains a dict with the following keys:
> >>> record[0].keys()
> [u'GBSeq_moltype',
>  u'GBSeq_source',
>  u'GBSeq_sequence',
>  u'GBSeq_primary-accession',
>  u'GBSeq_definition',
>  u'GBSeq_accession-version',
>  u'GBSeq_topology',
>  u'GBSeq_length',
>  u'GBSeq_feature-table',
>  u'GBSeq_create-date',
>  u'GBSeq_other-seqids',
>  u'GBSeq_division',
>  u'GBSeq_taxonomy',
>  u'GBSeq_comment',
>  u'GBSeq_source-db',
>  u'GBSeq_references',
>  u'GBSeq_update-date',
>  u'GBSeq_organism',
>  u'GBSeq_locus']
>
> If you got the same response, then you can just do:
> >>> record[0]['GBSeq_locus']
> 'NP_997807'
>
> I hope this helps.
>
> David
>
> 2011/6/6 Sheila the angel <from.d.putto at gmail.com>
>
>> Hi All,
>>
>> I am new to BioPython. I have simple question 'How can I process XML files
>> in Biopython?'
>> For example I have NCBI Reference Sequence ID 'NP_997807.1'
>> I want to download the 'xml' file and want to extract certain information
>> (e.g. GeneID, amino acid length etc.).
>> To download the file I did
>>
>> from Bio import Entrez
>> handle = Entrez.efetch(db="protein", id= "NP_997807.1", retmode="xml")
>> record = Entrez.read(handle)
>> handle.close()
>>
>> Now I have no clue how to extract certain information (like GeneID) :(
>> plz help
>>
>> --
>> Cheers
>>
>> Sheila d. Angela
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>



From p.j.a.cock at googlemail.com  Mon Jun  6 15:16:23 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 16:16:23 +0100
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTi=xNcQKa0MuKAdfK2dOyjLmCBcYcg@mail.gmail.com>
References: <BANLkTimLGc0aLPj+8Qs9RN+yqLANabZctg@mail.gmail.com>
	<BANLkTi=p0WEJ_DTk_o-5LmrY=5tJk-u9Vg@mail.gmail.com>
	<BANLkTi=xNcQKa0MuKAdfK2dOyjLmCBcYcg@mail.gmail.com>
Message-ID: <BANLkTinLipX-71yTynSRF3+DGytyacoR+Q@mail.gmail.com>

On Mon, Jun 6, 2011 at 4:10 PM, Sheila the angel <from.d.putto at gmail.com> wrote:
> @David- Yes it works but few small question
> 1. how to extract the information not sored in directly in record[0].keys()
> for an example
> record[0]['GBSeq_feature-table']
> gives output which seems parsed in XML. From this how can I extract the
> 'GBQualifier_name' ?
>
> 2. just out of curiosity ?'why we use record[0] to extract information e.g.
> record[0]['GBSeq_definition'] ?'

This is because the parser gave you a list, and we want the first element
(element zero), which was a dictionary, and we picked the key GBSeq_definition
This is what I meant by the Bio.Entrez parser turns the XML into Python
objects (lists and dicts containing strings/numbers). The structure comes
from the XML itself.

As I said, if you know beforehand exactly which XML element you want,
one of the Python standard libraries might be more direct.

Peter



From dilara.ally at gmail.com  Mon Jun  6 16:18:44 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Mon, 06 Jun 2011 09:18:44 -0700
Subject: [Biopython] installation failure on mac OS10.6.7
Message-ID: <4DECFDE4.8040705@gmail.com>

Hi,

I was trying to install Biopython on mac OS 10.6.7.  I checked the 
archives and installed Apple's Xcode ver4.0.2.  But I got this error 
message:


building 'Bio.cpairwise2' extension
gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 
-g -O2 -DNDEBUG -g -O3 -IBio 
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c 
Bio/cpairwise2module.c -o 
build/temp.macosx-10.3-fat-2.6/Bio/cpairwise2module.o
unable to execute gcc-4.0: No such file or directory
error: command 'gcc-4.0' failed with exit status 1

Thanks so much for the help.

Cheers, Dilara


From p.j.a.cock at googlemail.com  Mon Jun  6 16:38:01 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 17:38:01 +0100
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <4DECFDE4.8040705@gmail.com>
References: <4DECFDE4.8040705@gmail.com>
Message-ID: <BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>

On Mon, Jun 6, 2011 at 5:18 PM, Dilara Ally <dilara.ally at gmail.com> wrote:
> Hi,
>
> I was trying to install Biopython on mac OS 10.6.7. ?I checked the archives
> and installed Apple's Xcode ver4.0.2. ?But I got this error message:
>
>
> building 'Bio.cpairwise2' extension
> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g
> -O2 -DNDEBUG -g -O3 -IBio
> -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
> Bio/cpairwise2module.c -o
> build/temp.macosx-10.3-fat-2.6/Bio/cpairwise2module.o
> unable to execute gcc-4.0: No such file or directory
> error: command 'gcc-4.0' failed with exit status 1
>
> Thanks so much for the help.
>
> Cheers, Dilara

That's strange - I have it under /usr/bin/gcc-4.0

When you installed X Code, did you tick the optional 10.4 SDK as recommended
here http://biopython.org/wiki/Download ?


Peter



From dilara.ally at gmail.com  Mon Jun  6 16:46:55 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Mon, 06 Jun 2011 09:46:55 -0700
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
Message-ID: <4DED047F.2090505@gmail.com>

I thought I did.  How can I find out if it has 10.4 SDK?

Thanks.

Dilara

On 6/6/11 9:38 AM, Peter Cock wrote:
> On Mon, Jun 6, 2011 at 5:18 PM, Dilara Ally<dilara.ally at gmail.com>  wrote:
>> Hi,
>>
>> I was trying to install Biopython on mac OS 10.6.7.  I checked the archives
>> and installed Apple's Xcode ver4.0.2.  But I got this error message:
>>
>>
>> building 'Bio.cpairwise2' extension
>> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g
>> -O2 -DNDEBUG -g -O3 -IBio
>> -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
>> Bio/cpairwise2module.c -o
>> build/temp.macosx-10.3-fat-2.6/Bio/cpairwise2module.o
>> unable to execute gcc-4.0: No such file or directory
>> error: command 'gcc-4.0' failed with exit status 1
>>
>> Thanks so much for the help.
>>
>> Cheers, Dilara
> That's strange - I have it under /usr/bin/gcc-4.0
>
> When you installed X Code, did you tick the optional 10.4 SDK as recommended
> here http://biopython.org/wiki/Download ?
>
>
> Peter
>


From ilancaster at gmail.com  Mon Jun  6 16:56:13 2011
From: ilancaster at gmail.com (Ian Lancaster)
Date: Mon, 6 Jun 2011 12:56:13 -0400
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
Message-ID: <5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>

The 10.4 SDK support option was removed in Xcode 4, along with gcc 4.0 support necessary for building numpy and others. Xcode 3 installs Apple's gcc 4.0, but Xcode 4 installs only 4.2. The easiest solution I've found is to start clean by removing Xcode 4, install Xcode 3 (which is free), and then upgrade back to Xcode 4. Then you will have both the required gcc 4.0 and 4.2. 

http://stackoverflow.com/questions/5333490/how-can-we-restore-ppc-ppc64-as-well-as-full-10-4-10-5-sdk-support-to-xcode-4

Ian

Sorry for duplicates, I forgot to cc the list at first.

On Jun 6, 2011, at 12:38 PM, Peter Cock wrote:

> On Mon, Jun 6, 2011 at 5:18 PM, Dilara Ally <dilara.ally at gmail.com> wrote:
>> Hi,
>> 
>> I was trying to install Biopython on mac OS 10.6.7.  I checked the archives
>> and installed Apple's Xcode ver4.0.2.  But I got this error message:
>> 
>> 
>> building 'Bio.cpairwise2' extension
>> gcc-4.0 -fno-strict-aliasing -fno-common -dynamic -arch ppc -arch i386 -g
>> -O2 -DNDEBUG -g -O3 -IBio
>> -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
>> Bio/cpairwise2module.c -o
>> build/temp.macosx-10.3-fat-2.6/Bio/cpairwise2module.o
>> unable to execute gcc-4.0: No such file or directory
>> error: command 'gcc-4.0' failed with exit status 1
>> 
>> Thanks so much for the help.
>> 
>> Cheers, Dilara
> 
> That's strange - I have it under /usr/bin/gcc-4.0
> 
> When you installed X Code, did you tick the optional 10.4 SDK as recommended
> here http://biopython.org/wiki/Download ?
> 
> 
> Peter
> 
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython




From p.j.a.cock at googlemail.com  Mon Jun  6 16:59:05 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 17:59:05 +0100
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
Message-ID: <BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>

On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> The 10.4 SDK support option was removed in Xcode 4, along with gcc 4.0
> support necessary for building numpy and others. Xcode 3 installs Apple's
> gcc 4.0, but Xcode 4 installs only 4.2. The easiest solution I've found is to
> start clean by removing Xcode 4, install Xcode 3 (which is free), and then
> upgrade back to Xcode 4. Then you will have both the required gcc 4.0 and 4.2.
>
> http://stackoverflow.com/questions/5333490/how-can-we-restore-ppc-ppc64-as-well-as-full-10-4-10-5-sdk-support-to-xcode-4
>
> Ian

Hi Ian,

That's a very interesting link - do you have anything specific on what it is
that numpy (and therefore likely also Biopython) doesn't like?

Thank you,

Peter


From devaniranjan at gmail.com  Mon Jun  6 17:53:51 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Mon, 6 Jun 2011 13:53:51 -0400
Subject: [Biopython] _align in pairwise
Message-ID: <BANLkTik+mh2PCH5TFAD5aYXYnA8smcv_9w@mail.gmail.com>

I want to align one sequence to several multiple sequences using pairwise
alignment --I am trying to use _align but getting stumped by the variables I
need to specify.

Can someone give me some info on that? --Thanks a lot


From p.j.a.cock at googlemail.com  Mon Jun  6 18:01:28 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 19:01:28 +0100
Subject: [Biopython] _align in pairwise
In-Reply-To: <BANLkTik+mh2PCH5TFAD5aYXYnA8smcv_9w@mail.gmail.com>
References: <BANLkTik+mh2PCH5TFAD5aYXYnA8smcv_9w@mail.gmail.com>
Message-ID: <BANLkTinEgOZBjFuciO_2pLwYXLhOPusigA@mail.gmail.com>

On Mon, Jun 6, 2011 at 6:53 PM, George Devaniranjan
<devaniranjan at gmail.com> wrote:
> I want to align one sequence to several multiple sequences using pairwise
> alignment --I am trying to use _align but getting stumped by the variables I
> need to specify.
>
> Can someone give me some info on that? --Thanks a lot

As a general rule, anything in python starting with a single underscore
is a private method/function/variable and should not be used.

Have you looked at the help, either from within Python or here:
http://www.biopython.org/DIST/docs/api/Bio.pairwise2-module.html

Peter


From p.j.a.cock at googlemail.com  Mon Jun  6 18:23:05 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 19:23:05 +0100
Subject: [Biopython] _align in pairwise
In-Reply-To: <BANLkTim4nwoaHYcXphN1k836sUXkOmyN6w@mail.gmail.com>
References: <BANLkTik+mh2PCH5TFAD5aYXYnA8smcv_9w@mail.gmail.com>
	<BANLkTinEgOZBjFuciO_2pLwYXLhOPusigA@mail.gmail.com>
	<BANLkTim4nwoaHYcXphN1k836sUXkOmyN6w@mail.gmail.com>
Message-ID: <BANLkTinsvxAhZxZ1=-kCHVFRHnLG-ExaCQ@mail.gmail.com>

Hi George,

Please try to CC the mailing list in your replies.

On Mon, Jun 6, 2011 at 7:08 PM, George Devaniranjan
<devaniranjan at gmail.com> wrote:
> oh thanks Peter --I am a newbie to python and used to C programming so even
> in python my use of classes is very limited and tend to use simple
> functions.
>
> what I want to do is.......
> I have a file containing 10 FASTA like sequences (actually 1000s but for now
> 10) and I want to calculate the alignment score for the first 1 with the
> other 9 using FASTA like symbols and also use a blossum like matrix to look
> up penalties.
>
> _align looked like a good candidate so I tried to use that--is there another
> way?
>
> Thanks a lot,
> George

Something like this? Check if you want global or local alignments:

http://lists.open-bio.org/pipermail/biopython/2009-January/004855.html

Peter


From ilancaster at gmail.com  Mon Jun  6 19:14:10 2011
From: ilancaster at gmail.com (Ian Lancaster)
Date: Mon, 6 Jun 2011 15:14:10 -0400
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
	<BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
Message-ID: <A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>

After gcc 4.0 the Wno-long-double option was removed, among others, which was apparently used in building python. However, I don't think the problem is with gcc per se, but the version of python. 

For instance, installing numpy with Apple's python2.6 and 2.5 failed on my machine with the gcc 4.2 compiler. Then I installed python2.7 from the official package at python.org; numpy and Biopython installed and tested fine (I used pip). This might be a better solution for Snow Leopard users, particularly those who have only installed Xcode 4. 

Ian

On Jun 6, 2011, at 12:59 PM, Peter Cock wrote:

> On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> 
> Hi Ian,
> 
> That's a very interesting link - do you have anything specific on what it is
> that numpy (and therefore likely also Biopython) doesn't like?
> 
> Thank you,
> 
> Peter




From mictadlo at gmail.com  Mon Jun  6 21:52:21 2011
From: mictadlo at gmail.com (Michal)
Date: Tue, 07 Jun 2011 07:52:21 +1000
Subject: [Biopython] IUPAC code contribution
Message-ID: <4DED4C15.4010705@gmail.com>

Hello,
I would like to contribute the following IUPAC function to Biopython:

def iupac_base(alignment):
     IUPAC = {
       ord('N'): 'N',
       ord('G'): 'G',
       ord('A'): 'A',
       ord('T'): 'T',
       ord('C'): 'C',
       ord('G') + ord('A'): 'R',
       ord('T') + ord('C'): 'Y',
       ord('A') + ord('C'): 'M',
       ord('G') + ord('T'): 'K',
       ord('G') + ord('C'): 'S',
       ord('A') + ord('T'): 'W',
       ord('A') + ord('C') + ord('T'): 'H',
       ord('G') + ord('T') + ord('C'): 'B',
       ord('G') + ord('C') + ord('A'): 'V',
       ord('G') + ord('A') + ord('T'): 'D',
       ord('G') + ord('A') + ord('T') + ord('C'): 'N'}

     return IUPAC[sum(map(ord, {}.fromkeys(alignment).keys()))]


a = iupac_base(['A','A','T','T','T'])

Cheers,
Michal


From mictadlo at gmail.com  Mon Jun  6 21:59:39 2011
From: mictadlo at gmail.com (Michal)
Date: Tue, 07 Jun 2011 07:59:39 +1000
Subject: [Biopython] multiprocessing problem with pysam
In-Reply-To: <20110515155346.GD2530@kunkel>
References: <4DA1137E.1090803@gmail.com> <20110410111510.GA2634@kunkel>
	<4DA2EC9D.7040004@gmail.com> <20110412013119.GF2053@kunkel>
	<4DCF660B.30309@gmail.com> <20110515155346.GD2530@kunkel>
Message-ID: <4DED4DCB.8070605@gmail.com>

On 05/16/2011 01:53 AM, Brad Chapman wrote:
> Michal;
>
> [multiprocessing]
> multiprocessing is sensitive to passing or calling complex class
> objects. My suggestion is to use functions without associated state
> attributes and pass in your information as standard python objects
> (strings, lists, dicts). I use a little decorator to make writing
> the functions passed easier:
>
> import functools
> def map_wrap(f):
>      @functools.wraps(f)
>      def wrapper(*args, **kwargs):
>          return apply(f, *args, **kwargs)
>      return wrapper
>
> Then would write your function as:
>
> @map_wrap
> def run_test(bam_filename, cultivars, ref_name):
>      bam_fh = pysam.Samfile(bam_filename, "rb")
>      print os.getpid(), ref_name, cultivars
>      return (os.getpid(), ref_name)
>
> and call it with:
>
> cultivars = 'Ja,Ea,As'.replace(' ', '').split(',')
> bam_filename = "/media/usb/tests/test.bam"
> bamfile = pysam.Samfile(bam_filename, "rb")
> ref_names = bamfile.references
> bamfile.close()
>
> pool = Pool()
> results = dict(pool.imap(run_test, ((bam_filename, cultivars, ref)
>                                      for ref in ref_names)))
> pool.close()
>
> Hope this helps,
> Brad
Thank you Brad it works and I also found the following solution:

import os
from multiprocessing import Pool
from pprint import pprint
import functools


def calc_p(fname, start_pos, end_pos, reference_name):
     print os.getpid()
     print "fname", fname
     print "reference_name", reference_name
     print "start_pos", start_pos
     print "end_pos", end_pos
     print
     return (reference_name, [os.getpid(), 'x1', 'x2'])


if __name__ == '__main__':
     pool = Pool()

     fname = "ex1.txt"
     references = ['Test1', 'Test2', 'Test3', 'Test4']

     run_test = functools.partial(calc_p, fname, 100, 120)
     result = dict(pool.imap_unordered(run_test, references))

     pprint(result)


Michal


From p.j.a.cock at googlemail.com  Mon Jun  6 22:18:29 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 6 Jun 2011 23:18:29 +0100
Subject: [Biopython] IUPAC code contribution
In-Reply-To: <4DED4C15.4010705@gmail.com>
References: <4DED4C15.4010705@gmail.com>
Message-ID: <BANLkTincLfkH+dbbPP_eWkNJTPDi7JWBQA@mail.gmail.com>

On Mon, Jun 6, 2011 at 10:52 PM, Michal <mictadlo at gmail.com> wrote:
> Hello,
> I would like to contribute the following IUPAC function to Biopython:
>
> def iupac_base(alignment):
> ? ?IUPAC = {
> ? ? ?ord('N'): 'N',
> ? ? ?ord('G'): 'G',
> ? ? ?ord('A'): 'A',
> ? ? ?ord('T'): 'T',
> ? ? ?ord('C'): 'C',
> ? ? ?ord('G') + ord('A'): 'R',
> ? ? ?ord('T') + ord('C'): 'Y',
> ? ? ?ord('A') + ord('C'): 'M',
> ? ? ?ord('G') + ord('T'): 'K',
> ? ? ?ord('G') + ord('C'): 'S',
> ? ? ?ord('A') + ord('T'): 'W',
> ? ? ?ord('A') + ord('C') + ord('T'): 'H',
> ? ? ?ord('G') + ord('T') + ord('C'): 'B',
> ? ? ?ord('G') + ord('C') + ord('A'): 'V',
> ? ? ?ord('G') + ord('A') + ord('T'): 'D',
> ? ? ?ord('G') + ord('A') + ord('T') + ord('C'): 'N'}
>
> ? ?return IUPAC[sum(map(ord, {}.fromkeys(alignment).keys()))]
>
>
> a = iupac_base(['A','A','T','T','T'])
>
> Cheers,
> Michal

Well it would need some documentation at least (e.g. a docstring).
What is is meant to do? It looks like you just want a reverse lookup
of Bio.Data.IUPACData.ambiguous_dna_values - e.g.

from Bio.Data.IUPACData import ambiguous_dna_values
rev_map = dict((frozenset(v),k) for (k,v) in ambiguous_dna_values.iteritems())
assert rev_map[frozenset('CG')] == rev_map[frozenset('GC')]

Peter



From dilara.ally at gmail.com  Mon Jun  6 22:29:15 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Mon, 6 Jun 2011 15:29:15 -0700
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
	<BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
	<A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>
Message-ID: <BANLkTimKRCXUE6aHeZi=gnFe1rWfyv=ysw@mail.gmail.com>

Hi Ian,

I've installed python2.7 and because of an earlier email  I removed Xcode4.0
and installed  Xcode3.0 +10.4 sdk then upgraded to Xcode4.0.  I also changed
the version of numpy and tested to see if I could import it.  There was no
problem importing numpy.

I tried to install biopython by directing entering the directory
biopython-1.57 and typing the command python setup.py install but got this
message:

creating build/lib.macosx-10.6-intel-2.7
error: could not create 'build/lib.macosx-10.6-intel-2.7': Permission denied

Then when I tried the easy install using this command:

sudo easy_install -f http://biopython.org/DIST/ biopython

I got the following error:  Is it still having trouble with the gcc 4.2
compiler

Searching for biopython
Reading http://biopython.org/DIST/
Best match: biopython 1.57
Downloading http://biopython.org/DIST/biopython-1.57.zip
Processing biopython-1.57.zip
Running biopython-1.57/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-8RE8Sh/biopython-1.57/egg-dist-tmp-YMF_hu
warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
warning: no previously-included files found matching 'Tests/Graphics/*.eps'
warning: no previously-included files found matching 'Tests/Graphics/*.svg'
warning: no previously-included files found matching 'Tests/Graphics/*.png'
warning: no previously-included files matching '*' found under directory
'Tests/UnitTests'
warning: no previously-included files matching '.cvsignore' found under
directory '*'
warning: no previously-included files matching '.gitignore' found under
directory '*'
warning: no previously-included files matching '*.pyc' found under directory
'*'
unable to execute gcc-4.2: No such file or directory
error: Setup script exited with error: command 'gcc-4.2' failed with exit
status 1


I'm stumped.

Thanks for the help.

Dilara



On Mon, Jun 6, 2011 at 12:14 PM, Ian Lancaster <ilancaster at gmail.com> wrote:

> After gcc 4.0 the Wno-long-double option was removed, among others, which
> was apparently used in building python. However, I don't think the problem
> is with gcc per se, but the version of python.
>
> For instance, installing numpy with Apple's python2.6 and 2.5 failed on my
> machine with the gcc 4.2 compiler. Then I installed python2.7 from the
> official package at python.org; numpy and Biopython installed and tested
> fine (I used pip). This might be a better solution for Snow Leopard users,
> particularly those who have only installed Xcode 4.
>
> Ian
>
> On Jun 6, 2011, at 12:59 PM, Peter Cock wrote:
>
> > On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster <ilancaster at gmail.com>
> wrote:
> >
> > Hi Ian,
> >
> > That's a very interesting link - do you have anything specific on what it
> is
> > that numpy (and therefore likely also Biopython) doesn't like?
> >
> > Thank you,
> >
> > Peter
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From ilancaster at gmail.com  Mon Jun  6 23:10:43 2011
From: ilancaster at gmail.com (Ian Lancaster)
Date: Mon, 6 Jun 2011 19:10:43 -0400
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <BANLkTimKRCXUE6aHeZi=gnFe1rWfyv=ysw@mail.gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
	<BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
	<A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>
	<BANLkTimKRCXUE6aHeZi=gnFe1rWfyv=ysw@mail.gmail.com>
Message-ID: <AD366D51-805F-4A99-B8F1-BF06A12D6B3D@gmail.com>

First of all, make sure everything is in place. Type which gcc-4.2; it should be in /usr/bin. Which easy_install and which python should points to /Library/Frameworks/Python.framework/Versions/2.7/bin if you used the python.org installer. 

You shouldn't have to use sudo to install python packages, unless you are still pointed at the system version of python. I suspect this is the case based on the permissions error. Add the correct python to your path by adding to the end of ~/.bash_profile

	PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"
	export PATH"

When you run python the shell prompt should display the GCC version in the beginning. You can explicitly set the compiler for distutils before running easy_install with the command export CC=gcc-4.2. Then easy_install biopython.

Also, if you are going to be managing more python packages (why not) pip is much better at this than easy_install, and actually supports uninstallation. Easy_install pip, then pip install biopython or whatever. Not necessary, but useful. www.pip-installer.org

Ian

On Jun 6, 2011, at 6:29 PM, Dilara Ally wrote:

> Hi Ian, 
> 
> I've installed python2.7 and because of an earlier email  I removed Xcode4.0 and installed  Xcode3.0 +10.4 sdk then upgraded to Xcode4.0.  I also changed the version of numpy and tested to see if I could import it.  There was no problem importing numpy.
> 
> I tried to install biopython by directing entering the directory biopython-1.57 and typing the command python setup.py install but got this message:
> 
> creating build/lib.macosx-10.6-intel-2.7
> error: could not create 'build/lib.macosx-10.6-intel-2.7': Permission denied
> 
> Then when I tried the easy install using this command:  
> sudo easy_install -f http://biopython.org/DIST/ biopython
> I got the following error:  Is it still having trouble with the gcc 4.2 compiler
> 
> Searching for biopython
> Reading http://biopython.org/DIST/
> Best match: biopython 1.57
> Downloading http://biopython.org/DIST/biopython-1.57.zip
> Processing biopython-1.57.zip
> Running biopython-1.57/setup.py -q bdist_egg --dist-dir /tmp/easy_install-8RE8Sh/biopython-1.57/egg-dist-tmp-YMF_hu
> warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
> warning: no previously-included files found matching 'Tests/Graphics/*.eps'
> warning: no previously-included files found matching 'Tests/Graphics/*.svg'
> warning: no previously-included files found matching 'Tests/Graphics/*.png'
> warning: no previously-included files matching '*' found under directory 'Tests/UnitTests'
> warning: no previously-included files matching '.cvsignore' found under directory '*'
> warning: no previously-included files matching '.gitignore' found under directory '*'
> warning: no previously-included files matching '*.pyc' found under directory '*'
> unable to execute gcc-4.2: No such file or directory
> error: Setup script exited with error: command 'gcc-4.2' failed with exit status 1
> 
> 
> I'm stumped.
> 
> Thanks for the help.
> 
> Dilara
> 
> 
> 
> On Mon, Jun 6, 2011 at 12:14 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> After gcc 4.0 the Wno-long-double option was removed, among others, which was apparently used in building python. However, I don't think the problem is with gcc per se, but the version of python.
> 
> For instance, installing numpy with Apple's python2.6 and 2.5 failed on my machine with the gcc 4.2 compiler. Then I installed python2.7 from the official package at python.org; numpy and Biopython installed and tested fine (I used pip). This might be a better solution for Snow Leopard users, particularly those who have only installed Xcode 4.
> 
> Ian
> 
> On Jun 6, 2011, at 12:59 PM, Peter Cock wrote:
> 
> > On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> >
> > Hi Ian,
> >
> > That's a very interesting link - do you have anything specific on what it is
> > that numpy (and therefore likely also Biopython) doesn't like?
> >
> > Thank you,
> >
> > Peter
> 
> 
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 




From mjldehoon at yahoo.com  Tue Jun  7 02:24:18 2011
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Mon, 6 Jun 2011 19:24:18 -0700 (PDT)
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <BANLkTikaPRc=34QkHdB5VzHz7k0ynCk=kw@mail.gmail.com>
Message-ID: <449273.3301.qm@web161220.mail.bf1.yahoo.com>

--- On Mon, 6/6/11, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> > And, if that is correct, what is the advantage of
> > using Bio.Entrez.parse
> > over using another Python XML lib?
> 
> If you're not scared of XML, not much.
> 
That is a misconception, to say the least.
Bio.Entrez parses the DTD associated with the XML file, and is therefore able to store the information in the XML file as a Python object in a sensible way. In addition, Bio.Entrez.parse can handle multi-gigabyte XML files (such as the ones from the Entrez Gene database). I'd like to see you do that with another Python XML lib.

--Michiel.


From p.j.a.cock at googlemail.com  Tue Jun  7 07:47:27 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 7 Jun 2011 08:47:27 +0100
Subject: [Biopython] processing XML files in Biopython
In-Reply-To: <449273.3301.qm@web161220.mail.bf1.yahoo.com>
References: <BANLkTikaPRc=34QkHdB5VzHz7k0ynCk=kw@mail.gmail.com>
	<449273.3301.qm@web161220.mail.bf1.yahoo.com>
Message-ID: <BANLkTim+rf2N3-wRtrAERpKayL5sbmAppw@mail.gmail.com>

On Tue, Jun 7, 2011 at 3:24 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> --- On Mon, 6/6/11, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> > And, if that is correct, what is the advantage of
>> > using Bio.Entrez.parse
>> > over using another Python XML lib?
>>
>> If you're not scared of XML, not much.
>>
> That is a misconception, to say the least.
> Bio.Entrez parses the DTD associated with the XML file, and
> is therefore able to store the information in the XML file as a
> Python object in a sensible way. In addition, Bio.Entrez.parse
> can handle multi-gigabyte XML files (such as the ones from
> the Entrez Gene database). I'd like to see you do that with
> another Python XML lib.

I was probably being too glib. My point was if you are already
experienced with another Python XML lib, you may find it more
productive to use that. The particular case where you only want
to pull out one or two fields is an interesting one, because here
there is no need to parse all the other data into objects in
memory.

Peter


From devaniranjan at gmail.com  Tue Jun  7 13:39:17 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 7 Jun 2011 09:39:17 -0400
Subject: [Biopython] shuffle sequences
Message-ID: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>

Hello everyone,
I need to 'shuffle' a sequence so that I can calculate the statistical
alignment scores--I tried the random.shuffle opetion but it does not seem to
work

I defined the sequence as a string like the following

w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
random.shuffle(w)


also like this...
my_protein=IUPAC.protein
from Bio.Seq import Seq
myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)

random.shuffle(myseq)

Both don't seem to work--where am I going wrong?

Thanks a lot,
George


From anaryin at gmail.com  Tue Jun  7 14:46:28 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Tue, 7 Jun 2011 16:46:28 +0200
Subject: [Biopython] shuffle sequences
In-Reply-To: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
References: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
Message-ID: <BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>

Hey George,

random.shuffle works on lists or other datatypes that support item
assignment. Therefore, neither a string nor Seq will work. I would extract
the sequence out of Seq and build a new sequence object with that.

Cheers,

Jo?o [...] Rodrigues
http://nmr.chem.uu.nl/~joao



On Tue, Jun 7, 2011 at 3:39 PM, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Hello everyone,
> I need to 'shuffle' a sequence so that I can calculate the statistical
> alignment scores--I tried the random.shuffle opetion but it does not seem
> to
> work
>
> I defined the sequence as a string like the following
>
> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
> random.shuffle(w)
>
>
> also like this...
> my_protein=IUPAC.protein
> from Bio.Seq import Seq
> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>
> random.shuffle(myseq)
>
> Both don't seem to work--where am I going wrong?
>
> Thanks a lot,
> George
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



From eric.talevich at gmail.com  Tue Jun  7 14:56:37 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 7 Jun 2011 10:56:37 -0400
Subject: [Biopython] IUPAC code contribution
In-Reply-To: <BANLkTincLfkH+dbbPP_eWkNJTPDi7JWBQA@mail.gmail.com>
References: <4DED4C15.4010705@gmail.com>
	<BANLkTincLfkH+dbbPP_eWkNJTPDi7JWBQA@mail.gmail.com>
Message-ID: <BANLkTinmH1+Y3fTfqKvWXJE6R68xHgh1BA@mail.gmail.com>

On Mon, Jun 6, 2011 at 6:18 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Mon, Jun 6, 2011 at 10:52 PM, Michal <mictadlo at gmail.com> wrote:
> > Hello,
> > I would like to contribute the following IUPAC function to Biopython:
> >
> > def iupac_base(alignment):
> >    IUPAC = {
> >      ord('N'): 'N',
> >      ord('G'): 'G',
> >      ord('A'): 'A',
> >      ord('T'): 'T',
> >      ord('C'): 'C',
> >      ord('G') + ord('A'): 'R',
> >      ord('T') + ord('C'): 'Y',
> >      ord('A') + ord('C'): 'M',
> >      ord('G') + ord('T'): 'K',
> >      ord('G') + ord('C'): 'S',
> >      ord('A') + ord('T'): 'W',
> >      ord('A') + ord('C') + ord('T'): 'H',
> >      ord('G') + ord('T') + ord('C'): 'B',
> >      ord('G') + ord('C') + ord('A'): 'V',
> >      ord('G') + ord('A') + ord('T'): 'D',
> >      ord('G') + ord('A') + ord('T') + ord('C'): 'N'}
> >
> >    return IUPAC[sum(map(ord, {}.fromkeys(alignment).keys()))]
> >
> >
> > a = iupac_base(['A','A','T','T','T'])
> >
> > Cheers,
> > Michal
>
> Well it would need some documentation at least (e.g. a docstring).
> What is is meant to do? It looks like you just want a reverse lookup
> of Bio.Data.IUPACData.ambiguous_dna_values - e.g.
>
> from Bio.Data.IUPACData import ambiguous_dna_values
> rev_map = dict((frozenset(v),k) for (k,v) in
> ambiguous_dna_values.iteritems())
> assert rev_map[frozenset('CG')] == rev_map[frozenset('GC')]
>
>
This is also a good candidate for a Cookbook entry on the Biopython wiki:
http://biopython.org/wiki/Category:Cookbook

Then others can easily comment on it, describe use cases and suggest
alternatives.

-Eric


From devaniranjan at gmail.com  Tue Jun  7 13:55:36 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 7 Jun 2011 09:55:36 -0400
Subject: [Biopython] correction and follow up to previous question
Message-ID: <BANLkTimrJ_em-Si7Zr8gFABu3p+_=7s+1Q@mail.gmail.com>

Sorry guys--It seems to work when I define the seqence as  a LIST

however I have another  doubt......

the top is the original seqence the bottom the shuffled seqence--while some
residues are shuffled, its not "very" shuffled
is this "normal" ?
First time I am doing this so I just wondered......

Thanks once again.
George


From anaryin at gmail.com  Tue Jun  7 15:01:16 2011
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Tue, 7 Jun 2011 17:01:16 +0200
Subject: [Biopython] correction and follow up to previous question
In-Reply-To: <BANLkTimrJ_em-Si7Zr8gFABu3p+_=7s+1Q@mail.gmail.com>
References: <BANLkTimrJ_em-Si7Zr8gFABu3p+_=7s+1Q@mail.gmail.com>
Message-ID: <BANLkTim0Z1vF3LsLWO635rfsxOva_nUCJQ@mail.gmail.com>

Hey George,

>From the Python Docs:

random.shuffle(*x*[, *random*])
>
> Shuffle the sequence *x* in place. The optional argument *random* is a
> 0-argument function returning a random float in [0.0, 1.0); by default, this
> is the function random()<http://docs.python.org/library/random.html#random.random>
> .
>
> Note that for even rather small len(x), the total number of permutations
> of *x* is larger than the period of most random number generators; this
> implies that most permutations of a long sequence can never be generated.
>
This might be the answer to your last question. A more efficient combination
perhaps would be to use random.choice and then append to a list.. perhaps
this leads to better randomized sequences, but I'm talking out of thin air,
not based on experience..

Cheers

Jo?o [...] Rodrigues
http://nmr.chem.uu.nl/~joao



On Tue, Jun 7, 2011 at 3:55 PM, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Sorry guys--It seems to work when I define the seqence as  a LIST
>
> however I have another  doubt......
>
> the top is the original seqence the bottom the shuffled seqence--while some
> residues are shuffled, its not "very" shuffled
> is this "normal" ?
> First time I am doing this so I just wondered......
>
> Thanks once again.
> George
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



From devaniranjan at gmail.com  Tue Jun  7 15:01:41 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 7 Jun 2011 11:01:41 -0400
Subject: [Biopython] shuffle sequences
In-Reply-To: <BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>
References: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
	<BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>
Message-ID: <BANLkTim+5jbv3BLsSopNwVoPcKd-u6EcqA@mail.gmail.com>

Hello Jo?o,

Thanks for the answer but I am confused--"new sequence object with that"
so I still need to create a seq object?
I tried this ...
myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)

I was thinking if it would be possible to have FOR loop and loop throught
the entire sequence then shuffle it and then write the shuffled list (going
though it one by one using another FOR loop) to a seq object.

Thank you,
George

On Tue, Jun 7, 2011 at 10:46 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hey George,
>
> random.shuffle works on lists or other datatypes that support item
> assignment. Therefore, neither a string nor Seq will work. I would extract
> the sequence out of Seq and build a new sequence object with that.
>
> Cheers,
>
> Jo?o [...] Rodrigues
> http://nmr.chem.uu.nl/~joao
>
>
>
> On Tue, Jun 7, 2011 at 3:39 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hello everyone,
>> I need to 'shuffle' a sequence so that I can calculate the statistical
>> alignment scores--I tried the random.shuffle opetion but it does not seem
>> to
>> work
>>
>> I defined the sequence as a string like the following
>>
>> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
>> random.shuffle(w)
>>
>>
>> also like this...
>> my_protein=IUPAC.protein
>> from Bio.Seq import Seq
>> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>>
>> random.shuffle(myseq)
>>
>> Both don't seem to work--where am I going wrong?
>>
>> Thanks a lot,
>> George
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>



From idoerg at gmail.com  Tue Jun  7 15:11:05 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Tue, 7 Jun 2011 11:11:05 -0400
Subject: [Biopython] shuffle sequences
In-Reply-To: <BANLkTim+5jbv3BLsSopNwVoPcKd-u6EcqA@mail.gmail.com>
References: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
	<BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>
	<BANLkTim+5jbv3BLsSopNwVoPcKd-u6EcqA@mail.gmail.com>
Message-ID: <BANLkTin5-jX8ia6CsEFC9W0rErc2nja1Cw@mail.gmail.com>

probably a good solution wouls be to convert to  a list and then back to a
string (or a Seq object).

To shuffle w:
w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
wl=list(w)
random.shuffle(wl)
w=''.join(wl)

And with a Seq object:
myseq=Seq('KVFGRCELAAAMKRHGL')
lms = list(myseq)
random.shuffle(lms)
myseq = Seq(''.join(lms))

On Tue, Jun 7, 2011 at 11:01 AM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hello Jo?o,
>
> Thanks for the answer but I am confused--"new sequence object with that"
> so I still need to create a seq object?
> I tried this ...
> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>
> I was thinking if it would be possible to have FOR loop and loop throught
> the entire sequence then shuffle it and then write the shuffled list (going
> though it one by one using another FOR loop) to a seq object.
>
> Thank you,
> George
>
> On Tue, Jun 7, 2011 at 10:46 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:
>
> > Hey George,
> >
> > random.shuffle works on lists or other datatypes that support item
> > assignment. Therefore, neither a string nor Seq will work. I would
> extract
> > the sequence out of Seq and build a new sequence object with that.
> >
> > Cheers,
> >
> > Jo?o [...] Rodrigues
> > http://nmr.chem.uu.nl/~joao
> >
> >
> >
> > On Tue, Jun 7, 2011 at 3:39 PM, George Devaniranjan <
> > devaniranjan at gmail.com> wrote:
> >
> >> Hello everyone,
> >> I need to 'shuffle' a sequence so that I can calculate the statistical
> >> alignment scores--I tried the random.shuffle opetion but it does not
> seem
> >> to
> >> work
> >>
> >> I defined the sequence as a string like the following
> >>
> >> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
> >> random.shuffle(w)
> >>
> >>
> >> also like this...
> >> my_protein=IUPAC.protein
> >> from Bio.Seq import Seq
> >> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
> >>
> >> random.shuffle(myseq)
> >>
> >> Both don't seem to work--where am I going wrong?
> >>
> >> Thanks a lot,
> >> George
> >> _______________________________________________
> >> Biopython mailing list  -  Biopython at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biopython
> >>
> >
> >
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html



From devaniranjan at gmail.com  Tue Jun  7 15:24:43 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 7 Jun 2011 11:24:43 -0400
Subject: [Biopython] shuffle sequences
In-Reply-To: <BANLkTin5-jX8ia6CsEFC9W0rErc2nja1Cw@mail.gmail.com>
References: <BANLkTimu=Vw-kQ8zP9Fa89oj2LwqNRzduQ@mail.gmail.com>
	<BANLkTimcqOTJuCucwBaf_BfR9KRUy8qS5w@mail.gmail.com>
	<BANLkTim+5jbv3BLsSopNwVoPcKd-u6EcqA@mail.gmail.com>
	<BANLkTin5-jX8ia6CsEFC9W0rErc2nja1Cw@mail.gmail.com>
Message-ID: <BANLkTim9T+LSUm4d=m8=Yv2nVmZ69a4ojw@mail.gmail.com>

Thanks Iddo and Jo?o,
I think this works and it seems to shuffle the sequence well to
differentiate between the original and shuffled (very diff scores for
alignment.)

George

On Tue, Jun 7, 2011 at 11:11 AM, Iddo Friedberg <idoerg at gmail.com> wrote:

> probably a good solution wouls be to convert to  a list and then back to a
> string (or a Seq object).
>
> To shuffle w:
> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
> wl=list(w)
> random.shuffle(wl)
> w=''.join(wl)
>
> And with a Seq object:
> myseq=Seq('KVFGRCELAAAMKRHGL')
> lms = list(myseq)
> random.shuffle(lms)
> myseq = Seq(''.join(lms))
>
>
> On Tue, Jun 7, 2011 at 11:01 AM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hello Jo?o,
>>
>> Thanks for the answer but I am confused--"new sequence object with that"
>> so I still need to create a seq object?
>> I tried this ...
>> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>>
>> I was thinking if it would be possible to have FOR loop and loop throught
>> the entire sequence then shuffle it and then write the shuffled list
>> (going
>> though it one by one using another FOR loop) to a seq object.
>>
>> Thank you,
>> George
>>
>> On Tue, Jun 7, 2011 at 10:46 AM, Jo?o Rodrigues <anaryin at gmail.com>
>> wrote:
>>
>> > Hey George,
>> >
>> > random.shuffle works on lists or other datatypes that support item
>> > assignment. Therefore, neither a string nor Seq will work. I would
>> extract
>> > the sequence out of Seq and build a new sequence object with that.
>> >
>> > Cheers,
>> >
>> > Jo?o [...] Rodrigues
>> > http://nmr.chem.uu.nl/~joao
>> >
>> >
>> >
>> > On Tue, Jun 7, 2011 at 3:39 PM, George Devaniranjan <
>> > devaniranjan at gmail.com> wrote:
>> >
>> >> Hello everyone,
>> >> I need to 'shuffle' a sequence so that I can calculate the statistical
>> >> alignment scores--I tried the random.shuffle opetion but it does not
>> seem
>> >> to
>> >> work
>> >>
>> >> I defined the sequence as a string like the following
>> >>
>> >> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
>> >> random.shuffle(w)
>> >>
>> >>
>> >> also like this...
>> >> my_protein=IUPAC.protein
>> >> from Bio.Seq import Seq
>> >> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>> >>
>> >> random.shuffle(myseq)
>> >>
>> >> Both don't seem to work--where am I going wrong?
>> >>
>> >> Thanks a lot,
>> >> George
>> >> _______________________________________________
>> >> Biopython mailing list  -  Biopython at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/biopython
>> >>
>> >
>> >
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>



From eric.talevich at gmail.com  Tue Jun  7 15:25:55 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 7 Jun 2011 11:25:55 -0400
Subject: [Biopython] correction and follow up to previous question
In-Reply-To: <BANLkTim0Z1vF3LsLWO635rfsxOva_nUCJQ@mail.gmail.com>
References: <BANLkTimrJ_em-Si7Zr8gFABu3p+_=7s+1Q@mail.gmail.com>
	<BANLkTim0Z1vF3LsLWO635rfsxOva_nUCJQ@mail.gmail.com>
Message-ID: <BANLkTinS_VakXd_YB=0W=TQd=Yi2PgTd_A@mail.gmail.com>

 On Tue, Jun 7, 2011 at 3:55 PM, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Sorry guys--It seems to work when I define the seqence as  a LIST
>
> however I have another  doubt......
>
> the top is the original seqence the bottom the shuffled seqence--while
some
> residues are shuffled, its not "very" shuffled
> is this "normal" ?

With random.shuffle, all sequence combinations are supposed to be equally
probable. This means a sequence that's similar to the input is possible, as
is a sequence that's very different.

>>> stuff = list('ASDFSDFG')
>>> random.shuffle(stuff)
>>> ''.join(stuff)
'GFSFADDS'
>>> random.shuffle(stuff)
>>> ''.join(stuff)
'FADDSGSF'

In theory, anything is possible.
http://dilbert.com/strips/comic/2001-10-25/


On Tue, Jun 7, 2011 at 11:01 AM, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hey George,
>
> From the Python Docs:
>
> random.shuffle(*x*[, *random*])
> >
> > Shuffle the sequence *x* in place. The optional argument *random* is a
> > 0-argument function returning a random float in [0.0, 1.0); by default,
> this
> > is the function random()<
> http://docs.python.org/library/random.html#random.random>
> > .
> >
> > Note that for even rather small len(x), the total number of permutations
> > of *x* is larger than the period of most random number generators; this
> > implies that most permutations of a long sequence can never be generated.
> >
> This might be the answer to your last question. A more efficient
> combination
> perhaps would be to use random.choice and then append to a list.. perhaps
> this leads to better randomized sequences, but I'm talking out of thin air,
> not based on experience..
>
>
According to the docs, the pseudo-RNG implementation has a cycle of
 2**19937-1. If I'm understanding random.shuffle correctly, a string of
length k has k! permutations. So:

>>> 2**19937-1 < math.factorial(2081)
True
>>> 2**19937-1 < math.factorial(2080)
False

It should work as expected for lists of up to 2080 elements, and after that,
gradually become less purely "random" (but still behave fairly well for most
use cases in biology). So random.shufffle is an acceptable choice for
protein sequences, but not for whole genomes. But for whole genomes you'd
probably want to use a more clever HMM-based model for generating random
sequences, anyway.

Cheers,
Eric



From dilara.ally at gmail.com  Wed Jun  8 17:37:48 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Wed, 08 Jun 2011 10:37:48 -0700
Subject: [Biopython] installation failure on mac OS10.6.7
In-Reply-To: <AD366D51-805F-4A99-B8F1-BF06A12D6B3D@gmail.com>
References: <4DECFDE4.8040705@gmail.com>
	<BANLkTi=Pv-9ui6pXxsVbuay-cDBpCTDhOw@mail.gmail.com>
	<5340FB2A-DCB4-478F-8A03-81684011CE4A@gmail.com>
	<BANLkTinp+oD2Em=jM6KxnrewqX40VBbopQ@mail.gmail.com>
	<A91F5EAE-A193-4569-88A4-475C5E2BBA18@gmail.com>
	<BANLkTimKRCXUE6aHeZi=gnFe1rWfyv=ysw@mail.gmail.com>
	<AD366D51-805F-4A99-B8F1-BF06A12D6B3D@gmail.com>
Message-ID: <4DEFB36C.9080002@gmail.com>

thanks a bunch!

On 6/6/11 4:10 PM, Ian Lancaster wrote:
> First of all, make sure everything is in place. Type which gcc-4.2; it should be in /usr/bin. Which easy_install and which python should points to /Library/Frameworks/Python.framework/Versions/2.7/bin if you used the python.org installer.
>
> You shouldn't have to use sudo to install python packages, unless you are still pointed at the system version of python. I suspect this is the case based on the permissions error. Add the correct python to your path by adding to the end of ~/.bash_profile
>
> 	PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"
> 	export PATH"
>
> When you run python the shell prompt should display the GCC version in the beginning. You can explicitly set the compiler for distutils before running easy_install with the command export CC=gcc-4.2. Then easy_install biopython.
>
> Also, if you are going to be managing more python packages (why not) pip is much better at this than easy_install, and actually supports uninstallation. Easy_install pip, then pip install biopython or whatever. Not necessary, but useful. www.pip-installer.org
>
> Ian
>
> On Jun 6, 2011, at 6:29 PM, Dilara Ally wrote:
>
>> Hi Ian,
>>
>> I've installed python2.7 and because of an earlier email  I removed Xcode4.0 and installed  Xcode3.0 +10.4 sdk then upgraded to Xcode4.0.  I also changed the version of numpy and tested to see if I could import it.  There was no problem importing numpy.
>>
>> I tried to install biopython by directing entering the directory biopython-1.57 and typing the command python setup.py install but got this message:
>>
>> creating build/lib.macosx-10.6-intel-2.7
>> error: could not create 'build/lib.macosx-10.6-intel-2.7': Permission denied
>>
>> Then when I tried the easy install using this command:
>> sudo easy_install -f http://biopython.org/DIST/ biopython
>> I got the following error:  Is it still having trouble with the gcc 4.2 compiler
>>
>> Searching for biopython
>> Reading http://biopython.org/DIST/
>> Best match: biopython 1.57
>> Downloading http://biopython.org/DIST/biopython-1.57.zip
>> Processing biopython-1.57.zip
>> Running biopython-1.57/setup.py -q bdist_egg --dist-dir /tmp/easy_install-8RE8Sh/biopython-1.57/egg-dist-tmp-YMF_hu
>> warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
>> warning: no previously-included files found matching 'Tests/Graphics/*.eps'
>> warning: no previously-included files found matching 'Tests/Graphics/*.svg'
>> warning: no previously-included files found matching 'Tests/Graphics/*.png'
>> warning: no previously-included files matching '*' found under directory 'Tests/UnitTests'
>> warning: no previously-included files matching '.cvsignore' found under directory '*'
>> warning: no previously-included files matching '.gitignore' found under directory '*'
>> warning: no previously-included files matching '*.pyc' found under directory '*'
>> unable to execute gcc-4.2: No such file or directory
>> error: Setup script exited with error: command 'gcc-4.2' failed with exit status 1
>>
>>
>> I'm stumped.
>>
>> Thanks for the help.
>>
>> Dilara
>>
>>
>>
>> On Mon, Jun 6, 2011 at 12:14 PM, Ian Lancaster<ilancaster at gmail.com>  wrote:
>> After gcc 4.0 the Wno-long-double option was removed, among others, which was apparently used in building python. However, I don't think the problem is with gcc per se, but the version of python.
>>
>> For instance, installing numpy with Apple's python2.6 and 2.5 failed on my machine with the gcc 4.2 compiler. Then I installed python2.7 from the official package at python.org; numpy and Biopython installed and tested fine (I used pip). This might be a better solution for Snow Leopard users, particularly those who have only installed Xcode 4.
>>
>> Ian
>>
>> On Jun 6, 2011, at 12:59 PM, Peter Cock wrote:
>>
>>> On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster<ilancaster at gmail.com>  wrote:
>>>
>>> Hi Ian,
>>>
>>> That's a very interesting link - do you have anything specific on what it is
>>> that numpy (and therefore likely also Biopython) doesn't like?
>>>
>>> Thank you,
>>>
>>> Peter
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>


From eric.talevich at gmail.com  Fri Jun 10 16:33:00 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Fri, 10 Jun 2011 12:33:00 -0400
Subject: [Biopython] Deprecating and renaming some keyword args in
	Phylo/NewickIO
Message-ID: <BANLkTikD1nbj1GCvTWhbtx3sOQ26uMOYuA@mail.gmail.com>

Folks,

I'd like to rename several optional arguments used for the Newick parser and
writer in Bio.Phylo. The old argument names will be supported in Biopython
1.58, but trigger a deprecation warning, and then be removed in version
1.59.

The changed functions are in Bio.Phylo.NewickIO.

Parser.parse:
  values_are_support  =>  values_are_confidence
(This isn't currently accessible through Phylo.read/parse or
NewickIO.read/parse, but I will enable that in the next release.)

Writer.write:
  support_as_branchlengths  =>  confidence_as_branch_length
  max_support  =>  max_confidence
  branchlengths_only  =>  branch_length_only


Example:

tree = Phylo.read(infile, 'newick', values_are_support=True)
Phylo.write(tree, outfile, 'newick', support_as_branchlengths=True,
max_support=100)

becomes:

tree = Phylo.read(infile, 'newick', values_are_confidence=True)
Phylo.write(tree, outfile, 'newick', confidence_as_branch_length=True,
max_confidence=100)


Why? NewickIO was originally ported from Bio.Nexus.Trees, where tree node
objects have an attribute called 'support', equivalent to clade.confidence.
Since this attribute is called 'confidence' in Bio.Phylo, these original
argument names no longer make sense. Oops. Also, branch_length grew an
underscore in Bio.Phylo.

So, does anyone have a problem with deprecating these arguments in the next
release, and removing them after that?

Thanks,
Eric


From matsen at fhcrc.org  Tue Jun 14 03:08:01 2011
From: matsen at fhcrc.org (Erick Matsen)
Date: Mon, 13 Jun 2011 20:08:01 -0700
Subject: [Biopython] programmer position open in our group (Seattle, WA)
Message-ID: <BANLkTimpGoEZMv8csAqxOEZttsfSVmG5+A@mail.gmail.com>

Hello there Biopython community--


We are looking for another top programmer to join our group. The full
text of the ad is below, or see the online version at
http://matsen.fhcrc.org/programmer-ad.html


Thanks!

Erick

----

Advance biology with the tools you love

Our group at the Fred Hutchinson Cancer Research Center in Seattle is
looking for an experienced programmer to write code and analyze data.
We develop methods for the evolutionary analysis of next-generation
DNA sequence data for HIV research and the study of the human
microbiome (bacteria that live on and inside of us). And we love
coding, especially in OCaml and Python.

Your job will be to develop, deploy, and apply a computational
pipeline for metagenomics annotation using phylogenetics. This will
include:

    A framework to automatically select collections of sequences for
evolutionary comparison using phylogenetic and taxonomic criteria
    Implementation of high performance phylogenetic models
    Implementation of methods to infer gene function and taxonomic
identity from phylogenetic trees
    Application of machine learning techniques to phylogenetic placement data

You will be joining a core group of one group leader and two
programmers, as well as a larger community of programmers and many
biologists. There is a lot of knowledge here, and you will have
support while you are learning the ropes. On the other hand, in order
to succeed at this job you will need to be able to read scientific
papers and work through references to find the necessary background.
Scientific curiosity strictly required.

You will also need some serious coding chops. Your code should be DRY,
well documented, and robust. Long-time linux hacker a big plus.

If you are not already aware, biology is a tremendously exciting area
right now, and this is an opportunity to work at the forefront. The
work environment will be dynamic, and we are always looking for better
ways to do our work. On the other hand we?re serious about helping
biologists with their data and sometimes that just means turning the
crank on data analysis. All finalized code will be open source, and
you will be required to feed as much code as possible into Biopython
or other relevant projects.

Fred Hutchinson Cancer Research Center, home of about 190 faculty
including three Nobel laureates, is an independent, nonprofit research
institution dedicated to the development and advancement of biomedical
research. The environment is lively yet casual, with a strong emphasis
on collaborative work. The center has great benefits and a lovely
campus next to Lake Union within walking distance from downtown.
Powerful computing resources and a helpful IT staff await you.

Although the FHCRC is a large facility, this will be much more like an
informal startup-style job. You?ll be expected to come into work for
design discussions, but other than that your schedule will be your
own, as long as those commits keep coming. Competitive salary, which
will scale according to your level of experience.

You can find out more about our work by visiting:

    http://matsen.fhcrc.org/
    http://github.com/matsen
    http://github.com/fhcrc

Requirements

    BS in a relevant field or at least four years relevant work experience
    a high level of linux proficiency (at least three years)
    top-notch programming skills, with at least a year of Python experience
    experience using a VCS, preferably git
    SQL experience a plus
    the ability to work independently with a long-range goal in mind
    interest in bioinformatics

How to apply

Please send a CV and significant code sample, preferably in Python, to
Nerreda Chavez at nchavez at fhcrc.org. The code should be DRY, well
documented, and show that you can use some non-trivial features of
your chosen language.

-- 
Frederick "Erick" Matsen, Assistant Member
Fred Hutchinson Cancer Research Center
http://matsen.fhcrc.org/



From b.invergo at gmail.com  Tue Jun 14 13:15:52 2011
From: b.invergo at gmail.com (Brandon Invergo)
Date: Tue, 14 Jun 2011 15:15:52 +0200
Subject: [Biopython] introducing PAML for Biopython
Message-ID: <BANLkTi=nVuwk87yAsmGs2T+z=DU64O17qA@mail.gmail.com>

Hi everyone,

I have written a Python interface to the PAML (Phylogenetic Analysis
by Maximum Likelihood) package of programs by Ziheng Yang which is in
the process of being added to Biopython. In advance of adding it, it
would be great if some people would be willing to take it for a
test-drive to make sure things are working the way you would like them
to, that it's useful, that it's not buggy, etc. For the moment, it can
be had as a branch of Biopython here:
https://github.com/brandoninvergo/biopython/tree/paml-branch
(If you click Downloads you can download the source code as a .tar.gz file)

The PAML interface is located in Bio.Phylo.PAML and includes the
following modules: codeml, baseml, yn00 and chi2. I have not written
implementations of the evolver or mcmctree programs from the package.
Evolver requires menu interaction from the user, so it can't be
scripted easily. As for mcmctree, I will profess complete ignorance in
how people use the program, so I was not sure of the best way to
implement it (particularly in parsing the results). If you use
mcmctree and you would like me to implement an interface to it, feel
free to contact me and we can discuss it.


If you're interested in using the library, I have not yet written
documentation, however usage would be something like this (codeml,
baseml, and yn00 all function similarly):

> from Bio.Phylo.PAML import codeml
> cml = codeml.Codeml()
> cml.alignment = "path/to/alignment"  #can use either relative or absolute paths; they all get converted to relative paths to avoid the path-length limits imposed in PAML
> cml.tree = "path/to/tree"
> cml.working_dir = "path/to/working_directory"
> cml.out_file = "path/to/output_file"
#or, alternatively:
> cml = codeml.Codeml(alignment="path/to/alignment", tree="path/to/tree", working_dir="path/to/working_dir", out_file="path/to/out_file")

# view all options
> cml.print_options()

# read in an existing control file
> cml.read_ctl_file("path/to/control_file")

# set an option
> cml.set_option("clock", 1)
> cml.set_option("NSsites", [0,1,2])
> cml.set_option("aaRatefile", None)

# get an option value
> cml.get_option("clock")

# write all options to a control file (this is done automatically when
you do the run() method, so you probably won't have to do this)
> cml.ctl_file = "path/to/ctl_file"
> cml.write_ctl_file()


# run the program, which returns the results in dict format
> results = cml.run()

# or, to see all of codeml's output to the screen
> results = cml.run(verbose=True)

# or, to specify the location of the executable (ie if it's not in
your path or if you use multiple versions of it)
> results = cml.run(command = "path/to/codeml")

# or, to skip parsing the results
> cml.run(parse = False)

# parse an existing results file
> results = codeml.read("path/to/results_file")



The results are stored in a giant dictionary. I will have to describe
all the contents in the documentation but for now I would recommend
just exploring it to see what's there. For each program, I tried to
parse out as much as possible, on the assumption that I don't know
what *you* need to know from the output file. So, the results dict
probably contains far more than anyone needs. Still, if you find that
you need something that has not been parsed, please let me know and
I'll try to implement it  (I have not parsed Naive Emperical Bayes or
Bayes Empirical Bayes results, for example, or the various codon usage
statistics in the beginning of the file).
nssites = results.get("NSsites")
m0 = nssites.get(0)
m0_maxlnl = m0.get("max lnL")
etc...

I do recommend using the results.get(key) method rather than
results[key] because if codeml encounters an error, the keys won't be
added to the results dictionary and results[key] will raise an
exception.

At the moment, the chi2 program in PAML doesn't properly take
command-line arguments so it's not easily scriptable. Since using PAML
programs calls for a lot of likelihood ratio testing, I went ahead and
reimplemented it in pure Python from the original C code (with
permission). In most cases, it works fine however I have found that if
you have many degrees of freedom, such as in the case of the FMutSel
model testing (41 df), it takes an unacceptably long time to compute.
I've been told that the next version of PAML will include a chi2 which
takes both the test statistic and the d.f. as command line arguments,
so I'll be able to just write an interface to it.

Ok, I think that sums it up for now. I hope that you find this to be
useful! Please let me know if you have any problems, suggestions,
bugs, etc., especially in the parsing!

Thanks!
Brandon Invergo


From from.d.putto at gmail.com  Thu Jun 16 11:43:06 2011
From: from.d.putto at gmail.com (Sheila the angel)
Date: Thu, 16 Jun 2011 13:43:06 +0200
Subject: [Biopython] processing genbank file
Message-ID: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>

Hi to all,
>From a genbank file I want to extract certain information. Here is my code

#---------------------------------------------------------------------------------------------------------
from Bio import SeqIO
handle = open('NP_954888.1.gb', "rU")
for gb_record in SeqIO.parse(handle, 'gb'):
 for gb_feature in gb_record.features:
if gb_feature.type == 'CDS':
 gene=gb_feature.qualifiers['gene'][0]
                 db_xref=gb_feature.qualifiers['db_xref']
                                print gene, db_xref

print gb_record.annotations['organism']

#====================================================

Is there any simple way to print information like gene name, GeneID etc. or
I have to use this loop method :( for an example to print organism name I
need to do only gb_record.annotations['organism'] while to print 'gene' id I
need the for loop !!!!
Another problem is the db_xref=gb_feature.qualifiers['db_xref'] gives me
all /db_xref entries in CDS field while I want only /db_xref="GeneID:309165"
(or only the GeneID)...how to do that

Thanks in Advance

--
Cheers
Sheila


From p.j.a.cock at googlemail.com  Thu Jun 16 11:52:02 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 Jun 2011 12:52:02 +0100
Subject: [Biopython] processing genbank file
In-Reply-To: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>
References: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>
Message-ID: <BANLkTinQe8+_PW6bC37Qgt-tLRGCe5bS+Q@mail.gmail.com>

On Thu, Jun 16, 2011 at 12:43 PM, Sheila the angel
<from.d.putto at gmail.com> wrote:
> Hi to all,
> >From a genbank file I want to extract certain information. Here is my code
>
> #---------------------------------------------------------------------------------------------------------
> from Bio import SeqIO
> handle = open('NP_954888.1.gb', "rU")
> for gb_record in SeqIO.parse(handle, 'gb'):

If you've only got one record in the file, you can get rid of one loop:

gb_record = SeqIO.read('NP_954888.1.gb', 'gb')

Since there will in generally be many features in a GenBank file,
you do need this loop to look at each potential gene:

> ?for gb_feature in gb_record.features:
> if gb_feature.type == 'CDS':
> ?gene=gb_feature.qualifiers['gene'][0]
> ? ? ? ? ? ? ? ? db_xref=gb_feature.qualifiers['db_xref']

Note in the above not all CDS features will have a gene or db_xref
qualifier - you may get a KeyError exception with some files.

> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?print gene, db_xref
>
> print gb_record.annotations['organism']
>
> #====================================================
>
> Is there any simple way to print information like gene name, GeneID etc. or
> I have to use this loop method :( for an example to print organism name I
> need to do only gb_record.annotations['organism'] while to print 'gene' id I
> need the for loop !!!!

You will need some loops in general: One single GenBank file can hold
multiple records, each of which can hold multiple features, each of which
can have multiple names and database cross-references.

> Another problem is the db_xref=gb_feature.qualifiers['db_xref'] gives me
> all /db_xref entries in CDS field while I want only /db_xref="GeneID:309165"
> (or only the GeneID)...how to do that
>
> Thanks in Advance

Since you can get multiple /db_xref (or other qualifiers), when the parser
was designed a list was used for the values. You could filter on what the
entries start with, e.g. db_xref.startswith("GeneID:")

Peter



From from.d.putto at gmail.com  Thu Jun 16 12:28:34 2011
From: from.d.putto at gmail.com (Sheila the angel)
Date: Thu, 16 Jun 2011 14:28:34 +0200
Subject: [Biopython] processing genbank file
In-Reply-To: <BANLkTinQe8+_PW6bC37Qgt-tLRGCe5bS+Q@mail.gmail.com>
References: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>
	<BANLkTinQe8+_PW6bC37Qgt-tLRGCe5bS+Q@mail.gmail.com>
Message-ID: <BANLkTikozeKazjZJdFJi-bFizMijt-cLyA@mail.gmail.com>

So if I have only one file which contains only 1 record (say 'NP_954888.1.gb'
) and I want to extract information like  'gene' name I can't do it in one
line e.g.
#------------------------------------------------------------------------------
gene=gb_record.features['CDS'].qualifiers['gene'][0]     #or
something similar to this will not work
#-----------------------------------------------------------------------------

But I have to use loop as
#-----------------------------------------------------------------------------
gb_record = SeqIO.read('NP_954888.1.gb', 'gb')
for gb_feature in gb_record.features:
      if gb_feature.type == 'CDS':
      gene=gb_feature.qualifiers['gene'][0]
      print gene
#-----------------------------------------------------------------------------

?????


On Thu, Jun 16, 2011 at 1:52 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Jun 16, 2011 at 12:43 PM, Sheila the angel
> <from.d.putto at gmail.com> wrote:
> > Hi to all,
> > >From a genbank file I want to extract certain information. Here is my
> code
> >
> >
> #---------------------------------------------------------------------------------------------------------
> > from Bio import SeqIO
> > handle = open('NP_954888.1.gb', "rU")
> > for gb_record in SeqIO.parse(handle, 'gb'):
>
> If you've only got one record in the file, you can get rid of one loop:
>
> gb_record = SeqIO.read('NP_954888.1.gb', 'gb')
>
> Since there will in generally be many features in a GenBank file,
> you do need this loop to look at each potential gene:
>
> >  for gb_feature in gb_record.features:
> > if gb_feature.type == 'CDS':
> >  gene=gb_feature.qualifiers['gene'][0]
> >                 db_xref=gb_feature.qualifiers['db_xref']
>
> Note in the above not all CDS features will have a gene or db_xref
> qualifier - you may get a KeyError exception with some files.
>
> >                                print gene, db_xref
> >
> > print gb_record.annotations['organism']
> >
> > #====================================================
> >
> > Is there any simple way to print information like gene name, GeneID etc.
> or
> > I have to use this loop method :( for an example to print organism name I
> > need to do only gb_record.annotations['organism'] while to print 'gene'
> id I
> > need the for loop !!!!
>
> You will need some loops in general: One single GenBank file can hold
> multiple records, each of which can hold multiple features, each of which
> can have multiple names and database cross-references.
>
> > Another problem is the db_xref=gb_feature.qualifiers['db_xref'] gives me
> > all /db_xref entries in CDS field while I want only
> /db_xref="GeneID:309165"
> > (or only the GeneID)...how to do that
> >
> > Thanks in Advance
>
> Since you can get multiple /db_xref (or other qualifiers), when the parser
> was designed a list was used for the values. You could filter on what the
> entries start with, e.g. db_xref.startswith("GeneID:")
>
> Peter
>


From p.j.a.cock at googlemail.com  Thu Jun 16 13:24:02 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 Jun 2011 14:24:02 +0100
Subject: [Biopython] processing genbank file
In-Reply-To: <BANLkTikozeKazjZJdFJi-bFizMijt-cLyA@mail.gmail.com>
References: <BANLkTik6YHPuFTNHbJj_HngMxw36QFqxrQ@mail.gmail.com>
	<BANLkTinQe8+_PW6bC37Qgt-tLRGCe5bS+Q@mail.gmail.com>
	<BANLkTikozeKazjZJdFJi-bFizMijt-cLyA@mail.gmail.com>
Message-ID: <BANLkTinHhokSZOF3c+L80MfBr7S+egEUQg@mail.gmail.com>

On Thu, Jun 16, 2011 at 1:28 PM, Sheila the angel
<from.d.putto at gmail.com> wrote:
> So if I have only one file which contains only 1 record (say
> 'NP_954888.1.gb' ) and I want to extract?information like
>??'gene' name I can't do it in one line e.g.
> #------------------------------------------------------------------------------
> gene=gb_record.features['CDS'].qualifiers['gene'][0] ? ? #or
> something?similar?to this will not work

Supposing there was a neat built in way to filter the features by type,
in general there would still be multiple CDS features - often 1000s,
so you'd need to choose from them.

> #-----------------------------------------------------------------------------
> But I have to use loop as
> #-----------------------------------------------------------------------------
> gb_record = SeqIO.read('NP_954888.1.gb', 'gb')
> for gb_feature in gb_record.features:
> ? ? ? if gb_feature.type == 'CDS':
> ? ? ? gene=gb_feature.qualifiers['gene'][0]
> ? ? ? print gene
> #-----------------------------------------------------------------------------
> ?????

I've checked your example NP_954888 and it is actually a GenPept
file (a protein GenBank file), and it does have just one CDS feature.

Do you prefer this syntax?

gb_record = SeqIO.read('NP_954888.1.gb', 'gb')
cds_features = [f for f in gb_record.features if f.type=="CDS"]
assert len(cds_features)==1
print cds_features[0].qualifiers['gene'][0]

Peter



From bjorn_johansson at bio.uminho.pt  Mon Jun 20 06:36:14 2011
From: bjorn_johansson at bio.uminho.pt (=?ISO-8859-1?Q?Bj=F6rn_Johansson?=)
Date: Mon, 20 Jun 2011 07:36:14 +0100
Subject: [Biopython] common substrings
Message-ID: <BANLkTi=Np0bXa-qPVpNwJcnF196Sycb36Q@mail.gmail.com>

Hi,

I am interested in finding perfect substrings between two sequences that are
longer than a certain specified cut off value. I would like to return the
positions in each sequence and the substring.

The code below is a working implementation that is based on dynamic
programming. I would like to have a faster implementation if possible. I
wonder if someone has a comment on the implementation, if there are better
ways to do it or shortcuts that can be made. In the code below, every
character is compared in both strings. I don't think there is anything like
this in biopython? The pairwise2 comes close, but seems overkill for this
purpose?

Most code and examples I find by google is about the longest common
substring problem, which is slightly different from this.

Thanks for any feedback,
Bjorn


def CommonSubstrings(S1, S2, limit=30):

    M = [[0]*(len(S2)) for i in xrange(len(S1))]

    matches=[]

    for x in xrange(1,len(S1)):
        for y in xrange(1,len(S2)):

            upperleftcell = M[x-1][y-1]

            if S1[x-1] == S2[y-1]:
                M[x][y] = upperleftcell + 1
            else:
                M[x][y] = 0
                if upperleftcell>limit:
                    matches.append((x-1-upperleftcell,y-1-upperleftcell,
upperleftcell))

    for x in xrange(1,len(S1)):
        if M[x][len(S2)-1]>limit:

matches.append(((x-M[x][len(S2)-1]),len(S2)-1-M[x][len(S2)-1],M[x][len(S2)-1]))
            #print M[x][len(S2)-1]

    for y in xrange(1,len(S2)):
        if M[len(S1)-1][y]>limit:

matches.append((len(S1)-1-M[len(S1)-1][y],y-M[len(S1)-1][y]-1,M[len(S1)-1][y]))
            #print M[len(S1)-1][y]

    return matches

x='''TTCTAGAACTAGTGGATCCCCCGGGCTGCAGATGAGTGAAGGCCCCGTCAAATTCGAAAAAAATACCGTCATATCTGTCTTTGGTGCGTCAGGTGATCTGGCAAAGAAGAAGACTTTTCCCGCCTTATTTGGGCTTTTCAGAGAAGGTTACCTTGATCCATCTACCAAGATCTTCGGTTATGCCCGGTCCAAATTGTCCATGGAGGAGGACCTGAAGTCCCGTGTCCTACCCCACTTGAAAAAACCTCACGGTGAAGCCGATGACTCTAAGGTCGAACAGTTCTTCAAGATGGTCAGCTACATTTCGGGAAATTACGACACAGATGAAGGCTTCGACGAATTAAGAACGCAGATCGAGAAATTCGAGAAAAGTGCCAACGTCGATGTCCCACACCGTCTCTTCTATCTGGCCTTGCCGCCAAGCGTTTTTTTGACGGTGGCCAAGCAGATCAAGAGTCGTGTGTACGCAGAGAATGGCATCACCCGTGTAATCGTAGAGAAACCTTTCGGCCACGACCTGGCCTCTGCCAGGGAGCTGCAAAAAAACCTGGGGCCCCTCTTTAAAGAAGAAGAGTTGTACAGAATTGACCATTACTTGGGTAAAGAGTTGGTCAAGAATCTTTTAGTCTTGAGGTTCGGTAACCAGTTTTTGAATGCCTCGTGGAATAGAGACAACATTCAAAGCGTTCAGATTTCGTTTAAAGAGAGGTTCGGCACCGAAGGCCGTGGCGGCTATTTCGACTCTATAGGCATAATCAGAGACGTGATGCAGAACCATCTGTTACAAATCATGACTCTCTTGACTATGGAAAGACCGGTGTCTTTTGACCCGGAATCTATTCGTGACGAAAAGGTTAAGGTTCTAAAGGCCGTGGCCCCCATCGACACGGACGACGTCCTCTTGGGCCAGTACGGTAAATCTGAGGACGGGTCTAAGCCCGCCTACGTGGATGATGACACTGTAGACAAGGACTCTAAATGTGTCACTTTTGCAGCAATGACTTTCAACATCGAAAACGAGCGTTGGGAGGGCGTCCCCATCATGATGCGTGCCGGTAAGGCTTTGAATGAGTCCAAGGTGGAGATCAGACTGCAGTACAAAGCGGTCGCATCGGGTGTCTTCAAAGACATTCCAAATAACGAACTGGTCATCAGAGTGCAGCCCGATGCCGCTGTGTACCTAAAGTTTAATGCTAAGACCCCTGGTCTGTCAAATGCTACCCAAGTCACAGATCTGAATCTAACTTACGCAAGCAGGTACCAAGACTTTTGGATTCCAGAGGCTTACGAGGTGTTGATAAGAGACGCCCTACTGGGTGACCATTCCAACTTTGTCAGAGATGACGAATTGGATATCAGTTGGGGCATATTCACCCCATTACTGAAGCACATAGAGCGTCCGGACGGTCCAACACCGGAAATTTACCCCTACGGATCAAGAGGTCCAAAGGGATTGAAGGAATATATGCAAAAACACAAGTATGTTATGCCCGAAAAGCACCCTTACGCTTGGCCCGTGACTAAGCCAGAAGATACGAAGGATAATTAGCTGCAGGAATTCGATATCAAGCTTATCGATA'''

y='''GACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGTATGATCCAATATCAAAGGAAATGATAGCATTGAAGGATGAGACTAATCCAATTGAGGAGTGGCAGCATATAGAACAGCTAAAGGGTAGTGCTGAAGGAAGCATACGATACCCCGCATGGAATGGGATAATATCACAGGAGGTACTAGACTACCTTTCATCCTACATAAATAGACGCATATAAGTACGCATTTAAGCATAAACACGCACTATGCCGTTCTTCTCATGTATATATATATACAGGCAACACGCAGATATAGGTGCGACGTGAACAGTGAGCTGTATGTGCGCAGCTCGCGTTGCATTTTCGGAAGCGCTCGTTTTCGGAAACGCTTTGAAGTTCCTATTCCGAAGTTCCTATTCTCTAGAAAGTATAGGAACTTCAGAGCGCTTTTGAAAACCAAAAGCGCTCTGAAGACGCACTTTCAAAAAACCAAAAACGCACCGGACTGTAACGAGCTACTAAAATATTGCGAATACCGCTTCCACAAACATTGCTCAAAAGTATCTCTTTGCTATATATCTCTGTGCTATATCCCTATATAACCTACCCATCCACCTTTCGCTCCTTGAACTTGCATCTAAACTCGACCTCTACATTTTTTATGTTTATCTCTAGTATTACTCTTTAGACAAAAAAATTGTAGTAAGAACTATTCATAGAGTGAATCGAAAACAATACGAAAATGTAAACATTTCCTATACGTAGTATATAGAGACAAAATAGAAGAAACCGTTCATAATTTTCTGACCAATGAAGAATCATCAACGCTATCACTTTCTGTTCACAAAGTATGCGCAATCCACATCGGTATAGAATATAATCGGGGATGCCTTTATCTTGAAAAAATGCACCCGCAGCTTCGCTAGTAATCAGTAAACGCGGGAAGTGGAGTCAGGCTTTTTTTATGGAAGAGAAAATAGACACCAAAGTAGCCTTCTTCTAACCTTAACGGACCTACAGTGCAAAAAGTTATCAAGAGACTGCATTATAGAGCGCACAAAGGAGAAAAAAAGTAATCTAAGATGCTTTGTTAGAAAAATAGCGCTCTCGGGATGCATTTTTGTAGAACAAAAAAGAAGTATAGATTCTTTGTTGGTAAAATAGCGCTCTCGCGTTGCATTTCTGTTCTGTAAAAATGCAGCTCAGATTCTTTGTTTGAAAAATTAGCGCTCTCGCGTTGCATTTTTGTTTTACAAAAATGAAGCACAGATTCTTCGTTGGTAAAATAGCGCTTTCGCGTTGCATTTCTGTTCTGTAAAAATGCAGCTCAGATTCTTTGTTTGAAAAATTAGCGCTCTCGCGTTGCATTTTTGTTCTACAAAATGAAGCACAGATGCTTCGTTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTACCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCCTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGAGCTCAGTTTATCATTATCAATACTCGCCATTTCAAAGAATACGTAAATAATTAATAGTAGTGATTTTCCTAACTTTATTTAGTCAAAAAATTAGCCTTTTAATTCTGCTGTAACCCGTACATGCCCAAAATAGGGGGCGGGTTACACAGAATATATAACATCGTAGGTGTCTGGGTGAACAGTTTATTCCTGGCATCCACTAAATATAATGGAGCCCGCTTTTTAAGCTGGCATCCAGAAAAAAAAAGAATCCCAGCACCAAAATATTGTTTTCTTCACCAACCATCAGTTCATAGGTCCATTCTCTTAGCGCAACTACAGAGAACAGGGGCACAAACAGGCAAAAAACGGGCACAACCTCAATGGAGTGATGCAACCTGCCTGGAGTAAATGATGACACAAGGCAATTGACCCACGCATGTATCTATCTCATTTTCTTACACCTTCTATTACCTTCTGCTCTCTCTGATTTGGAAAAAGCTGAAAAAAAAGGTTGAAACCAGTTCCCTGAAATTATTCCCCTACTTGACTAATAAGTATATAAAGACGGTAGGTATTGATTGTAATTCTGTAAATCTATTTCTTAAACTTCTTAAATTCTACTTTTATAGTTAGTCTTTTTTTTAGTTTTAAAACACCAGAACTTAGTTTCGACGGATTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGATATCAAGCTTATCGATACCGTCGACCTCGAGTCATGTAATTAGTTATGTCACGCTTACATTCACGCCCTCCCCCCACATCCGCTCTAACCGAAAAGGAAGGAGTTAGACAACCTGAAGTCTAGGTCCCTATTTATTTTTTTATAGTTATGTTAGTATTAAGAACGTTATTTATATTTCAAATTTTTCTTTTTTTTCTGTACAGACGCGTGTACGCATGTAACATTATACTGAAAACCTTGCTTGAGAAGGTTTTGGGACGCTCGAAGGCTTTAATTTGCGGCCGGTACCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCGACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAACGCGAATTTTAACAAAATATTAACGTTTACAATTTCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATCGACGGTCGAGGAGAACTTCTAGTATATCCACATACCTAATATTATTGCCTTATTAAAAATGGAATCCCAACAATTACATCAAAATCCACATTCTCTTCAAAATCAATTGTCCTGTACTTCCTTGTTCATGTGTGTTCAAAAACGTTATATTTATAGGATAATTATACTCTATTTCTCAACAAGTAATTGGTTGTTTGGCCGAGCGGTCTAAGGCGCCTGATTCAAGAAATATCTTGACCGCAGTTAACTGTGGGAATACTCAGGTATCGTAAGATGCAAGAGTTCGAATCTCTTAGCAACCATTATTTTTTTCCTCAACATAACGAGAACACACAGGGGCGCTATCGCACAGAATCAAATTCGATGACTGGAAATTTTTTGTTAATTTCAGAGGTCGCCTGACGCATATACCTTTTTCAACTGAAAAATTGGGAGAAAAAGGAAAGGTGAGAGGCCGGAACCGGCTTTTCATATAGAATAGAGAAGCGTTCATGACTAAATGCTTGCATCACAATACTTGAAGTTGACAATATTATTTAAGGACCTATTGTTTTTTCCAATAGGTGGTTAGCAATCGTCTTACTTTCTAACTTTTCTTACCTTTTACATTTCAGCAATATATATATATATTTCAAGGATATACCATTCTAATGTCTGCCCCTATGTCTGCCCCTAAGAAGATCGTCGTTTTGCCAGGTGACCACGTTGGTCAAGAAATCACAGCCGAAGCCATTAAGGTTCTTAAAGCTATTTCTGATGTTCGTTCCAATGTCAAGTTCGATTTCGAAAATCATTTAATTGGTGGTGCTGCTATCGATGCTACAGGTGTCCCACTTCCAGATGAGGCGCTGGAAGCCTCCAAGAAGGTTGATGCCGTTTTGTTAGGTGCTGTGGCTGGTCCTAAATGGGGTACCGGTAGTGTTAGACCTGAACAAGGTTTACTAAAAATCCGTAAAGAACTTCAATTGTACGCCAACTTAAGACCATGTAACTTTGCATCCGACTCTCTTTTAGACTTATCTCCAATCAAGCCACAATTTGCTAAAGGTACTGACTTCGTTGTTGTCAGAGAATTAGTGGGAGGTATTTACTTTGGTAAGAGAAAGGAAGACGATGGTGATGGTGTCGCTTGGGATAGTGAACAATACACCGTTCCAGAAGTGCAAAGAATCACAAGAATGGCCGCTTTCATGGCCCTACAACATGAGCCACCATTGCCTATTTGGTCCTTGGATAAAGCTAATCTTTTGGCCTCTTCAAGATTATGGAGAAAAACTGTGGAGGAAACCATCAAGAACGAATTCCCTACATTGAAGGTTCAACATCAATTGATTGATTCTGCCGCCATGATCCTAGTTAAGAACCCAACCCACCTAAATGGTATTATAATCACCAGCAACATGTTTGGTGATATCATCTCCGATGAAGCCTCCGTTATCCCAGGTTCCTTGGGTTTGTTGCCATCTGCGTCCTTGGCCTCTTTGCCAGACAAGAACACCGCATTTGGTTTGTACGAACCATGCCACGGTTCTGCTCCAGATTTGCCAAAGAATAAGGTTGACCCTATCGCCACTATCTTGTCTGCTGCAATGATGTTGAAATTGTCATTGAACTTGCCTGAAGAAGGTAAGGCCATTGAAGATGCAGTTAAAAAGGTTTTGGATGCAGGTATCAGAACTGGTGATTTAGGTGGTTCCAACAGTACCACCGAAGTCGGTGATGCTGTCGCCGAAGAAGTTAAGAAAATCCTTGCTTAAAAAGATTCTCTTTTTTTATGATATTTGTACATAAACTTTATAAATGAAATTCATAATAGAAACGACACGAAATTACAAAATGGAATATGTTCATAGGGTAGACGAAACTATATACGCAATCTACATACATTTATCAAGAAGGAGAAAAAGGAGGATAGTAAAGGAATACAGGTAAGCAAATTGATACTAATGGCTCAACGTGATAAGGAAAAAGAATTGCACTTTAACATTAATATTGACAAGGAGGAGGGCACCACACAAAAAGTTAGGTGTAACAGAAAATCATGAAACTACGATTCCTAATTTGATATTGGAGGATTTTCTCTAAAAAAAAAAAAATACAACAAATAAAAAACACTCAATGACCTGACCATTTGATGGAGTTTAAGTCAATACCTTCTTGAAGCATTTCCCATAATGGTGAAAGTTCCCTCAAGAATTTTACTCTGTCAGAAACGGCCTTACGACGTAGTCGATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGTTAAGCCAGCCCCGACACCCGCCAACACCCGCTGACGCGCCCTGACGGGCTTGTCTGCTCCCGGCATCCGCTTACAGACAAGCTGTGACCGTCTCCGGGAGCTGCATGTGTCAGAGGTTTTCACCGTCATCACCGAAACGCGCGA'''

c = CommonSubstrings(x,y)

"def CommonSubstrings(S1, S2, limit=30):

    M = [[0]*(len(S2)) for i in xrange(len(S1))]

    matches=[]

    for x in xrange(1,len(S1)):
        for y in xrange(1,len(S2)):

            upperleftcell = M[x-1][y-1]

            if S1[x-1] == S2[y-1]:
                M[x][y] = upperleftcell + 1
            else:
                M[x][y] = 0
                if upperleftcell>limit:
                    matches.append((x-1-upperleftcell,y-1-upperleftcell,
upperleftcell))

    for x in xrange(1,len(S1)):
        if M[x][len(S2)-1]>limit:

matches.append(((x-M[x][len(S2)-1]),len(S2)-1-M[x][len(S2)-1],M[x][len(S2)-1]))
            #print M[x][len(S2)-1]

    for y in xrange(1,len(S2)):
        if M[len(S1)-1][y]>limit:

matches.append((len(S1)-1-M[len(S1)-1][y],y-M[len(S1)-1][y]-1,M[len(S1)-1][y]))
            #print M[len(S1)-1][y]

    return matches

x='''TTCTAGAACTAGTGGATCCCCCGGGCTGCAGATGAGTGAAGGCCCCGTCAAATTCGAAAAAAATACCGTCATATCTGTCTTTGGTGCGTCAGGTGATCTGGCAAAGAAGAAGACTTTTCCCGCCTTATTTGGGCTTTTCAGAGAAGGTTACCTTGATCCATCTACCAAGATCTTCGGTTATGCCCGGTCCAAATTGTCCATGGAGGAGGACCTGAAGTCCCGTGTCCTACCCCACTTGAAAAAACCTCACGGTGAAGCCGATGACTCTAAGGTCGAACAGTTCTTCAAGATGGTCAGCTACATTTCGGGAAATTACGACACAGATGAAGGCTTCGACGAATTAAGAACGCAGATCGAGAAATTCGAGAAAAGTGCCAACGTCGATGTCCCACACCGTCTCTTCTATCTGGCCTTGCCGCCAAGCGTTTTTTTGACGGTGGCCAAGCAGATCAAGAGTCGTGTGTACGCAGAGAATGGCATCACCCGTGTAATCGTAGAGAAACCTTTCGGCCACGACCTGGCCTCTGCCAGGGAGCTGCAAAAAAACCTGGGGCCCCTCTTTAAAGAAGAAGAGTTGTACAGAATTGACCATTACTTGGGTAAAGAGTTGGTCAAGAATCTTTTAGTCTTGAGGTTCGGTAACCAGTTTTTGAATGCCTCGTGGAATAGAGACAACATTCAAAGCGTTCAGATTTCGTTTAAAGAGAGGTTCGGCACCGAAGGCCGTGGCGGCTATTTCGACTCTATAGGCATAATCAGAGACGTGATGCAGAACCATCTGTTACAAATCATGACTCTCTTGACTATGGAAAGACCGGTGTCTTTTGACCCGGAATCTATTCGTGACGAAAAGGTTAAGGTTCTAAAGGCCGTGGCCCCCATCGACACGGACGACGTCCTCTTGGGCCAGTACGGTAAATCTGAGGACGGGTCTAAGCCCGCCTACGTGGATGATGACACTGTAGACAAGGACTCTAAATGTGTCACTTTTGCAGCAATGACTTTCAACATCGAAAACGAGCGTTGGGAGGGCGTCCCCATCATGATGCGTGCCGGTAAGGCTTTGAATGAGTCCAAGGTGGAGATCAGACTGCAGTACAAAGCGGTCGCATCGGGTGTCTTCAAAGACATTCCAAATAACGAACTGGTCATCAGAGTGCAGCCCGATGCCGCTGTGTACCTAAAGTTTAATGCTAAGACCCCTGGTCTGTCAAATGCTACCCAAGTCACAGATCTGAATCTAACTTACGCAAGCAGGTACCAAGACTTTTGGATTCCAGAGGCTTACGAGGTGTTGATAAGAGACGCCCTACTGGGTGACCATTCCAACTTTGTCAGAGATGACGAATTGGATATCAGTTGGGGCATATTCACCCCATTACTGAAGCACATAGAGCGTCCGGACGGTCCAACACCGGAAATTTACCCCTACGGATCAAGAGGTCCAAAGGGATTGAAGGAATATATGCAAAAACACAAGTATGTTATGCCCGAAAAGCACCCTTACGCTTGGCCCGTGACTAAGCCAGAAGATACGAAGGATAATTAGCTGCAGGAATTCGATATCAAGCTTATCGATA'''

y='''GACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGTATGATCCAATATCAAAGGAAATGATAGCATTGAAGGATGAGACTAATCCAATTGAGGAGTGGCAGCATATAGAACAGCTAAAGGGTAGTGCTGAAGGAAGCATACGATACCCCGCATGGAATGGGATAATATCACAGGAGGTACTAGACTACCTTTCATCCTACATAAATAGACGCATATAAGTACGCATTTAAGCATAAACACGCACTATGCCGTTCTTCTCATGTATATATATATACAGGCAACACGCAGATATAGGTGCGACGTGAACAGTGAGCTGTATGTGCGCAGCTCGCGTTGCATTTTCGGAAGCGCTCGTTTTCGGAAACGCTTTGAAGTTCCTATTCCGAAGTTCCTATTCTCTAGAAAGTATAGGAACTTCAGAGCGCTTTTGAAAACCAAAAGCGCTCTGAAGACGCACTTTCAAAAAACCAAAAACGCACCGGACTGTAACGAGCTACTAAAATATTGCGAATACCGCTTCCACAAACATTGCTCAAAAGTATCTCTTTGCTATATATCTCTGTGCTATATCCCTATATAACCTACCCATCCACCTTTCGCTCCTTGAACTTGCATCTAAACTCGACCTCTACATTTTTTATGTTTATCTCTAGTATTACTCTTTAGACAAAAAAATTGTAGTAAGAACTATTCATAGAGTGAATCGAAAACAATACGAAAATGTAAACATTTCCTATACGTAGTATATAGAGACAAAATAGAAGAAACCGTTCATAATTTTCTGACCAATGAAGAATCATCAACGCTATCACTTTCTGTTCACAAAGTATGCGCAATCCACATCGGTATAGAATATAATCGGGGATGCCTTTATCTTGAAAAAATGCACCCGCAGCTTCGCTAGTAATCAGTAAACGCGGGAAGTGGAGTCAGGCTTTTTTTATGGAAGAGAAAATAGACACCAAAGTAGCCTTCTTCTAACCTTAACGGACCTACAGTGCAAAAAGTTATCAAGAGACTGCATTATAGAGCGCACAAAGGAGAAAAAAAGTAATCTAAGATGCTTTGTTAGAAAAATAGCGCTCTCGGGATGCATTTTTGTAGAACAAAAAAGAAGTATAGATTCTTTGTTGGTAAAATAGCGCTCTCGCGTTGCATTTCTGTTCTGTAAAAATGCAGCTCAGATTCTTTGTTTGAAAAATTAGCGCTCTCGCGTTGCATTTTTGTTTTACAAAAATGAAGCACAGATTCTTCGTTGGTAAAATAGCGCTTTCGCGTTGCATTTCTGTTCTGTAAAAATGCAGCTCAGATTCTTTGTTTGAAAAATTAGCGCTCTCGCGTTGCATTTTTGTTCTACAAAATGAAGCACAGATGCTTCGTTCAGGTGGCACTTTTCGGGGAAATGTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTACCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCCTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGAGCTCAGTTTATCATTATCAATACTCGCCATTTCAAAGAATACGTAAATAATTAATAGTAGTGATTTTCCTAACTTTATTTAGTCAAAAAATTAGCCTTTTAATTCTGCTGTAACCCGTACATGCCCAAAATAGGGGGCGGGTTACACAGAATATATAACATCGTAGGTGTCTGGGTGAACAGTTTATTCCTGGCATCCACTAAATATAATGGAGCCCGCTTTTTAAGCTGGCATCCAGAAAAAAAAAGAATCCCAGCACCAAAATATTGTTTTCTTCACCAACCATCAGTTCATAGGTCCATTCTCTTAGCGCAACTACAGAGAACAGGGGCACAAACAGGCAAAAAACGGGCACAACCTCAATGGAGTGATGCAACCTGCCTGGAGTAAATGATGACACAAGGCAATTGACCCACGCATGTATCTATCTCATTTTCTTACACCTTCTATTACCTTCTGCTCTCTCTGATTTGGAAAAAGCTGAAAAAAAAGGTTGAAACCAGTTCCCTGAAATTATTCCCCTACTTGACTAATAAGTATATAAAGACGGTAGGTATTGATTGTAATTCTGTAAATCTATTTCTTAAACTTCTTAAATTCTACTTTTATAGTTAGTCTTTTTTTTAGTTTTAAAACACCAGAACTTAGTTTCGACGGATTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGATATCAAGCTTATCGATACCGTCGACCTCGAGTCATGTAATTAGTTATGTCACGCTTACATTCACGCCCTCCCCCCACATCCGCTCTAACCGAAAAGGAAGGAGTTAGACAACCTGAAGTCTAGGTCCCTATTTATTTTTTTATAGTTATGTTAGTATTAAGAACGTTATTTATATTTCAAATTTTTCTTTTTTTTCTGTACAGACGCGTGTACGCATGTAACATTATACTGAAAACCTTGCTTGAGAAGGTTTTGGGACGCTCGAAGGCTTTAATTTGCGGCCGGTACCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCGACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAACGCGAATTTTAACAAAATATTAACGTTTACAATTTCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATCGACGGTCGAGGAGAACTTCTAGTATATCCACATACCTAATATTATTGCCTTATTAAAAATGGAATCCCAACAATTACATCAAAATCCACATTCTCTTCAAAATCAATTGTCCTGTACTTCCTTGTTCATGTGTGTTCAAAAACGTTATATTTATAGGATAATTATACTCTATTTCTCAACAAGTAATTGGTTGTTTGGCCGAGCGGTCTAAGGCGCCTGATTCAAGAAATATCTTGACCGCAGTTAACTGTGGGAATACTCAGGTATCGTAAGATGCAAGAGTTCGAATCTCTTAGCAACCATTATTTTTTTCCTCAACATAACGAGAACACACAGGGGCGCTATCGCACAGAATCAAATTCGATGACTGGAAATTTTTTGTTAATTTCAGAGGTCGCCTGACGCATATACCTTTTTCAACTGAAAAATTGGGAGAAAAAGGAAAGGTGAGAGGCCGGAACCGGCTTTTCATATAGAATAGAGAAGCGTTCATGACTAAATGCTTGCATCACAATACTTGAAGTTGACAATATTATTTAAGGACCTATTGTTTTTTCCAATAGGTGGTTAGCAATCGTCTTACTTTCTAACTTTTCTTACCTTTTACATTTCAGCAATATATATATATATTTCAAGGATATACCATTCTAATGTCTGCCCCTATGTCTGCCCCTAAGAAGATCGTCGTTTTGCCAGGTGACCACGTTGGTCAAGAAATCACAGCCGAAGCCATTAAGGTTCTTAAAGCTATTTCTGATGTTCGTTCCAATGTCAAGTTCGATTTCGAAAATCATTTAATTGGTGGTGCTGCTATCGATGCTACAGGTGTCCCACTTCCAGATGAGGCGCTGGAAGCCTCCAAGAAGGTTGATGCCGTTTTGTTAGGTGCTGTGGCTGGTCCTAAATGGGGTACCGGTAGTGTTAGACCTGAACAAGGTTTACTAAAAATCCGTAAAGAACTTCAATTGTACGCCAACTTAAGACCATGTAACTTTGCATCCGACTCTCTTTTAGACTTATCTCCAATCAAGCCACAATTTGCTAAAGGTACTGACTTCGTTGTTGTCAGAGAATTAGTGGGAGGTATTTACTTTGGTAAGAGAAAGGAAGACGATGGTGATGGTGTCGCTTGGGATAGTGAACAATACACCGTTCCAGAAGTGCAAAGAATCACAAGAATGGCCGCTTTCATGGCCCTACAACATGAGCCACCATTGCCTATTTGGTCCTTGGATAAAGCTAATCTTTTGGCCTCTTCAAGATTATGGAGAAAAACTGTGGAGGAAACCATCAAGAACGAATTCCCTACATTGAAGGTTCAACATCAATTGATTGATTCTGCCGCCATGATCCTAGTTAAGAACCCAACCCACCTAAATGGTATTATAATCACCAGCAACATGTTTGGTGATATCATCTCCGATGAAGCCTCCGTTATCCCAGGTTCCTTGGGTTTGTTGCCATCTGCGTCCTTGGCCTCTTTGCCAGACAAGAACACCGCATTTGGTTTGTACGAACCATGCCACGGTTCTGCTCCAGATTTGCCAAAGAATAAGGTTGACCCTATCGCCACTATCTTGTCTGCTGCAATGATGTTGAAATTGTCATTGAACTTGCCTGAAGAAGGTAAGGCCATTGAAGATGCAGTTAAAAAGGTTTTGGATGCAGGTATCAGAACTGGTGATTTAGGTGGTTCCAACAGTACCACCGAAGTCGGTGATGCTGTCGCCGAAGAAGTTAAGAAAATCCTTGCTTAAAAAGATTCTCTTTTTTTATGATATTTGTACATAAACTTTATAAATGAAATTCATAATAGAAACGACACGAAATTACAAAATGGAATATGTTCATAGGGTAGACGAAACTATATACGCAATCTACATACATTTATCAAGAAGGAGAAAAAGGAGGATAGTAAAGGAATACAGGTAAGCAAATTGATACTAATGGCTCAACGTGATAAGGAAAAAGAATTGCACTTTAACATTAATATTGACAAGGAGGAGGGCACCACACAAAAAGTTAGGTGTAACAGAAAATCATGAAACTACGATTCCTAATTTGATATTGGAGGATTTTCTCTAAAAAAAAAAAAATACAACAAATAAAAAACACTCAATGACCTGACCATTTGATGGAGTTTAAGTCAATACCTTCTTGAAGCATTTCCCATAATGGTGAAAGTTCCCTCAAGAATTTTACTCTGTCAGAAACGGCCTTACGACGTAGTCGATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAGTTAAGCCAGCCCCGACACCCGCCAACACCCGCTGACGCGCCCTGACGGGCTTGTCTGCTCCCGGCATCCGCTTACAGACAAGCTGTGACCGTCTCCGGGAGCTGCATGTGTCAGAGGTTTTCACCGTCATCACCGAAACGCGCGA'''

c = CommonSubstrings(x,y)

#print x
#print y

for a in c:
    print a[0],a[0]+a[2],x[a[0]:a[0]+a[2]]
    print a[1],a[1]+a[2],y[a[1]:a[1]+a[2]]print x
print y

for a in c:
    print a[0],a[0]+a[2],x[a[0]:a[0]+a[2]]
    print a[1],a[1]+a[2],y[a[1]:a[1]+a[2]]



From devaniranjan at gmail.com  Mon Jun 20 20:35:24 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Mon, 20 Jun 2011 16:35:24 -0400
Subject: [Biopython] ClastalW and creating own log odd table
Message-ID: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>

I want to try set up a log-odds matrix for my own and was experimenting with
the BIOPYTHON TUTURIOL


import os
from Bio import Clustalw
from Bio.Clustalw import MultipleAlignCL
cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
cline.set_output('test.aln')

alignment =Clustalw.do_alignment(cline)


The output was as follows..........

sh: clustalw: command not found
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
line 134, in do_alignment
    raise IOError("Output .aln file %s not produced, commandline: %s"
IOError: Output .aln file test.aln not produced, commandline: clustalw
./sequence.fasta -OUTFILE=test.aln


I am not sure where I am going wrong.
Thank you,
George


From idoerg at gmail.com  Mon Jun 20 20:43:56 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Mon, 20 Jun 2011 16:43:56 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
Message-ID: <BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>

George,

It seems like wither you do no have clustalw installed, or it is not
installed in your normal path. Clustalw is a 3rd party program,
unaffiliated with biopython. To download and install, go here:
http://www.clustal.org/

Iddo



On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> I want to try set up a log-odds matrix for my own and was experimenting
> with
> the BIOPYTHON TUTURIOL
>
>
> import os
> from Bio import Clustalw
> from Bio.Clustalw import MultipleAlignCL
> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
> cline.set_output('test.aln')
>
> alignment =Clustalw.do_alignment(cline)
>
>
> The output was as follows..........
>
> sh: clustalw: command not found
> Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
> line 134, in do_alignment
>    raise IOError("Output .aln file %s not produced, commandline: %s"
> IOError: Output .aln file test.aln not produced, commandline: clustalw
> ./sequence.fasta -OUTFILE=test.aln
>
>
> I am not sure where I am going wrong.
> Thank you,
> George
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html


From devaniranjan at gmail.com  Mon Jun 20 20:49:37 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Mon, 20 Jun 2011 16:49:37 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
	<BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
Message-ID: <BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>

Hi Iddo,

Thank you but when I do

from Bio import Clustalw

It does not raise an error, and under
Python2.4/Site-Packages/Bio/
There is a folder called ClustalW

So does it mean there is something extra to be installed than the above
which already exist?

Thank you,
George


On Mon, Jun 20, 2011 at 4:43 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> George,
>
> It seems like wither you do no have clustalw installed, or it is not
> installed in your normal path. Clustalw is a 3rd party program,
> unaffiliated with biopython. To download and install, go here:
> http://www.clustal.org/
>
> Iddo
>
>
>
> On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> I want to try set up a log-odds matrix for my own and was experimenting
>> with
>> the BIOPYTHON TUTURIOL
>>
>>
>> import os
>> from Bio import Clustalw
>> from Bio.Clustalw import MultipleAlignCL
>> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
>> cline.set_output('test.aln')
>>
>> alignment =Clustalw.do_alignment(cline)
>>
>>
>> The output was as follows..........
>>
>> sh: clustalw: command not found
>> Traceback (most recent call last):
>>  File "<stdin>", line 1, in ?
>>  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
>> line 134, in do_alignment
>>    raise IOError("Output .aln file %s not produced, commandline: %s"
>> IOError: Output .aln file test.aln not produced, commandline: clustalw
>> ./sequence.fasta -OUTFILE=test.aln
>>
>>
>> I am not sure where I am going wrong.
>> Thank you,
>> George
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>


From idoerg at gmail.com  Mon Jun 20 21:05:13 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Mon, 20 Jun 2011 17:05:13 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
	<BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
	<BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>
Message-ID: <BANLkTikV_Lce0zPYJCiXh=5kHQn0oEuvFA@mail.gmail.com>

Clustalw is a 3rd party package, it is not part of Biopython.

What you are importing via Python is not clustalw, but rather the Biopython
interface to clustalw.

./I


On Mon, Jun 20, 2011 at 4:49 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi Iddo,
>
> Thank you but when I do
>
> from Bio import Clustalw
>
> It does not raise an error, and under
> Python2.4/Site-Packages/Bio/
> There is a folder called ClustalW
>
> So does it mean there is something extra to be installed than the above
> which already exist?
>
> Thank you,
> George
>
>
>
> On Mon, Jun 20, 2011 at 4:43 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>
>> George,
>>
>> It seems like wither you do no have clustalw installed, or it is not
>> installed in your normal path. Clustalw is a 3rd party program,
>> unaffiliated with biopython. To download and install, go here:
>> http://www.clustal.org/
>>
>> Iddo
>>
>>
>>
>> On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <
>> devaniranjan at gmail.com> wrote:
>>
>>> I want to try set up a log-odds matrix for my own and was experimenting
>>> with
>>> the BIOPYTHON TUTURIOL
>>>
>>>
>>> import os
>>> from Bio import Clustalw
>>> from Bio.Clustalw import MultipleAlignCL
>>> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
>>> cline.set_output('test.aln')
>>>
>>> alignment =Clustalw.do_alignment(cline)
>>>
>>>
>>> The output was as follows..........
>>>
>>> sh: clustalw: command not found
>>> Traceback (most recent call last):
>>>  File "<stdin>", line 1, in ?
>>>  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
>>> line 134, in do_alignment
>>>    raise IOError("Output .aln file %s not produced, commandline: %s"
>>> IOError: Output .aln file test.aln not produced, commandline: clustalw
>>> ./sequence.fasta -OUTFILE=test.aln
>>>
>>>
>>> I am not sure where I am going wrong.
>>> Thank you,
>>> George
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>
>>
>>
>>
>> --
>> Iddo Friedberg
>> http://iddo-friedberg.net/contact.html
>>
>
>


-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html


From devaniranjan at gmail.com  Mon Jun 20 21:14:18 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Mon, 20 Jun 2011 17:14:18 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTikV_Lce0zPYJCiXh=5kHQn0oEuvFA@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
	<BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
	<BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>
	<BANLkTikV_Lce0zPYJCiXh=5kHQn0oEuvFA@mail.gmail.com>
Message-ID: <BANLkTinyNMzx8arv9vwqav19doy1KCL7kA@mail.gmail.com>

Thank you Iddo,
Could I also ask if I should install ClustalW within the
python2.4/site-packages
or somewhere else?
Thank you for your answers,
George


On Mon, Jun 20, 2011 at 5:05 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> Clustalw is a 3rd party package, it is not part of Biopython.
>
> What you are importing via Python is not clustalw, but rather the Biopython
> interface to clustalw.
>
> ./I
>
>
> On Mon, Jun 20, 2011 at 4:49 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hi Iddo,
>>
>> Thank you but when I do
>>
>> from Bio import Clustalw
>>
>> It does not raise an error, and under
>> Python2.4/Site-Packages/Bio/
>> There is a folder called ClustalW
>>
>> So does it mean there is something extra to be installed than the above
>> which already exist?
>>
>> Thank you,
>> George
>>
>>
>>
>> On Mon, Jun 20, 2011 at 4:43 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>>
>>> George,
>>>
>>> It seems like wither you do no have clustalw installed, or it is not
>>> installed in your normal path. Clustalw is a 3rd party program,
>>> unaffiliated with biopython. To download and install, go here:
>>> http://www.clustal.org/
>>>
>>> Iddo
>>>
>>>
>>>
>>> On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <
>>> devaniranjan at gmail.com> wrote:
>>>
>>>> I want to try set up a log-odds matrix for my own and was experimenting
>>>> with
>>>> the BIOPYTHON TUTURIOL
>>>>
>>>>
>>>> import os
>>>> from Bio import Clustalw
>>>> from Bio.Clustalw import MultipleAlignCL
>>>> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
>>>> cline.set_output('test.aln')
>>>>
>>>> alignment =Clustalw.do_alignment(cline)
>>>>
>>>>
>>>> The output was as follows..........
>>>>
>>>> sh: clustalw: command not found
>>>> Traceback (most recent call last):
>>>>  File "<stdin>", line 1, in ?
>>>>  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
>>>> line 134, in do_alignment
>>>>    raise IOError("Output .aln file %s not produced, commandline: %s"
>>>> IOError: Output .aln file test.aln not produced, commandline: clustalw
>>>> ./sequence.fasta -OUTFILE=test.aln
>>>>
>>>>
>>>> I am not sure where I am going wrong.
>>>> Thank you,
>>>> George
>>>> _______________________________________________
>>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>>
>>>
>>>
>>>
>>> --
>>> Iddo Friedberg
>>> http://iddo-friedberg.net/contact.html
>>>
>>
>>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>


From idoerg at gmail.com  Mon Jun 20 21:29:34 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Mon, 20 Jun 2011 17:29:34 -0400
Subject: [Biopython] ClastalW and creating own log odd table
In-Reply-To: <BANLkTinyNMzx8arv9vwqav19doy1KCL7kA@mail.gmail.com>
References: <BANLkTimWPD1P5BtXPFHMkbbjBBk+MgMaVg@mail.gmail.com>
	<BANLkTimg7BHeNsRb9Ue1aaxCA=aabY2cdg@mail.gmail.com>
	<BANLkTi=2-Wk1Gn=q04-3H18Uf-w4nXM79w@mail.gmail.com>
	<BANLkTikV_Lce0zPYJCiXh=5kHQn0oEuvFA@mail.gmail.com>
	<BANLkTinyNMzx8arv9vwqav19doy1KCL7kA@mail.gmail.com>
Message-ID: <BANLkTikN+AGytu=Ke0TE6mrVSf6XUXaVnA@mail.gmail.com>

For installation instrucitons go here:

http://www.clustal.org/

This varies with your operating system.

On Mon, Jun 20, 2011 at 5:14 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Thank you Iddo,
> Could I also ask if I should install ClustalW within the
> python2.4/site-packages
> or somewhere else?
> Thank you for your answers,
> George
>
>
>
> On Mon, Jun 20, 2011 at 5:05 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>
>> Clustalw is a 3rd party package, it is not part of Biopython.
>>
>> What you are importing via Python is not clustalw, but rather the
>> Biopython interface to clustalw.
>>
>> ./I
>>
>>
>> On Mon, Jun 20, 2011 at 4:49 PM, George Devaniranjan <
>> devaniranjan at gmail.com> wrote:
>>
>>> Hi Iddo,
>>>
>>> Thank you but when I do
>>>
>>> from Bio import Clustalw
>>>
>>> It does not raise an error, and under
>>> Python2.4/Site-Packages/Bio/
>>> There is a folder called ClustalW
>>>
>>> So does it mean there is something extra to be installed than the above
>>> which already exist?
>>>
>>> Thank you,
>>> George
>>>
>>>
>>>
>>> On Mon, Jun 20, 2011 at 4:43 PM, Iddo Friedberg <idoerg at gmail.com>wrote:
>>>
>>>> George,
>>>>
>>>> It seems like wither you do no have clustalw installed, or it is not
>>>> installed in your normal path. Clustalw is a 3rd party program,
>>>> unaffiliated with biopython. To download and install, go here:
>>>> http://www.clustal.org/
>>>>
>>>> Iddo
>>>>
>>>>
>>>>
>>>> On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <
>>>> devaniranjan at gmail.com> wrote:
>>>>
>>>>> I want to try set up a log-odds matrix for my own and was experimenting
>>>>> with
>>>>> the BIOPYTHON TUTURIOL
>>>>>
>>>>>
>>>>> import os
>>>>> from Bio import Clustalw
>>>>> from Bio.Clustalw import MultipleAlignCL
>>>>> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
>>>>> cline.set_output('test.aln')
>>>>>
>>>>> alignment =Clustalw.do_alignment(cline)
>>>>>
>>>>>
>>>>> The output was as follows..........
>>>>>
>>>>> sh: clustalw: command not found
>>>>> Traceback (most recent call last):
>>>>>  File "<stdin>", line 1, in ?
>>>>>  File
>>>>> "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
>>>>> line 134, in do_alignment
>>>>>    raise IOError("Output .aln file %s not produced, commandline: %s"
>>>>> IOError: Output .aln file test.aln not produced, commandline: clustalw
>>>>> ./sequence.fasta -OUTFILE=test.aln
>>>>>
>>>>>
>>>>> I am not sure where I am going wrong.
>>>>> Thank you,
>>>>> George
>>>>> _______________________________________________
>>>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Iddo Friedberg
>>>> http://iddo-friedberg.net/contact.html
>>>>
>>>
>>>
>>
>>
>> --
>> Iddo Friedberg
>> http://iddo-friedberg.net/contact.html
>>
>
>


-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html


From ssphatak at mdanderson.org  Mon Jun 20 22:25:15 2011
From: ssphatak at mdanderson.org (Sharangdhar Phatak)
Date: Mon, 20 Jun 2011 17:25:15 -0500
Subject: [Biopython] pubmed import
Message-ID: <1308608715.29480.34.camel@KVJ>

Hi, 
 I would like to download pubmed abstracts by using limits based on
publication dates. Can someone please provide a couple of pointers on
how to do so?

Regards,
Sharang



From devaniranjan at gmail.com  Tue Jun 21 18:01:31 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 21 Jun 2011 14:01:31 -0400
Subject: [Biopython] BLOCKS BLOSUM
Message-ID: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>

Hi,
This might not be the correct place to ask this question-but some of you may
have experience in this.
I went to the BLOCKS database and downloaded a text file that contains many
BLOCKS but I would like to see the structure of these blocks either in
VMD/Pymol
Is there a way to find the PDB ID of these blocks?

What I want is to use the same BLOCKS info and develop my own BLOSUM like
matrix using biopyhton.
Thank you and my apologies is this is not directly related to biopython.
(example of a block from the downloaded text file is given below)
George

NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN


From idoerg at gmail.com  Tue Jun 21 18:36:46 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Tue, 21 Jun 2011 14:36:46 -0400
Subject: [Biopython] BLOCKS BLOSUM
In-Reply-To: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
References: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
Message-ID: <BANLkTi=hu7FzXhZzxPwsHC1D7yG7i_J9rg@mail.gmail.com>

Go here:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc232

On Tue, Jun 21, 2011 at 2:01 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi,
> This might not be the correct place to ask this question-but some of you
> may
> have experience in this.
> I went to the BLOCKS database and downloaded a text file that contains many
> BLOCKS but I would like to see the structure of these blocks either in
> VMD/Pymol
> Is there a way to find the PDB ID of these blocks?
>
> What I want is to use the same BLOCKS info and develop my own BLOSUM like
> matrix using biopyhton.
> Thank you and my apologies is this is not directly related to biopython.
> (example of a block from the downloaded text file is given below)
> George
>
> NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
> NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
> NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
> NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
> NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
> NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html


From devaniranjan at gmail.com  Tue Jun 21 18:45:34 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Tue, 21 Jun 2011 14:45:34 -0400
Subject: [Biopython] BLOCKS BLOSUM
In-Reply-To: <BANLkTi=hu7FzXhZzxPwsHC1D7yG7i_J9rg@mail.gmail.com>
References: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
	<BANLkTi=hu7FzXhZzxPwsHC1D7yG7i_J9rg@mail.gmail.com>
Message-ID: <BANLkTinrbnEcZEZfKF9RgD9MaZ1P_fX11g@mail.gmail.com>

Hi Iddo,
I actaully want to see the fragments being used for the BLOCK in pymol or
VMD but as you can see below
(Is it a alpha helix or a beta sheet..etc)
NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN

I cant find the PDB ID these fragments came from.
The actual calcualtion of the matrix I think I can do.
Thank you,
George






On Tue, Jun 21, 2011 at 2:36 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> Go here:
>
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc232
>
> On Tue, Jun 21, 2011 at 2:01 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hi,
>> This might not be the correct place to ask this question-but some of you
>> may
>> have experience in this.
>> I went to the BLOCKS database and downloaded a text file that contains
>> many
>> BLOCKS but I would like to see the structure of these blocks either in
>> VMD/Pymol
>> Is there a way to find the PDB ID of these blocks?
>>
>> What I want is to use the same BLOCKS info and develop my own BLOSUM like
>> matrix using biopyhton.
>> Thank you and my apologies is this is not directly related to biopython.
>> (example of a block from the downloaded text file is given below)
>> George
>>
>> NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
>> NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
>> NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
>> NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
>> NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
>> NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
>> NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
>> NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
>> NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
>> NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
>> NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
>> NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
>> NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
>> NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>


From Aisling.ODriscoll at cit.ie  Tue Jun 21 20:07:07 2011
From: Aisling.ODriscoll at cit.ie (Aisling ODriscoll)
Date: Tue, 21 Jun 2011 21:07:07 +0100
Subject: [Biopython] Teaching BioPython
Message-ID: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>

Hi everyone,
 
I have been asked to deliver BioPython classes to biologists. Having a
computer science background myself (Python), I am not finding it easy to
tie python back to concepts that the biology students will relate to.
This will be very important as I'm not there to teach them to be expert
Python computer programmers - they're programming skills must relate to
their discipline. Has anyone delivered such a course? Even better would
someone have any lesson plans available which I could use as a starting
point?
 
I came across this post but the it's a bit old and the information
provided in the link no longer seems to be hosted.
http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
 
Any help appreciated. Thanks in advance. 
 
Aisling.
 



From idoerg at gmail.com  Tue Jun 21 20:28:02 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Tue, 21 Jun 2011 16:28:02 -0400
Subject: [Biopython] Teaching BioPython
In-Reply-To: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
Message-ID: <BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com>

Not exactly what you are looking for, but you may be able to grab some
examples from teh course at the Institut Pasteur, which is a programming
course for biologists using Python:

http://www.pasteur.fr/formation/infobio/python/

The same people used to have a biopython course, but it seems not to be
available online anymore. Maybe you can email them directly.

Iddo

On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll <Aisling.ODriscoll at cit.ie
> wrote:

> Hi everyone,
>
> I have been asked to deliver BioPython classes to biologists. Having a
> computer science background myself (Python), I am not finding it easy to
> tie python back to concepts that the biology students will relate to.
> This will be very important as I'm not there to teach them to be expert
> Python computer programmers - they're programming skills must relate to
> their discipline. Has anyone delivered such a course? Even better would
> someone have any lesson plans available which I could use as a starting
> point?
>
> I came across this post but the it's a bit old and the information
> provided in the link no longer seems to be hosted.
> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
>
> Any help appreciated. Thanks in advance.
>
> Aisling.
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html


From p.j.a.cock at googlemail.com  Tue Jun 21 20:33:08 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 21 Jun 2011 21:33:08 +0100
Subject: [Biopython] Teaching BioPython
In-Reply-To: <BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
	<BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com>
Message-ID: <C2B83F16-7FE2-4884-A9B4-4C1BC7D018E9@googlemail.com>



On 21 Jun 2011, at 21:28, Iddo Friedberg <idoerg at gmail.com> wrote:

> Not exactly what you are looking for, but you may be able to grab some
> examples from teh course at the Institut Pasteur, which is a programming
> course for biologists using Python:
> 
> http://www.pasteur.fr/formation/infobio/python/
> 
> The same people used to have a biopython course, but it seems not to be
> available online anymore. Maybe you can email them directly.

Unfortunately large parts of their Biopython material had become out of date.

> 
> On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll wrote:
> 
>> Hi everyone,
>> 
>> I have been asked to deliver BioPython classes to biologists. Having a
>> computer science background myself (Python), I am not finding it easy to
>> tie python back to concepts that the biology students will relate to.
>> This will be very important as I'm not there to teach them to be expert
>> Python computer programmers - they're programming skills must relate to
>> their discipline. Has anyone delivered such a course? Even better would
>> someone have any lesson plans available which I could use as a starting
>> point?
>> 
>> I came across this post but the it's a bit old and the information
>> provided in the link no longer seems to be hosted.
>> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
>> 
>> Any help appreciated. Thanks in advance.
>> 
>> Aisling.
>> 
>> 

I've not tried to do anything quite that ambitious. Have you got an idea of the amount of contact time you have to work with? That would make a big difference.

Peter


From idoerg at gmail.com  Tue Jun 21 20:34:08 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Tue, 21 Jun 2011 16:34:08 -0400
Subject: [Biopython] Teaching BioPython
In-Reply-To: <C2B83F16-7FE2-4884-A9B4-4C1BC7D018E9@googlemail.com>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
	<BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com>
	<C2B83F16-7FE2-4884-A9B4-4C1BC7D018E9@googlemail.com>
Message-ID: <BANLkTikC+50irwx1jnLrgq-_SwctEVV_AA@mail.gmail.com>

There is also Sebastian Bassi's book...
http://www.amazon.com/Bioinformatics-Chapman-Mathematical-Computational-Biology/dp/1584889292/ref=sr_1_1?ie=UTF8&s=books&qid=1308688427&sr=8-1

On Tue, Jun 21, 2011 at 4:33 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

>
>
> On 21 Jun 2011, at 21:28, Iddo Friedberg <idoerg at gmail.com> wrote:
>
> > Not exactly what you are looking for, but you may be able to grab some
> > examples from teh course at the Institut Pasteur, which is a programming
> > course for biologists using Python:
> >
> > http://www.pasteur.fr/formation/infobio/python/
> >
> > The same people used to have a biopython course, but it seems not to be
> > available online anymore. Maybe you can email them directly.
>
> Unfortunately large parts of their Biopython material had become out of
> date.
>
> >
> > On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll wrote:
> >
> >> Hi everyone,
> >>
> >> I have been asked to deliver BioPython classes to biologists. Having a
> >> computer science background myself (Python), I am not finding it easy to
> >> tie python back to concepts that the biology students will relate to.
> >> This will be very important as I'm not there to teach them to be expert
> >> Python computer programmers - they're programming skills must relate to
> >> their discipline. Has anyone delivered such a course? Even better would
> >> someone have any lesson plans available which I could use as a starting
> >> point?
> >>
> >> I came across this post but the it's a bit old and the information
> >> provided in the link no longer seems to be hosted.
> >> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
> >>
> >> Any help appreciated. Thanks in advance.
> >>
> >> Aisling.
> >>
> >>
>
> I've not tried to do anything quite that ambitious. Have you got an idea of
> the amount of contact time you have to work with? That would make a big
> difference.
>
> Peter




-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html


From Aisling.ODriscoll at cit.ie  Tue Jun 21 20:41:50 2011
From: Aisling.ODriscoll at cit.ie (Aisling ODriscoll)
Date: Tue, 21 Jun 2011 21:41:50 +0100
Subject: [Biopython] Teaching BioPython
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie><BANLkTim5k_79FTuzy3uQZGhJ2a8Opv3-qA@mail.gmail.com><C2B83F16-7FE2-4884-A9B4-4C1BC7D018E9@googlemail.com>
	<BANLkTikC+50irwx1jnLrgq-_SwctEVV_AA@mail.gmail.com>
Message-ID: <DA2A8F990E1A4745BBE58A7F7952347802E95F97@CITMAIL.cit.ie>


Thanks Iddo for providing links.

Peter, the contact time is 1 hour lecture and 2 hours lab. 

Thanks again. 

-----Original Message-----
From: Iddo Friedberg [mailto:idoerg at gmail.com]
Sent: Tue 21/06/2011 21:34
To: Peter Cock
Cc: Aisling ODriscoll; biopython at lists.open-bio.org
Subject: Re: [Biopython] Teaching BioPython
 
There is also Sebastian Bassi's book...
http://www.amazon.com/Bioinformatics-Chapman-Mathematical-Computational-Biology/dp/1584889292/ref=sr_1_1?ie=UTF8&s=books&qid=1308688427&sr=8-1

On Tue, Jun 21, 2011 at 4:33 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

>
>
> On 21 Jun 2011, at 21:28, Iddo Friedberg <idoerg at gmail.com> wrote:
>
> > Not exactly what you are looking for, but you may be able to grab some
> > examples from teh course at the Institut Pasteur, which is a programming
> > course for biologists using Python:
> >
> > http://www.pasteur.fr/formation/infobio/python/
> >
> > The same people used to have a biopython course, but it seems not to be
> > available online anymore. Maybe you can email them directly.
>
> Unfortunately large parts of their Biopython material had become out of
> date.
>
> >
> > On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll wrote:
> >
> >> Hi everyone,
> >>
> >> I have been asked to deliver BioPython classes to biologists. Having a
> >> computer science background myself (Python), I am not finding it easy to
> >> tie python back to concepts that the biology students will relate to.
> >> This will be very important as I'm not there to teach them to be expert
> >> Python computer programmers - they're programming skills must relate to
> >> their discipline. Has anyone delivered such a course? Even better would
> >> someone have any lesson plans available which I could use as a starting
> >> point?
> >>
> >> I came across this post but the it's a bit old and the information
> >> provided in the link no longer seems to be hosted.
> >> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
> >>
> >> Any help appreciated. Thanks in advance.
> >>
> >> Aisling.
> >>
> >>
>
> I've not tried to do anything quite that ambitious. Have you got an idea of
> the amount of contact time you have to work with? That would make a big
> difference.
>
> Peter




-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html




From eric.talevich at gmail.com  Wed Jun 22 00:29:55 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 21 Jun 2011 20:29:55 -0400
Subject: [Biopython] Teaching BioPython
In-Reply-To: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
Message-ID: <BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>

On Tue, Jun 21, 2011 at 4:07 PM, Aisling ODriscoll <Aisling.ODriscoll at cit.ie
> wrote:

> Hi everyone,
>
> I have been asked to deliver BioPython classes to biologists. Having a
> computer science background myself (Python), I am not finding it easy to
> tie python back to concepts that the biology students will relate to.
> This will be very important as I'm not there to teach them to be expert
> Python computer programmers - they're programming skills must relate to
> their discipline. Has anyone delivered such a course? Even better would
> someone have any lesson plans available which I could use as a starting
> point?
>
> I came across this post but the it's a bit old and the information
> provided in the link no longer seems to be hosted.
> http://lists.open-bio.org/pipermail/biopython/2009-August/005487.html
>
>
Hi Aisling,

I've run a few 2-hour workshops on Python and Biopython at the University of
Georgia using these slide sets:
http://www.slideshare.net/etalevich/biopython-programming-workshop-at-uga
http://www.slideshare.net/etalevich/python-workshop-1-uga-bioinformatics

I'm due to update the Biopython set soon with a section on Bio.Phylo, and I
can send that to you when it's done if you'd like (or post it here).

The second chapter of the official tutorial, Quick Start, is a good starting
point for designing your own lecture and lab, pulling in more detailed
material from the other chapters as needed.
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc6

Also: It's much easier to run a workshop if the participants have set up the
same environment on their own laptops, or the computers on site all have the
same software installed. Specifically, make sure everyone has IDLE and
Python 2.7 installed. Earlier I let students choose between ipython and
IDLE, and during the workshops I typed my examples into ipython -- this was
highly confusing for 100% of the students, including those who did have
ipython installed but weren't familiar with it. In IDLE, everyone has the
same environment and GUI, and the distinction between interpreter and script
is clear.

Cheers,
Eric


From eric.talevich at gmail.com  Wed Jun 22 00:47:45 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Tue, 21 Jun 2011 20:47:45 -0400
Subject: [Biopython] BLOCKS BLOSUM
In-Reply-To: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
References: <BANLkTimLS8h9DFd8qCKo9iEJD5RMWsOeUQ@mail.gmail.com>
Message-ID: <BANLkTinhfOXRfQ3E2s91jC=u_M+ud2ybUA@mail.gmail.com>

HI George,

If the PDB ID isn't listed with the blocks, then I don't know of an
immediate way to look up the source structure PDBID, but since the blocks
are highly conserved (by definition) you should be able to get a reliable
hit by BLASTing with any of the sequences in the block against NCBI's PDBAA
database. If you'd like to be more rigorous you can construct an HMM profile
from the BLOCKS alignment and use HMMer to search PDBAA. And, if secondary
structure is all you're worried about, you can also try a secondary
structure prediction program like JPred with any of the source sequences as
the query.

Best,
Eric

On Tue, Jun 21, 2011 at 2:01 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi,
> This might not be the correct place to ask this question-but some of you
> may
> have experience in this.
> I went to the BLOCKS database and downloaded a text file that contains many
> BLOCKS but I would like to see the structure of these blocks either in
> VMD/Pymol
> Is there a way to find the PDB ID of these blocks?
>
> What I want is to use the same BLOCKS info and develop my own BLOSUM like
> matrix using biopyhton.
> Thank you and my apologies is this is not directly related to biopython.
> (example of a block from the downloaded text file is given below)
> George
>
> NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
> NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
> NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
> NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
> NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
> NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From p.j.a.cock at googlemail.com  Wed Jun 22 07:46:53 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 22 Jun 2011 08:46:53 +0100
Subject: [Biopython] Teaching BioPython
In-Reply-To: <BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
	<BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>
Message-ID: <BANLkTimJgv7zcVmnED+oFz-wCbGZWpC1mg@mail.gmail.com>

On Wed, Jun 22, 2011 at 1:29 AM, Eric Talevich wrote:
> Hi Aisling,
>
> I've run a few 2-hour workshops on Python and Biopython at the University
> of Georgia using these slide sets:
> http://www.slideshare.net/etalevich/biopython-programming-workshop-at-uga
> http://www.slideshare.net/etalevich/python-workshop-1-uga-bioinformatics
>
> I'm due to update the Biopython set soon with a section on Bio.Phylo, and I
> can send that to you when it's done if you'd like (or post it here).
>
> The second chapter of the official tutorial, Quick Start, is a good starting
> point for designing your own lecture and lab, pulling in more detailed
> material from the other chapters as needed.
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc6

Certainly that could be a good basis - but you're going to have to
be selective given the limited contact time. Realistically you can
expect the students to type in and run some short examples, and
get a flavour of Python (and Biopython). For most of them that
will be all the take away - but a few could be tempted to learn more
(of Python or programming in general).

> Also: It's much easier to run a workshop if the participants have set up the
> same environment on their own laptops, or the computers on site all have
> the same software installed.

For a short course like yours, this is essential - otherwise you (Aisling)
could easily spend the first hour troubleshooting several different setups
and making sure everyone can start the examples.

> Specifically, make sure everyone has IDLE and
> Python 2.7 installed. Earlier I let students choose between ipython and
> IDLE, and during the workshops I typed my examples into ipython -- this
> was highly confusing for 100% of the students, including those who did
> have ipython installed but weren't familiar with it. In IDLE, everyone has
> the same environment and GUI, and the distinction between interpreter
> and script is clear.

Assuming your class are not using the Mac, I'd also use IDLE in a class.
Apple doesn't include it by default on the Mac for some reason.

It is likely your group be using a set of Windows machines, so the
installation of Python 2.7, NumPy and Biopython via the installers
should be easy. You might also look at the Enthought Python Distribution,
which I think comes with them all bundled (but not necessarily the latest
versions).

Peter


From Aisling.ODriscoll at cit.ie  Wed Jun 22 10:51:38 2011
From: Aisling.ODriscoll at cit.ie (Aisling ODriscoll)
Date: Wed, 22 Jun 2011 11:51:38 +0100
Subject: [Biopython] Teaching BioPython
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie><BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>
	<BANLkTimJgv7zcVmnED+oFz-wCbGZWpC1mg@mail.gmail.com>
Message-ID: <DA2A8F990E1A4745BBE58A7F7952347802E95F9A@CITMAIL.cit.ie>

Many thanks to all who have taken the time to reply and to provide links and advice. Apologies, I should have been more explicit about the course duration.
It will be a 1 hour lecture and 2 hours lab delivered over 11 weeks (excluding assessments). I will probably introduce them to a little Perl as well (but not too much because otherwide it will just become confusing for them I think) so I would imagine at least 8-9 weeks will be dedicated to Python/Biopython.
 
So I need to devise 8/9 weeks of lecture notes and 8/9 weeks 2 hour lab exercises and problems - While the first week or so might be dedicated to just getting to grips with Python (they have 4 non contact hours too per week so they can use them for this), I want to introduce them to BioPython and applying programming to biology-related problems as quickly as possible so that they can see the relevance of what they're doing. 
 
Kind Regards,
Aisling.

________________________________

From: Peter Cock [mailto:p.j.a.cock at googlemail.com]
Sent: Wed 22/06/2011 08:46
To: Eric Talevich
Cc: Aisling ODriscoll; biopython at lists.open-bio.org
Subject: Re: [Biopython] Teaching BioPython



On Wed, Jun 22, 2011 at 1:29 AM, Eric Talevich wrote:
> Hi Aisling,
>
> I've run a few 2-hour workshops on Python and Biopython at the University
> of Georgia using these slide sets:
> http://www.slideshare.net/etalevich/biopython-programming-workshop-at-uga
> http://www.slideshare.net/etalevich/python-workshop-1-uga-bioinformatics
>
> I'm due to update the Biopython set soon with a section on Bio.Phylo, and I
> can send that to you when it's done if you'd like (or post it here).
>
> The second chapter of the official tutorial, Quick Start, is a good starting
> point for designing your own lecture and lab, pulling in more detailed
> material from the other chapters as needed.
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc6

Certainly that could be a good basis - but you're going to have to
be selective given the limited contact time. Realistically you can
expect the students to type in and run some short examples, and
get a flavour of Python (and Biopython). For most of them that
will be all the take away - but a few could be tempted to learn more
(of Python or programming in general).

> Also: It's much easier to run a workshop if the participants have set up the
> same environment on their own laptops, or the computers on site all have
> the same software installed.

For a short course like yours, this is essential - otherwise you (Aisling)
could easily spend the first hour troubleshooting several different setups
and making sure everyone can start the examples.

> Specifically, make sure everyone has IDLE and
> Python 2.7 installed. Earlier I let students choose between ipython and
> IDLE, and during the workshops I typed my examples into ipython -- this
> was highly confusing for 100% of the students, including those who did
> have ipython installed but weren't familiar with it. In IDLE, everyone has
> the same environment and GUI, and the distinction between interpreter
> and script is clear.

Assuming your class are not using the Mac, I'd also use IDLE in a class.
Apple doesn't include it by default on the Mac for some reason.

It is likely your group be using a set of Windows machines, so the
installation of Python 2.7, NumPy and Biopython via the installers
should be easy. You might also look at the Enthought Python Distribution,
which I think comes with them all bundled (but not necessarily the latest
versions).

Peter





From p.j.a.cock at googlemail.com  Wed Jun 22 11:27:05 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 22 Jun 2011 12:27:05 +0100
Subject: [Biopython] Teaching BioPython
In-Reply-To: <DA2A8F990E1A4745BBE58A7F7952347802E95F9A@CITMAIL.cit.ie>
References: <DA2A8F990E1A4745BBE58A7F79523478082FBEEA@CITMAIL.cit.ie>
	<BANLkTinmTkSKL12qNdR00LyKusfxEjV7-Q@mail.gmail.com>
	<BANLkTimJgv7zcVmnED+oFz-wCbGZWpC1mg@mail.gmail.com>
	<DA2A8F990E1A4745BBE58A7F7952347802E95F9A@CITMAIL.cit.ie>
Message-ID: <BANLkTin15bWC+jD9HKmcEuWPPG-kxDmX9w@mail.gmail.com>

On Wed, Jun 22, 2011 at 11:51 AM, Aisling ODriscoll
<Aisling.ODriscoll at cit.ie> wrote:
> Many thanks to all who have taken the time to reply and to provide links and
> advice. Apologies, I should have been more explicit about the course
> duration.
> It will be a 1 hour lecture and 2 hours lab delivered over 11 weeks
> (excluding assessments). I will probably introduce them to a little Perl as
> well (but not?too much because otherwide it will just become?confusing for
> them?I think) so I would imagine at least 8-9 weeks will be dedicated to
> Python/Biopython.

Oh right - so a total of about 11 hours lectures and 22 hours in the lab.
That does make things much more interesting (and more work).

> So I need to devise 8/9 weeks of lecture notes and 8/9 weeks 2 hour lab
> exercises and problems - While the first week or so might be dedicated to
> just getting to grips with Python (they have 4 non contact hours too per
> week?so they can use them for this), I want to introduce them to BioPython
> and applying programming to biology-related problems as quickly as possible
> so that they can see the relevance of what they're doing.

I would start by looking at existing introductory Python materials, and probably
put a little more emphasis on string manipulation with biological sequence
examples. Maybe get them to write their own FASTA parser as an exercise,
before then bringing in Biopython.

I've never tried to teach (Bio)python on that scale - but if you find any errors
or omissions in our documentation (especially the Tutorial), we would
welcome feedback.

Peter



From mnemonico at posthocergopropterhoc.net  Mon Jun 27 07:00:37 2011
From: mnemonico at posthocergopropterhoc.net (A M Torres, Hugo)
Date: Mon, 27 Jun 2011 04:00:37 -0300
Subject: [Biopython] biopython cookbook error
Message-ID: <BANLkTim__OXzYwa5FXnaj8b_h0vrnOQTBG3STfdpvAUM_+o=TQ@mail.gmail.com>

Hi, I am new to this list excuse me if this is not the appropriate place to
report this:

I am just trying to teach myself some biopython and at section "2.4.1  Simple
FASTA parsing example" of the biopython tutorial it suggests us to run this
code:

from Bio import SeqIO
> for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
>     print seq_record.id
>     print repr(seq_record.seq)
>     print len(seq_record)
>
>
Which outputs the error:

Traceback (most recent call last):
> File "simple_parser_2_4_1.py", line 4, in <module>
> for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"): #this seems
> wrong in the tutorial
> File "/usr/lib/pymodules/python2.6/Bio/SeqIO/__init__.py", line 424, in
> parse
> raise TypeError("Need a file handle, not a string (i.e. not a filename)")
> TypeError: Need a file handle, not a string (i.e. not a filename)
>

Python novices like me might have a problem understanding what a "file
handle" is. I tryed this and it seems to work:

from Bio import SeqIO
>
> with open("ls_orchid.fasta", 'rU') as data:
>     for seq_record in SeqIO.parse(data, "fasta"):
>         print seq_record.id
>         print repr(seq_record.seq)
>         print len(seq_record)
>

Maybe someone here can help me notify whoever maintains the tutorial.

Thanks,

Hugo Torres


From chapmanb at 50mail.com  Mon Jun 27 10:38:34 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Mon, 27 Jun 2011 06:38:34 -0400
Subject: [Biopython] biopython cookbook error
In-Reply-To: <BANLkTim__OXzYwa5FXnaj8b_h0vrnOQTBG3STfdpvAUM_+o=TQ@mail.gmail.com>
References: <BANLkTim__OXzYwa5FXnaj8b_h0vrnOQTBG3STfdpvAUM_+o=TQ@mail.gmail.com>
Message-ID: <20110627103834.GA22214@sobchak>

Hugo;
Thanks for the e-mail and reporting the problem you were running
into.

> Hi, I am new to this list excuse me if this is not the appropriate place to
> report this:
> 
> I am just trying to teach myself some biopython and at section "2.4.1  Simple
> FASTA parsing example" of the biopython tutorial it suggests us to run this
> code:
[...]
> Which outputs the error:
[...]
> > TypeError: Need a file handle, not a string (i.e. not a filename)

It sounds like you have an old version of Biopython. SeqIO was
changed a few releases ago to support string filenames instead of
handles for the reason you mention: to make it easier for new Python
developers. See FAQ #14 for more information, and #3 for information
about checking your version of Biopython:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc5

If you have easy_install available, you can update with:

sudo easy_install -U biopython

Hope this helps,
Brad


From pjthorpe at gmail.com  Mon Jun 27 16:06:06 2011
From: pjthorpe at gmail.com (Peter Thorpe)
Date: Mon, 27 Jun 2011 17:06:06 +0100
Subject: [Biopython] Biopython Digest, Vol 102, Issue 16
In-Reply-To: <mailman.1.1309190402.19877.biopython@lists.open-bio.org>
References: <mailman.1.1309190402.19877.biopython@lists.open-bio.org>
Message-ID: <BANLkTik1CMoMX1CtBT6zzdXwLKu276UYoQ@mail.gmail.com>

On 27 June 2011 17:00, <biopython-request at lists.open-bio.org> wrote:

> Send Biopython mailing list submissions to
>        biopython at lists.open-bio.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.open-bio.org/mailman/listinfo/biopython
> or, via email, send a message with subject or body 'help' to
>        biopython-request at lists.open-bio.org
>
> You can reach the person managing the list at
>        biopython-owner at lists.open-bio.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biopython digest..."
>
>
> Today's Topics:
>
>   1. biopython cookbook error (A M Torres, Hugo)
>   2. Re: biopython cookbook error (Brad Chapman)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 27 Jun 2011 04:00:37 -0300
> From: "A M Torres, Hugo" <mnemonico at posthocergopropterhoc.net>
> Subject: [Biopython] biopython cookbook error
> To: biopython at lists.open-bio.org
> Message-ID:
>        <BANLkTim__OXzYwa5FXnaj8b_h0vrnOQTBG3STfdpvAUM_+o=TQ at mail.gmail.com
> >
> Content-Type: text/plain; charset=UTF-8
>
> Hi, I am new to this list excuse me if this is not the appropriate place to
> report this:
>
> I am just trying to teach myself some biopython and at section "2.4.1
>  Simple
> FASTA parsing example" of the biopython tutorial it suggests us to run this
> code:
>
> from Bio import SeqIO
> > for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
> >     print seq_record.id
> >     print repr(seq_record.seq)
> >     print len(seq_record)
> >
> >
> Which outputs the error:
>
> Traceback (most recent call last):
> > File "simple_parser_2_4_1.py", line 4, in <module>
> > for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"): #this seems
> > wrong in the tutorial
> > File "/usr/lib/pymodules/python2.6/Bio/SeqIO/__init__.py", line 424, in
> > parse
> > raise TypeError("Need a file handle, not a string (i.e. not a filename)")
> > TypeError: Need a file handle, not a string (i.e. not a filename)
> >
>
> Python novices like me might have a problem understanding what a "file
> handle" is. I tryed this and it seems to work:
>
> from Bio import SeqIO
> >
> > with open("ls_orchid.fasta", 'rU') as data:
> >     for seq_record in SeqIO.parse(data, "fasta"):
> >         print seq_record.id
> >         print repr(seq_record.seq)
> >         print len(seq_record)
> >
>
> Maybe someone here can help me notify whoever maintains the tutorial.
>
> Thanks,
>
> Hugo Torres
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 27 Jun 2011 06:38:34 -0400
> From: Brad Chapman <chapmanb at 50mail.com>
> Subject: Re: [Biopython] biopython cookbook error
> To: biopython at lists.open-bio.org
> Message-ID: <20110627103834.GA22214 at sobchak>
> Content-Type: text/plain; charset=us-ascii
>
> Hugo;
> Thanks for the e-mail and reporting the problem you were running
> into.
>
> > Hi, I am new to this list excuse me if this is not the appropriate place
> to
> > report this:
> >
> > I am just trying to teach myself some biopython and at section "2.4.1
>  Simple
> > FASTA parsing example" of the biopython tutorial it suggests us to run
> this
> > code:
> [...]
> > Which outputs the error:
> [...]
> > > TypeError: Need a file handle, not a string (i.e. not a filename)
>
> It sounds like you have an old version of Biopython. SeqIO was
> changed a few releases ago to support string filenames instead of
> handles for the reason you mention: to make it easier for new Python
> developers. See FAQ #14 for more information, and #3 for information
> about checking your version of Biopython:
>
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc5
>
> If you have easy_install available, you can update with:
>
> sudo easy_install -U biopython
>
> Hope this helps,
> Brad
>
>
> Subject: Re: [Biopython] biopython cookbook error

Hi All,

This is my first post too... The current version of biopython and current
cookbook example does work fine. So, as Brad says, you may be using an old
version.

Pete Thorpe

> ------------------------------
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>
> End of Biopython Digest, Vol 102, Issue 16
> ******************************************
>


From ajingnk at gmail.com  Mon Jun 27 21:53:30 2011
From: ajingnk at gmail.com (Jing Lu)
Date: Mon, 27 Jun 2011 14:53:30 -0700
Subject: [Biopython]  How to pull out the coordinates for het groups?
Message-ID: <BANLkTin3FZk4jybQVFnMhoVLOq6w0OvXXA@mail.gmail.com>

Hi,

I want to pull out ligand from pdb file, then for each ligand(or het group)
save it as pdb, and keep the header. I have try the following code, but it
didn't return the result I want. Could you please give me some suggestion?

''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
for filename in os.listdir(workdir):
        print filename
        if '.bio' in filename:
            parser = PDBParser(PERMISSIVE=1)
            structure = parser.get_structure(filename[:4], filename)
            structure_copy = copy.deepcopy(structure) # for each ligand
renew the structure

            het_id_all = get_het_id(structure_copy) # only return the
ligands of structure

            for het_id in het_id_all:
                for model in structure_copy:
                    for chain in model:
                        for residue in chain:
                            id = residue.id
                            if id[0] is not het_id:
                                chain.detach_child(id)
                        if len(chain) == 0:
                            model.detach_child(chain.id)

                name = './ligand/' + filename[:9] + '_' + het_id[2:] + '_' +
str(id[1]).zfill(4) + chain.id + '.pdb'
                save_structure(structure_copy, name)
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''


From dilara.ally at gmail.com  Mon Jun 27 22:33:42 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Mon, 27 Jun 2011 15:33:42 -0700
Subject: [Biopython] using a function on a batch of files
Message-ID: <4E090546.7080002@gmail.com>

Hi All

I'm a newbie to python and I'm interested in using a function on a batch 
of files.

I know that in R, you can set the working directory to the directory of 
interest.  Is there a way to do this in Python?  This would allow me to 
access files that were in a different location than where the script 
file is.  The reason I would be interested to do this is that I have a 
function that I want to apply to 400 different files.  If I were 
scripting in R (which I am familiar with) I could use the fn list.files 
that would list the files in the directory.  Then I could read them in 
one by one with a loop.  Apply the function and then write the files to 
a different directory.

What is the best way to do this in python?

Thanks for the help.

Cheers, Dilara


From idoerg at gmail.com  Mon Jun 27 23:09:17 2011
From: idoerg at gmail.com (Iddo Friedberg)
Date: Mon, 27 Jun 2011 19:09:17 -0400
Subject: [Biopython] using a function on a batch of files
In-Reply-To: <4E090546.7080002@gmail.com>
References: <4E090546.7080002@gmail.com>
Message-ID: <BANLkTikvT38XyREuFahv3XLriBKjN9o3hw@mail.gmail.com>

Hi Dilara,

Read up on the glob module. http://docs.python.org/library/glob.html

That being said, this kind of question is probably better directed to one of
the Python community resources: http://python.org/community/

This list is primarily for Biopython inquiries.

Cheers,

Iddo

On Mon, Jun 27, 2011 at 6:33 PM, Dilara Ally <dilara.ally at gmail.com> wrote:

> Hi All
>
> I'm a newbie to python and I'm interested in using a function on a batch of
> files.
>
> I know that in R, you can set the working directory to the directory of
> interest.  Is there a way to do this in Python?  This would allow me to
> access files that were in a different location than where the script file
> is.  The reason I would be interested to do this is that I have a function
> that I want to apply to 400 different files.  If I were scripting in R
> (which I am familiar with) I could use the fn list.files that would list the
> files in the directory.  Then I could read them in one by one with a loop.
>  Apply the function and then write the files to a different directory.
>
> What is the best way to do this in python?
>
> Thanks for the help.
>
> Cheers, Dilara
> ______________________________**_________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/**mailman/listinfo/biopython<http://lists.open-bio.org/mailman/listinfo/biopython>
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html


From eric.talevich at gmail.com  Mon Jun 27 23:18:10 2011
From: eric.talevich at gmail.com (Eric Talevich)
Date: Mon, 27 Jun 2011 19:18:10 -0400
Subject: [Biopython] using a function on a batch of files
In-Reply-To: <4E090546.7080002@gmail.com>
References: <4E090546.7080002@gmail.com>
Message-ID: <BANLkTi=KPMyTCjrTt2mL79xerMmt_cP9dg@mail.gmail.com>

Hi Dilara,

If the glob module doesn't do what you want, then os.listdir might be it:
http://docs.python.org/library/os.html#os.listdir

Usage:
for fname in os.listdir("path/to/files/"):     print fname

Cheers,
Eric

On Mon, Jun 27, 2011 at 6:33 PM, Dilara Ally <dilara.ally at gmail.com> wrote:

> Hi All
>
> I'm a newbie to python and I'm interested in using a function on a batch of
> files.
>
> I know that in R, you can set the working directory to the directory of
> interest.  Is there a way to do this in Python?  This would allow me to
> access files that were in a different location than where the script file
> is.  The reason I would be interested to do this is that I have a function
> that I want to apply to 400 different files.  If I were scripting in R
> (which I am familiar with) I could use the fn list.files that would list the
> files in the directory.  Then I could read them in one by one with a loop.
>  Apply the function and then write the files to a different directory.
>
> What is the best way to do this in python?
>
> Thanks for the help.
>
> Cheers, Dilara
> ______________________________**_________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/**mailman/listinfo/biopython<http://lists.open-bio.org/mailman/listinfo/biopython>
>


From laserson at mit.edu  Tue Jun 28 04:26:50 2011
From: laserson at mit.edu (Uri Laserson)
Date: Tue, 28 Jun 2011 00:26:50 -0400
Subject: [Biopython] Serialize SeqRecord to JSON?
In-Reply-To: <BANLkTiktqaj=7V_y-ajvfA+etqpKi1_SOA@mail.gmail.com>
References: <BANLkTinGvFuT8NCmO8-VkvMjwEWd7qzC-g@mail.gmail.com>
	<BANLkTiktqaj=7V_y-ajvfA+etqpKi1_SOA@mail.gmail.com>
Message-ID: <BANLkTinf1JpK9XVALja48=eEUgR83bgaPw@mail.gmail.com>

I am interested in easily loading SeqRecords into MongoDB, including all
annotations/features.

I made a hack where I convert everything to python dict and list types, and
back.  If anyone is interested, they can find it on my github page:

http://goo.gl/b3bts

It's worked well for me thus far.

Uri

...................................................................................
Uri Laserson
Graduate Student, Biomedical Engineering
Harvard-MIT Division of Health Sciences and Technology
M +1 917 742 8019
laserson at mit.edu


From devaniranjan at gmail.com  Wed Jun 29 16:15:17 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Wed, 29 Jun 2011 12:15:17 -0400
Subject: [Biopython] identify triplet sequences
Message-ID: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>

Hi,

Not sure if this is a python or  bio-python question -but suggestions are
most welcome.

I have some FASTA sequences....like
AAAAWWWHHHHH
TTTYYYYYHGGGG
NNNNNGGGGFFFF

I extract from each sequence triplets moving from 1st residue and extracting
the 2nd, 3rd as one triplet then 2/3/4 as another triplet then 3/4/5 as
another triplet ...ect
So for the 1st sequence given above.....
AAA
AAA
AAW
AWW
.
.
.
so on.....

Now my question for 20amino acids there will be 8000 possible unique
combinations (20^3)

How can I classify them using python/biopython and write them out to 8000
unique text files .....is there a way to classify them without writing 8000
IF/ELSIF statements?
I want to see which sets of triplets has the hightest occourence.

Thank you.


From w.arindrarto at gmail.com  Wed Jun 29 17:18:49 2011
From: w.arindrarto at gmail.com (Wibowo Arindrarto)
Date: Wed, 29 Jun 2011 19:18:49 +0200
Subject: [Biopython] identify triplet sequences
In-Reply-To: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>
References: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>
Message-ID: <BANLkTi=ySvjYgOo4mWmcAAVDHN2qRpbYVg@mail.gmail.com>

Hi George,

This is my first post, so greetings to everyone else as well. For your
question, do you need to name all 8000 combinations? If not, then you can
use a dictionary to enumerate the occurence of each amino acid triplet. You
don't have to take into account all possibilities, just the one you find in
your sequences.

I've made a somewhat short & dirty script to do the analysis you want. It
also generates a fasta file containing random amino acid sequences of a
certain length as a source for a demo analysis. Here it is:

#!/usr/bin/env python

import random

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC

# function to generate random protein sequence
def random_prot(length):
    seq = ''
    for i in xrange(length):
        seq += random.choice(IUPAC.protein.letters)
    return seq

# function to generate list of SeqRecord objects
def seqrecord_gen(num, length):
    seqs = []
    for i in xrange(num):
        seqs.append(SeqRecord(Seq(random_prot(length)),
                    id='fasta'+str(i+1),
                    name='',
                    description=''))
    SeqIO.write(seqs, 'random_proteins.fa', 'fasta')

# function to read fasta file and count triplets
def count_triplet(source):
    triplets = {}
    seqs = SeqIO.parse(source, 'fasta')

    for rec in seqs:
        step = 0
        while step + 3 <= len(rec.seq.tostring()):
            tri = rec.seq.tostring()[0+step:3+step]
            if tri not in triplets:
                triplets[tri] = 1
            else:
                triplets[tri] += 1
            step += 1

    with open('results', 'w') as output:
        for key in sorted(triplets, key=triplets.get, reverse=True):
            output.writelines("{0}: {1}\n".format(key, triplets[key]))

# generate mock file
seqrecord_gen(100, 30)
# count the triplet
count_triplet('random_proteins.fa')


You can also see the script here: https://gist.github.com/1054348 (in case
there are formatting problems with the mail's display). Just remove the
seqrecord_gen() call and replace run count_triplet() with your fasta file
name as the argument. You can see the output in 'results'

Hope that helps!
Wibowo Arindrarto (Bow)


On Wed, Jun 29, 2011 at 18:15, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Hi,
>
> Not sure if this is a python or  bio-python question -but suggestions are
> most welcome.
>
> I have some FASTA sequences....like
> AAAAWWWHHHHH
> TTTYYYYYHGGGG
> NNNNNGGGGFFFF
>
> I extract from each sequence triplets moving from 1st residue and
> extracting
> the 2nd, 3rd as one triplet then 2/3/4 as another triplet then 3/4/5 as
> another triplet ...ect
> So for the 1st sequence given above.....
> AAA
> AAA
> AAW
> AWW
> .
> .
> .
> so on.....
>
> Now my question for 20amino acids there will be 8000 possible unique
> combinations (20^3)
>
> How can I classify them using python/biopython and write them out to 8000
> unique text files .....is there a way to classify them without writing 8000
> IF/ELSIF statements?
> I want to see which sets of triplets has the hightest occourence.
>
> Thank you.
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From devaniranjan at gmail.com  Wed Jun 29 17:54:56 2011
From: devaniranjan at gmail.com (George Devaniranjan)
Date: Wed, 29 Jun 2011 13:54:56 -0400
Subject: [Biopython] identify triplet sequences
In-Reply-To: <BANLkTi=ySvjYgOo4mWmcAAVDHN2qRpbYVg@mail.gmail.com>
References: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>
	<BANLkTi=ySvjYgOo4mWmcAAVDHN2qRpbYVg@mail.gmail.com>
Message-ID: <BANLkTinO9m-7hzi6nCxjDuv5BUSDpobhPw@mail.gmail.com>

Hi Wibowo,
Thank you for your answer,
If I want to classify only based on 1st and 3rd charecters of the triplets
while allowing the central charecter to be anything/vary can I do that?
so  any of the following should be under one list..instead of being counted
as unique.
ACA
ARA
AEA
AGA
...etc
You are right I don't need all 8000 combinations, just the one's that occur
in the list.
Thank you,
George

On Wed, Jun 29, 2011 at 1:18 PM, Wibowo Arindrarto
<w.arindrarto at gmail.com>wrote:

> Hi George,
>
> This is my first post, so greetings to everyone else as well. For your
> question, do you need to name all 8000 combinations? If not, then you can
> use a dictionary to enumerate the occurence of each amino acid triplet. You
> don't have to take into account all possibilities, just the one you find in
> your sequences.
>
> I've made a somewhat short & dirty script to do the analysis you want. It
> also generates a fasta file containing random amino acid sequences of a
> certain length as a source for a demo analysis. Here it is:
>
> #!/usr/bin/env python
>
> import random
>
> from Bio import SeqIO
> from Bio.Seq import Seq
> from Bio.SeqRecord import SeqRecord
> from Bio.Alphabet import IUPAC
>
> # function to generate random protein sequence
> def random_prot(length):
>     seq = ''
>     for i in xrange(length):
>         seq += random.choice(IUPAC.protein.letters)
>     return seq
>
> # function to generate list of SeqRecord objects
> def seqrecord_gen(num, length):
>     seqs = []
>     for i in xrange(num):
>         seqs.append(SeqRecord(Seq(random_prot(length)),
>                     id='fasta'+str(i+1),
>                     name='',
>                     description=''))
>     SeqIO.write(seqs, 'random_proteins.fa', 'fasta')
>
> # function to read fasta file and count triplets
> def count_triplet(source):
>     triplets = {}
>     seqs = SeqIO.parse(source, 'fasta')
>
>     for rec in seqs:
>         step = 0
>         while step + 3 <= len(rec.seq.tostring()):
>             tri = rec.seq.tostring()[0+step:3+step]
>             if tri not in triplets:
>                 triplets[tri] = 1
>             else:
>                 triplets[tri] += 1
>             step += 1
>
>     with open('results', 'w') as output:
>         for key in sorted(triplets, key=triplets.get, reverse=True):
>             output.writelines("{0}: {1}\n".format(key, triplets[key]))
>
> # generate mock file
> seqrecord_gen(100, 30)
> # count the triplet
> count_triplet('random_proteins.fa')
>
>
> You can also see the script here: https://gist.github.com/1054348 (in case
> there are formatting problems with the mail's display). Just remove the
> seqrecord_gen() call and replace run count_triplet() with your fasta file
> name as the argument. You can see the output in 'results'
>
> Hope that helps!
> Wibowo Arindrarto (Bow)
>
>
> On Wed, Jun 29, 2011 at 18:15, George Devaniranjan <devaniranjan at gmail.com
> > wrote:
>
>> Hi,
>>
>> Not sure if this is a python or  bio-python question -but suggestions are
>> most welcome.
>>
>> I have some FASTA sequences....like
>> AAAAWWWHHHHH
>> TTTYYYYYHGGGG
>> NNNNNGGGGFFFF
>>
>> I extract from each sequence triplets moving from 1st residue and
>> extracting
>> the 2nd, 3rd as one triplet then 2/3/4 as another triplet then 3/4/5 as
>> another triplet ...ect
>> So for the 1st sequence given above.....
>> AAA
>> AAA
>> AAW
>> AWW
>> .
>> .
>> .
>> so on.....
>>
>> Now my question for 20amino acids there will be 8000 possible unique
>> combinations (20^3)
>>
>> How can I classify them using python/biopython and write them out to 8000
>> unique text files .....is there a way to classify them without writing
>> 8000
>> IF/ELSIF statements?
>> I want to see which sets of triplets has the hightest occourence.
>>
>> Thank you.
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>


From w.arindrarto at gmail.com  Wed Jun 29 18:12:28 2011
From: w.arindrarto at gmail.com (Wibowo Arindrarto)
Date: Wed, 29 Jun 2011 20:12:28 +0200
Subject: [Biopython] identify triplet sequences
In-Reply-To: <BANLkTinO9m-7hzi6nCxjDuv5BUSDpobhPw@mail.gmail.com>
References: <BANLkTikz+Z-3Z-5Mm-xVd-BLzyuL-PmEbQ@mail.gmail.com>
	<BANLkTi=ySvjYgOo4mWmcAAVDHN2qRpbYVg@mail.gmail.com>
	<BANLkTinO9m-7hzi6nCxjDuv5BUSDpobhPw@mail.gmail.com>
Message-ID: <BANLkTi=aS+ADjdY6eWtCkPN5C=F80qB6mA@mail.gmail.com>

Hi George,

That can be done by modifying this line:

tri = rec.seq.tostring()[0+step:3+step]

into this:

tri = rec.seq.tostring()[0+step:3+step:2]

Alternatively, if you want a prettier output ('A*A' instead of 'AA' for all
triplets starting and ending with 'A') you can replace it with these
instead:

tri = rec.seq.tostring()[0+step]
tri += '*'
tri += rec.seq.tostring()[2+step]

Hope that helps!
Bow


On Wed, Jun 29, 2011 at 19:54, George Devaniranjan
<devaniranjan at gmail.com>wrote:

> Hi Wibowo,
> Thank you for your answer,
> If I want to classify only based on 1st and 3rd charecters of the triplets
> while allowing the central charecter to be anything/vary can I do that?
> so  any of the following should be under one list..instead of being counted
> as unique.
> ACA
> ARA
> AEA
> AGA
> ...etc
> You are right I don't need all 8000 combinations, just the one's that occur
> in the list.
> Thank you,
> George
>
>
> On Wed, Jun 29, 2011 at 1:18 PM, Wibowo Arindrarto <w.arindrarto at gmail.com
> > wrote:
>
>> Hi George,
>>
>> This is my first post, so greetings to everyone else as well. For your
>> question, do you need to name all 8000 combinations? If not, then you can
>> use a dictionary to enumerate the occurence of each amino acid triplet. You
>> don't have to take into account all possibilities, just the one you find in
>> your sequences.
>>
>> I've made a somewhat short & dirty script to do the analysis you want. It
>> also generates a fasta file containing random amino acid sequences of a
>> certain length as a source for a demo analysis. Here it is:
>>
>> #!/usr/bin/env python
>>
>> import random
>>
>> from Bio import SeqIO
>> from Bio.Seq import Seq
>> from Bio.SeqRecord import SeqRecord
>> from Bio.Alphabet import IUPAC
>>
>> # function to generate random protein sequence
>> def random_prot(length):
>>     seq = ''
>>     for i in xrange(length):
>>         seq += random.choice(IUPAC.protein.letters)
>>     return seq
>>
>> # function to generate list of SeqRecord objects
>> def seqrecord_gen(num, length):
>>     seqs = []
>>     for i in xrange(num):
>>         seqs.append(SeqRecord(Seq(random_prot(length)),
>>                     id='fasta'+str(i+1),
>>                     name='',
>>                     description=''))
>>     SeqIO.write(seqs, 'random_proteins.fa', 'fasta')
>>
>> # function to read fasta file and count triplets
>> def count_triplet(source):
>>     triplets = {}
>>     seqs = SeqIO.parse(source, 'fasta')
>>
>>     for rec in seqs:
>>         step = 0
>>         while step + 3 <= len(rec.seq.tostring()):
>>             tri = rec.seq.tostring()[0+step:3+step]
>>             if tri not in triplets:
>>                 triplets[tri] = 1
>>             else:
>>                 triplets[tri] += 1
>>             step += 1
>>
>>     with open('results', 'w') as output:
>>         for key in sorted(triplets, key=triplets.get, reverse=True):
>>             output.writelines("{0}: {1}\n".format(key, triplets[key]))
>>
>> # generate mock file
>> seqrecord_gen(100, 30)
>> # count the triplet
>> count_triplet('random_proteins.fa')
>>
>>
>> You can also see the script here: https://gist.github.com/1054348 (in
>> case there are formatting problems with the mail's display). Just remove the
>> seqrecord_gen() call and replace run count_triplet() with your fasta file
>> name as the argument. You can see the output in 'results'
>>
>> Hope that helps!
>> Wibowo Arindrarto (Bow)
>>
>>
>> On Wed, Jun 29, 2011 at 18:15, George Devaniranjan <
>> devaniranjan at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> Not sure if this is a python or  bio-python question -but suggestions are
>>> most welcome.
>>>
>>> I have some FASTA sequences....like
>>> AAAAWWWHHHHH
>>> TTTYYYYYHGGGG
>>> NNNNNGGGGFFFF
>>>
>>> I extract from each sequence triplets moving from 1st residue and
>>> extracting
>>> the 2nd, 3rd as one triplet then 2/3/4 as another triplet then 3/4/5 as
>>> another triplet ...ect
>>> So for the 1st sequence given above.....
>>> AAA
>>> AAA
>>> AAW
>>> AWW
>>> .
>>> .
>>> .
>>> so on.....
>>>
>>> Now my question for 20amino acids there will be 8000 possible unique
>>> combinations (20^3)
>>>
>>> How can I classify them using python/biopython and write them out to 8000
>>> unique text files .....is there a way to classify them without writing
>>> 8000
>>> IF/ELSIF statements?
>>> I want to see which sets of triplets has the hightest occourence.
>>>
>>> Thank you.
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>
>>
>>
>


From babbanmia at gmail.com  Wed Jun 29 18:54:38 2011
From: babbanmia at gmail.com (Babban Mia)
Date: Wed, 29 Jun 2011 14:54:38 -0400
Subject: [Biopython] DIHEDRAL ANGLES from PDB
Message-ID: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>

Hello Everyone


I am looking for a tool that can calculate dihedral angle with in a python
script between four atoms in PDB file.

I hope Biopython has something to offer.

Please advise.


Best


From babbanmia at gmail.com  Wed Jun 29 18:54:38 2011
From: babbanmia at gmail.com (Babban Mia)
Date: Wed, 29 Jun 2011 14:54:38 -0400
Subject: [Biopython] DIHEDRAL ANGLES from PDB
Message-ID: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>

Hello Everyone


I am looking for a tool that can calculate dihedral angle with in a python
script between four atoms in PDB file.

I hope Biopython has something to offer.

Please advise.


Best


From p.j.a.cock at googlemail.com  Wed Jun 29 21:10:02 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jun 2011 22:10:02 +0100
Subject: [Biopython] DIHEDRAL ANGLES from PDB
In-Reply-To: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>
References: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>
Message-ID: <BANLkTikpw94xJaU68FZBTwZMoX2u8=4c+w@mail.gmail.com>

On Wed, Jun 29, 2011 at 7:54 PM, Babban Mia <babbanmia at gmail.com> wrote:
> Hello Everyone
>
>
> I am looking for a tool that can calculate dihedral angle with in a python
> script between four atoms in PDB file.
>
> I hope Biopython has something to offer.
>
> Please advise.
>
> Best

Yes, try this:
http://www.warwick.ac.uk/go/peter_cock/python/ramachandran/

Peter


From p.j.a.cock at googlemail.com  Wed Jun 29 21:10:02 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jun 2011 22:10:02 +0100
Subject: [Biopython] DIHEDRAL ANGLES from PDB
In-Reply-To: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>
References: <BANLkTikwsJf4OT+D585urnENMWnP8d=X4w@mail.gmail.com>
Message-ID: <BANLkTikpw94xJaU68FZBTwZMoX2u8=4c+w@mail.gmail.com>

On Wed, Jun 29, 2011 at 7:54 PM, Babban Mia <babbanmia at gmail.com> wrote:
> Hello Everyone
>
>
> I am looking for a tool that can calculate dihedral angle with in a python
> script between four atoms in PDB file.
>
> I hope Biopython has something to offer.
>
> Please advise.
>
> Best

Yes, try this:
http://www.warwick.ac.uk/go/peter_cock/python/ramachandran/

Peter


From dilara.ally at gmail.com  Wed Jun 29 22:55:35 2011
From: dilara.ally at gmail.com (Dilara Ally)
Date: Wed, 29 Jun 2011 15:55:35 -0700
Subject: [Biopython] multiple sequence blast
Message-ID: <4E0BAD67.70305@gmail.com>

Hi All

I'm new to biopython and python.  I have 1000 files each with 100 
contigs and I'm interested in blasting each one of those contigs.  I can 
get a single file with multiple sequences to blast each file and then 
write the output.  But the problem comes with reading the file from a 
loop in the first place.  Thanks in advance for the help.  If I don't 
use the loop but instead assign fname=allfiles[1] then it will work.  
Does it have something to do with lists vs seq records??
Cheers, Dilara

Here is the code:

from Bio import SeqIO
from Bio.Blast import NCBIWWW
import time
import os

allfiles=os.listdir("/Users/dally/Desktop/NextGenData/Python_Scripts/pract_input/")
for fname in allfiles:
     print fname
     handle = open(fname, "rU") <==it doesn't recognize the file just 
the name?
     contigs =list(SeqIO.parse(handle,"fasta"))
     handle.close()
     i = 0
     start=time.time()
     for seq_record in contigs:
         print seq_record.id
         print seq_record.seq
         result_handle=NCBIWWW.qblast("blastn", "nr", 
seq_record.format("fasta"),hitlist_size=10)
         filename = "contig_%i.xml" % (i+1)
         print filename
         save_file = open(filename, "w")
         save_file.write(result_handle.read())
         save_file.close()
         result_handle.close()
         end=time.clock()
         elapsed=end-start
         min=elapsed/60 #CONVERT TO MINUTE
         print "Your stuff took", elapsed, "seconds to run, which is the 
same as ",min, "minutes"


From chapmanb at 50mail.com  Thu Jun 30 10:42:27 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Thu, 30 Jun 2011 06:42:27 -0400
Subject: [Biopython] multiple sequence blast
In-Reply-To: <4E0BAD67.70305@gmail.com>
References: <4E0BAD67.70305@gmail.com>
Message-ID: <20110630104227.GA2883@sobchak>

Dilara;
Thanks for the message. It would be helpful if you'd include the
error message traceback that you got stuck on; this will help
pinpoint the problem.

>From reading your code, my guess is that you are getting and IOError
about files not existing. When you do os.listdir, it only includes
the name of the files, not the full path to where they are located.

> allfiles=os.listdir("/Users/dally/Desktop/NextGenData/Python_Scripts/pract_input/")
> for fname in allfiles:
>     print fname
>     handle = open(fname, "rU") <==it doesn't recognize the file just the name?

You can fix this by using os.path.join with the directory name and
fname. For instance:

>>> dirname = "biopython"
>>> allfiles = os.listdir(dirname)
>>> print allfiles
['CONTRIB', 'Scripts', 'Doc', '.git', 'MANIFEST.in', 'Bio', 'BioSQL', 'README', 
'DEPRECATED', 'Tests', 'NEWS', 'setup.py', '.gitignore', 'do2to3.py', 'LICENSE']
>>> print [os.path.join(dirname, f) for f in allfiles]
['biopython/CONTRIB', 'biopython/Scripts', 'biopython/Doc', 'biopython/.git', 'biopython/MANIFEST.in', 
'biopython/Bio', 'biopython/BioSQL', 'biopython/README', 'biopython/DEPRECATED', 'biopython/Tests', 
'biopython/NEWS', 'biopython/setup.py', 'biopython/.gitignore', 'biopython/do2to3.py', 'biopython/LICENSE']

Hope this helps,
Brad