From darkarcanis at mail.ru  Sun Jan 12 09:04:59 2014
From: darkarcanis at mail.ru (Evgeniy Alekseev)
Date: Sun, 12 Jan 2014 18:04:59 +0400
Subject: [Biopython] Biopython packages in Archlinux
Message-ID: <1427507.T7rLfSDXj6@arcanis>

Hello everyone,

First, thank you for developing this useful module.

I'm one of Archlinux Trusted User [1]. Today I moved packages python-biopython 
and python2-biopython which provide biopython module in Archlinux from user 
repository (AUR) into official ([community]) [2] and will maintain it.

I want ask someone, who can do it, to edit wiki page [3] and add something 
like that:
-----------------wiki text------------------------
Archlinux
Biopython is avaible in an official repository. The package named python-
biopython (for python3) or python2-biopython (for python2) and they can be 
installed using pacman:
   pacman -S python-biopython
or
   pacman -S python2-biopython
-----------------wiki text------------------------

Thank you!

Also if you have an additional request feel free to contact me and ask it.

Links:
[1] https://wiki.archlinux.org/index.php/Trusted%20Users
[2] https://www.archlinux.org/packages/biopython
[3] http://biopython.org/wiki/Download
-- 
? ?????????, ?.????????.
Sincerely yours, E.Alekseev.

e-mail: darkarcanis at mail.ru
ICQ: 407-398-235
Jabber: arcanis at jabber.ru
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From eric.talevich at gmail.com  Sun Jan 12 21:43:54 2014
From: eric.talevich at gmail.com (Eric Talevich)
Date: Sun, 12 Jan 2014 18:43:54 -0800
Subject: [Biopython] Biopython packages in Archlinux
In-Reply-To: <1427507.T7rLfSDXj6@arcanis>
References: <1427507.T7rLfSDXj6@arcanis>
Message-ID: <CAMC681=KFeKr1JaFXfvTniEJiFZZnJnouiu3WvD9jBatRxkWaw@mail.gmail.com>

On Sun, Jan 12, 2014 at 6:04 AM, Evgeniy Alekseev <darkarcanis at mail.ru>wrote:

> Hello everyone,
>
> First, thank you for developing this useful module.
>
> I'm one of Archlinux Trusted User [1]. Today I moved packages
> python-biopython
> and python2-biopython which provide biopython module in Archlinux from user
> repository (AUR) into official ([community]) [2] and will maintain it.
>
> I want ask someone, who can do it, to edit wiki page [3] and add something
> like that:
> -----------------wiki text------------------------
> Archlinux
> Biopython is avaible in an official repository. The package named python-
> biopython (for python3) or python2-biopython (for python2) and they can be
> installed using pacman:
>    pacman -S python-biopython
> or
>    pacman -S python2-biopython
> -----------------wiki text------------------------
>
> Thank you!
>
> Also if you have an additional request feel free to contact me and ask it.
>
> Links:
> [1] https://wiki.archlinux.org/index.php/Trusted%20Users
> [2] https://www.archlinux.org/packages/biopython
> [3] http://biopython.org/wiki/Download
> --
> ? ?????????, ?.????????.
> Sincerely yours, E.Alekseev.
>

Thanks for creating these packages, Evgeniy. I've added an edited version
of your notes to the wiki here:
http://biopython.org/wiki/Download#Archlinux

Cheers,
Eric


From mike.thon at gmail.com  Mon Jan 13 10:09:41 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Mon, 13 Jan 2014 16:09:41 +0100
Subject: [Biopython] iterating over FeatureLocation
Message-ID: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>

I need to iterate over all the features of a sequence, and then iterate over the locations/sublocations in each feature.  I?m not sure how to work with the sublocations though:

I need to do something like this:

for feat in seq.features:
	for loc in feat.locations:
		start = loc.start
		?

which does not work but maybe shows what I need to do.  Can anyone help me out?

From p.j.a.cock at googlemail.com  Mon Jan 13 10:38:54 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 13 Jan 2014 15:38:54 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
Message-ID: <CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>

On Mon, Jan 13, 2014 at 3:09 PM, Michael Thon <mike.thon at gmail.com> wrote:
> I need to iterate over all the features of a sequence, and then
> iterate over the locations/sublocations in each feature.  I?m not
> sure how to work with the sublocations though:
>
> I need to do something like this:
>
> for feat in seq.features:
>         for loc in feat.locations:
>                 start = loc.start
>                 ?
>
> which does not work but maybe shows what I need to do.
> Can anyone help me out?

Are you talking about join locations? Could you give an example
(e.g. link to a GenBank file) and what you want to look at?

Peter

P.S. This changed a bit back in Biopython 1.62 with the introduction
of the CompoundLocation object.


From mike.thon at gmail.com  Mon Jan 13 11:07:45 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Mon, 13 Jan 2014 17:07:45 +0100
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
Message-ID: <D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>

Here are two examples from the GenBank format file (not from GenBank though)


     CDS             order(6621..6658,6739..6985)
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_14847-RA:cds"
                     /label=?CDS"

     CDS             419..2374
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_05899-RA:cds"
                     /label=?CDS"

if the feature is a simple feature, then I just need to access its start and end.  If its a compound feature then I need to iterate over each segment, accessing the start and end.

What I am doing at the moment is this:

if feat._sub_features:
	for sf in feat.sub_features:
		start = sf.location.start
		?
else:
	start = feat.location.start
	?

it works, I think.  Is there a better way?

Also, is there an easy way to get the sequence represented by the seqfeature, if it is made up of CompoundLocations?  These features are CDSs where each sub-feature is an exon.  I need to splice them all together and get the translation.

Thanks

On Jan 13, 2014, at 4:38 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Jan 13, 2014 at 3:09 PM, Michael Thon <mike.thon at gmail.com> wrote:
>> I need to iterate over all the features of a sequence, and then
>> iterate over the locations/sublocations in each feature.  I?m not
>> sure how to work with the sublocations though:
>> 
>> I need to do something like this:
>> 
>> for feat in seq.features:
>>        for loc in feat.locations:
>>                start = loc.start
>>                ?
>> 
>> which does not work but maybe shows what I need to do.
>> Can anyone help me out?
> 
> Are you talking about join locations? Could you give an example
> (e.g. link to a GenBank file) and what you want to look at?
> 
> Peter
> 
> P.S. This changed a bit back in Biopython 1.62 with the introduction
> of the CompoundLocation object.



From p.j.a.cock at googlemail.com  Mon Jan 13 11:18:01 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 13 Jan 2014 16:18:01 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
Message-ID: <CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>

On Mon, Jan 13, 2014 at 4:07 PM, Michael Thon <mike.thon at gmail.com> wrote:
> Here are two examples from the GenBank format file (not from GenBank though)
>
>
>      CDS             order(6621..6658,6739..6985)
>                      /Source="maker"
>                      /codon_start=1
>                      /ID="CFIO01_14847-RA:cds"
>                      /label=?CDS"
>
>      CDS             419..2374
>                      /Source="maker"
>                      /codon_start=1
>                      /ID="CFIO01_05899-RA:cds"
>                      /label=?CDS"
>
> if the feature is a simple feature, then I just need to access its start and end.
> If its a compound feature then I need to iterate over each segment, accessing the start and end.
>
> What I am doing at the moment is this:
>
> if feat._sub_features:
>         for sf in feat.sub_features:
>                 start = sf.location.start
>                 ?
> else:
>         start = feat.location.start
>         ?
>
> it works, I think.  Is there a better way?

Don't do that :) Python variables/methods/etc starting with a single
underscore are by convention private and should not generally be
used. In this case, ._sub_features is an internal detail for the behind
the scenes backwards compatibility for the now deprecated property
.sub_features (don't use that either).

Instead use the location object itself directly, it now holds any
sub-location information using a CompoundLocation object.
See the .parts attribute, which gives a list of simple locations.

e.g.

for part in feat.location.parts:
    start = part.start
    ...

>
> Also, is there an easy way to get the sequence represented by the seqfeature,
> if it is made up of CompoundLocations?  These features are CDSs where each
> sub-feature is an exon.  I need to splice them all together and get the translation.
>

Yes, where `feat` is a SubFeature object use `feat.extract(the_parent_sequence)`
to get the spliced sequence, which you can then translate. See the section
"Sequence described by a feature or location" in the Tutorial,

http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

On reflection, the Tutorial could do with a bit more detail on how to use
a CompoundLocation, but I did try to cover this in the docstrings.

Regards,

Peter


From jere_2001 at ig.com.br  Mon Jan 13 22:04:42 2014
From: jere_2001 at ig.com.br (Jeremias Ponciano da Silva)
Date: Tue, 14 Jan 2014 01:04:42 -0200
Subject: [Biopython] Monte Carlo Simulation
Message-ID: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>

Hi people!
I'm doing a Monte Carlo Simulation, must take a DNA sequence and this
sequence can randomize N times, and with these seguencias plot on a Normal
chart monte carlo simulation, one would have any suggestions?

-- 
*Jeremias Ponciano*

From mike.thon at gmail.com  Tue Jan 14 05:20:00 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Tue, 14 Jan 2014 11:20:00 +0100
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
Message-ID: <AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>

Hi Peter - Thanks for your help.  Here is another problem.  Here is the block of features in my GenBank file for a gene:

     gene            complement(1..588)
                     /Source="maker"
                     /ID="CFIO01_14176"
                     /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
                     -gene-0.30"
                     /label="CFIO01_14176"
     CDS             order(complement(200..588),complement(1..124))
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_14176-RA:cds"
                     /label="CDS"
     mRNA            complement(1..588)
                     /Source="maker"
                     /ID="CFIO01_14176-RA"
                     /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
                     -gene-0.30-mRNA-1"
                     /_AED="0.06"
                     /_QI="0|0|0|1|1|1|2|0|171"
                     /_eAED="0.06"
                     /label="CFIO01_14176-RA"
 
Now, here is the CDS feature after is was parsed by BioPython:

                    
(Pdb) feat.location.parts
[FeatureLocation(ExactPosition(0), ExactPosition(124), strand=-1), FeatureLocation(ExactPosition(199), ExactPosition(588), strand=-1)]

Note that two positions have changed.  The CDS segments are (complement(200..588),complement(1..124)) but the positions in SeqFeature object are 0..124 and 199..588

I checked some other features too and it looks like BioPython adds 1 to the start of each segment.  For the features on the complementary strand it subtracts 1.  

When I translate the feature into a protein sequence like this: str(feat.extract(seq).seq.translate()) , the sequence is correct so this must not be a bug. so, how to I access the exact values that are in the genbank formatted file?  

On Jan 13, 2014, at 5:18 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Jan 13, 2014 at 4:07 PM, Michael Thon <mike.thon at gmail.com> wrote:
>> Here are two examples from the GenBank format file (not from GenBank though)
>> 
>> 
>>     CDS             order(6621..6658,6739..6985)
>>                     /Source="maker"
>>                     /codon_start=1
>>                     /ID="CFIO01_14847-RA:cds"
>>                     /label=?CDS"
>> 
>>     CDS             419..2374
>>                     /Source="maker"
>>                     /codon_start=1
>>                     /ID="CFIO01_05899-RA:cds"
>>                     /label=?CDS"
>> 
>> if the feature is a simple feature, then I just need to access its start and end.
>> If its a compound feature then I need to iterate over each segment, accessing the start and end.
>> 
>> What I am doing at the moment is this:
>> 
>> if feat._sub_features:
>>        for sf in feat.sub_features:
>>                start = sf.location.start
>>                ?
>> else:
>>        start = feat.location.start
>>        ?
>> 
>> it works, I think.  Is there a better way?
> 
> Don't do that :) Python variables/methods/etc starting with a single
> underscore are by convention private and should not generally be
> used. In this case, ._sub_features is an internal detail for the behind
> the scenes backwards compatibility for the now deprecated property
> .sub_features (don't use that either).
> 
> Instead use the location object itself directly, it now holds any
> sub-location information using a CompoundLocation object.
> See the .parts attribute, which gives a list of simple locations.
> 
> e.g.
> 
> for part in feat.location.parts:
>    start = part.start
>    ...
> 
>> 
>> Also, is there an easy way to get the sequence represented by the seqfeature,
>> if it is made up of CompoundLocations?  These features are CDSs where each
>> sub-feature is an exon.  I need to splice them all together and get the translation.
>> 
> 
> Yes, where `feat` is a SubFeature object use `feat.extract(the_parent_sequence)`
> to get the spliced sequence, which you can then translate. See the section
> "Sequence described by a feature or location" in the Tutorial,
> 
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
> 
> On reflection, the Tutorial could do with a bit more detail on how to use
> a CompoundLocation, but I did try to cover this in the docstrings.
> 
> Regards,
> 
> Peter



From mike.thon at gmail.com  Tue Jan 14 05:25:56 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Tue, 14 Jan 2014 11:25:56 +0100
Subject: [Biopython] Monte Carlo Simulation
In-Reply-To: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>
References: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>
Message-ID: <F31ABAEC-5C0B-49CD-8DE8-E8D1A3C06CB0@gmail.com>

Check out:
http://stackoverflow.com/questions/976882/shuffling-a-list-of-objects-in-python

Something like this should work:

from random import shuffle

x = ?GCAT?
s = list(x)
shuffle(s)


On Jan 14, 2014, at 4:04 AM, Jeremias Ponciano da Silva <jere_2001 at ig.com.br> wrote:

> Hi people!
> I'm doing a Monte Carlo Simulation, must take a DNA sequence and this
> sequence can randomize N times, and with these seguencias plot on a Normal
> chart monte carlo simulation, one would have any suggestions?
> 
> -- 
> *Jeremias Ponciano*
> _______________________________________________
> 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  Tue Jan 14 06:18:12 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 14 Jan 2014 11:18:12 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
	<AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
Message-ID: <CAKVJ-_7m4JQtnQj=jMa=Yyy4RQHW2SmrQkxbMyzOucWwT-3vHw@mail.gmail.com>

On Tue, Jan 14, 2014 at 10:20 AM, Michael Thon <mike.thon at gmail.com> wrote:
> Hi Peter - Thanks for your help.  Here is another problem.  Here is the
> block of features in my GenBank file for a gene:
>
>      gene            complement(1..588)
>                      /Source="maker"
>                      /ID="CFIO01_14176"
>
> /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
>                      -gene-0.30"
>                      /label="CFIO01_14176"
>      CDS             order(complement(200..588),complement(1..124))
>                      /Source="maker"
>                      /codon_start=1
>                      /ID="CFIO01_14176-RA:cds"
>                      /label="CDS"
>      mRNA            complement(1..588)
>                      /Source="maker"
>                      /ID="CFIO01_14176-RA"
>
> /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
>                      -gene-0.30-mRNA-1"
>                      /_AED="0.06"
>                      /_QI="0|0|0|1|1|1|2|0|171"
>                      /_eAED="0.06"
>                      /label="CFIO01_14176-RA"
>
> Now, here is the CDS feature after is was parsed by BioPython:
>
>
> (Pdb) feat.location.parts
> [FeatureLocation(ExactPosition(0), ExactPosition(124), strand=-1),
> FeatureLocation(ExactPosition(199), ExactPosition(588), strand=-1)]
>
> Note that two positions have changed.  The CDS segments are
> (complement(200..588),complement(1..124)) but the positions in SeqFeature
> object are 0..124 and 199..588
>
> I checked some other features too and it looks like BioPython adds 1 to the
> start of each segment.  For the features on the complementary strand it
> subtracts 1.

Not quite, no.

The Biopython SeqFeature location system uses Python counting as
in string slicing etc. This means that effectively all the start coordinates
you see are one less than the start coordinates in GenBank/EMBL
format files.

> When I translate the feature into a protein sequence like this:
> str(feat.extract(seq).seq.translate()) , the sequence is correct so this
> must not be a bug. so, how to I access the exact values that are in the
> genbank formatted file?

You must convert back from Python counting to GenBank/EMBL counting,

location.start + 1
location.end

However, for many things the Python counting is more natural once
you are used to it ;)

Peter

From jere_2001 at ig.com.br  Tue Jan 14 13:57:16 2014
From: jere_2001 at ig.com.br (Jeremias Ponciano da Silva)
Date: Tue, 14 Jan 2014 16:57:16 -0200
Subject: [Biopython] Monte Carlo Simulation
In-Reply-To: <F31ABAEC-5C0B-49CD-8DE8-E8D1A3C06CB0@gmail.com>
References: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>
	<F31ABAEC-5C0B-49CD-8DE8-E8D1A3C06CB0@gmail.com>
Message-ID: <CADtZUJ7aMiDWcx1jOQ6zRbJNtgbhT+p+whOfs8JX6yB4bgs1=w@mail.gmail.com>

Hi guys!
Thanks for the replies.
I can do randomization, even my biggest problem is how to make a plot of
Monte Carlo with the data I already have.


2014/1/14 Michael Thon <mike.thon at gmail.com>

> Check out:
>
> http://stackoverflow.com/questions/976882/shuffling-a-list-of-objects-in-python
>
> Something like this should work:
>
> from random import shuffle
>
> x = ?GCAT?
> s = list(x)
> shuffle(s)
>
>
> On Jan 14, 2014, at 4:04 AM, Jeremias Ponciano da Silva <
> jere_2001 at ig.com.br> wrote:
>
> > Hi people!
> > I'm doing a Monte Carlo Simulation, must take a DNA sequence and this
> > sequence can randomize N times, and with these seguencias plot on a
> Normal
> > chart monte carlo simulation, one would have any suggestions?
> >
> > --
> > *Jeremias Ponciano*
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
>
>


-- 
*Jeremias Ponciano*


From jere_2001 at ig.com.br  Tue Jan 14 14:41:24 2014
From: jere_2001 at ig.com.br (Jeremias Ponciano da Silva)
Date: Tue, 14 Jan 2014 17:41:24 -0200
Subject: [Biopython] Monte Carlo Simulation
In-Reply-To: <CADWfS5pux5+Qe7CmeKw5kdVYj==cz+HBaeS_N+xT0-UBFPHptg@mail.gmail.com>
References: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>
	<F31ABAEC-5C0B-49CD-8DE8-E8D1A3C06CB0@gmail.com>
	<CADtZUJ7aMiDWcx1jOQ6zRbJNtgbhT+p+whOfs8JX6yB4bgs1=w@mail.gmail.com>
	<CADWfS5pux5+Qe7CmeKw5kdVYj==cz+HBaeS_N+xT0-UBFPHptg@mail.gmail.com>
Message-ID: <CADtZUJ5631fGFx2k_6dk9NSmEjyg-tU-r7V7U61JRw6kyWZRHQ@mail.gmail.com>

Thanks Jared for the reply.
Seek a similarity of DNA, for example with the blast, getting this similar
sequence, eg 70%, I got to take this sequence, and do a test to see if it
is significant or not, making the randomization of this sample obtained, I
thought to do with Monte Carlo test to see if this within the normal 95% or
beyond 5%, which is what I seek.


2014/1/14 Jared Adolf-Bryfogle <jadolfbr at gmail.com>

> I think the distribution of your simulation will always be random - No
> monte carlo.  I'm not sure the problem your trying to solve.  If you want a
> monte carlo - based design algorithm on a structure, then you can try
> Rosetta:  https://www.rosettacommons.org/ (but I'm not sure if it does
> DNA design).
>
> Do you mean the combinations of sequences you get out?  Basically in
> either of these cases, the more times you choose a sequence, the more you
> sample the sequence space - however - your distribution will always be
> random, in that some sequences are not preferred.  Monte carlo is useful
> when you have a very large space to sample from, some constraints (such as
> a design algorithm and a dna structure), and you want to sample the range
> of possibilities.  In your case, you have no constraints, so,
> unfortunately, the result has no meaning...
>
> I would go back and see if Monte Carlo is what you really want?
>
>
> Jared Adolf-Bryfogle
> PhD Candidate
> Lab of Dr. Roland Dunbrack
> FCCC/DrexelMed
>
>
>
>
> On Tue, Jan 14, 2014 at 1:57 PM, Jeremias Ponciano da Silva <
> jere_2001 at ig.com.br> wrote:
>
>> Hi guys!
>> Thanks for the replies.
>> I can do randomization, even my biggest problem is how to make a plot of
>> Monte Carlo with the data I already have.
>>
>>
>> 2014/1/14 Michael Thon <mike.thon at gmail.com>
>>
>> > Check out:
>> >
>> >
>> http://stackoverflow.com/questions/976882/shuffling-a-list-of-objects-in-python
>> >
>> > Something like this should work:
>> >
>> > from random import shuffle
>> >
>> > x = ?GCAT?
>> > s = list(x)
>> > shuffle(s)
>> >
>> >
>> > On Jan 14, 2014, at 4:04 AM, Jeremias Ponciano da Silva <
>> > jere_2001 at ig.com.br> wrote:
>> >
>> > > Hi people!
>> > > I'm doing a Monte Carlo Simulation, must take a DNA sequence and this
>> > > sequence can randomize N times, and with these seguencias plot on a
>> > Normal
>> > > chart monte carlo simulation, one would have any suggestions?
>> > >
>> > > --
>> > > *Jeremias Ponciano*
>> > > _______________________________________________
>> > > Biopython mailing list  -  Biopython at lists.open-bio.org
>> > > http://lists.open-bio.org/mailman/listinfo/biopython
>> >
>> >
>>
>>
>> --
>> *Jeremias Ponciano*
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>


-- 
*Jeremias Ponciano*


From debruinjj at gmail.com  Thu Jan 16 06:48:47 2014
From: debruinjj at gmail.com (Jurgens de Bruin)
Date: Thu, 16 Jan 2014 13:48:47 +0200
Subject: [Biopython] Bio.PDB.PDBParser() Superimposer()
Message-ID: <CAMrqo6zww=ftqVOUCbYn=A3JUtnYWC3aciiCd2eJVfOccYXR-A@mail.gmail.com>

Hi,

I am trying to calculate the RMS for two pdb files but the proteins differ
in length. Currently I want to exclude the leading/trailing parts of the
longer sequence but I am having difficulty figuring out how I will be able
to do this.

Any help would be appreciated.


-- 
Regards/Groete/Mit freundlichen Gr??en/recuerdos/meilleures salutations/
distinti saluti/siong/du? y?/??????

Jurgens de Bruin


From anaryin at gmail.com  Thu Jan 16 06:59:43 2014
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Thu, 16 Jan 2014 12:59:43 +0100
Subject: [Biopython] Bio.PDB.PDBParser() Superimposer()
In-Reply-To: <CAMrqo6zww=ftqVOUCbYn=A3JUtnYWC3aciiCd2eJVfOccYXR-A@mail.gmail.com>
References: <CAMrqo6zww=ftqVOUCbYn=A3JUtnYWC3aciiCd2eJVfOccYXR-A@mail.gmail.com>
Message-ID: <CAJ9sUYN01JGb+TxKPVRt8PGaXXjgD33_TRLxycAWwxNfkVws7A@mail.gmail.com>

Hi Jurgens,

When you pass the two sequences to the Superimposer I guess you can trim
the sequence to that which you want (pass a list of residues that is sliced
to those that you want to include). The only requirement would be that both
have the same number of atoms.

If this doesn't make much sense I can give an example with code.

Cheers,

Jo?o


2014/1/16 Jurgens de Bruin <debruinjj at gmail.com>

> Hi,
>
> I am trying to calculate the RMS for two pdb files but the proteins differ
> in length. Currently I want to exclude the leading/trailing parts of the
> longer sequence but I am having difficulty figuring out how I will be able
> to do this.
>
> Any help would be appreciated.
>
>
> --
> Regards/Groete/Mit freundlichen Gr??en/recuerdos/meilleures salutations/
> distinti saluti/siong/du? y?/??????
>
> Jurgens de Bruin
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From debruinjj at gmail.com  Thu Jan 16 07:18:28 2014
From: debruinjj at gmail.com (Jurgens de Bruin)
Date: Thu, 16 Jan 2014 14:18:28 +0200
Subject: [Biopython] Bio.PDB.PDBParser() Superimposer()
In-Reply-To: <CAJ9sUYN01JGb+TxKPVRt8PGaXXjgD33_TRLxycAWwxNfkVws7A@mail.gmail.com>
References: <CAMrqo6zww=ftqVOUCbYn=A3JUtnYWC3aciiCd2eJVfOccYXR-A@mail.gmail.com>
	<CAJ9sUYN01JGb+TxKPVRt8PGaXXjgD33_TRLxycAWwxNfkVws7A@mail.gmail.com>
Message-ID: <CAMrqo6zSgOZFWJ3ZSBtEOTTGRbch6dShw4gtUpYBD7ZpxjEVvA@mail.gmail.com>

Hi Jo?o Rodrigues,

Thanks for the reply much appreciated, this does make sense but I would
greatly appreciate examples with some code.

Thanks


On 16 January 2014 13:59, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hi Jurgens,
>
> When you pass the two sequences to the Superimposer I guess you can trim
> the sequence to that which you want (pass a list of residues that is sliced
> to those that you want to include). The only requirement would be that both
> have the same number of atoms.
>
> If this doesn't make much sense I can give an example with code.
>
> Cheers,
>
> Jo?o
>
>
> 2014/1/16 Jurgens de Bruin <debruinjj at gmail.com>
>
>> Hi,
>>
>> I am trying to calculate the RMS for two pdb files but the proteins differ
>> in length. Currently I want to exclude the leading/trailing parts of the
>> longer sequence but I am having difficulty figuring out how I will be able
>> to do this.
>>
>> Any help would be appreciated.
>>
>>
>> --
>> Regards/Groete/Mit freundlichen Gr??en/recuerdos/meilleures salutations/
>> distinti saluti/siong/du? y?/??????
>>
>> Jurgens de Bruin
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>


-- 
Regards/Groete/Mit freundlichen Gr??en/recuerdos/meilleures salutations/
distinti saluti/siong/du? y?/??????

Jurgens de Bruin


From ishengomae at nm-aist.ac.tz  Fri Jan 17 02:11:41 2014
From: ishengomae at nm-aist.ac.tz (Edson Ishengoma)
Date: Fri, 17 Jan 2014 10:11:41 +0300
Subject: [Biopython] How to run PAL2NAL commandline via python
Message-ID: <CAKoVMyn1iLRQMffc5xvPb9HSs8e+YD180Yc20ApP9MjGhjmTFQ@mail.gmail.com>

Dear all,

I recently was introduced to pal2nal as a convenient tool to convert
aligned protein residues (from tblastn, for example) back to their original
nucleotide sequences. My boss suggested I use a python or perl script to
call the tool and feed the resulting nucleotide alignments to the 'codeml'
program to calculate Ka, Ks.

I don't know perl, so I would like to know how to do this from python -- a
python script which includes the way to feed the resulting codon alignments
to  PAML for "codeml" program to calculate Ka, Ks values.

I tried to check for the pre-existence of  Biopython wrapper for Pal2Nal I
didnt see one. I am on linux machine (Ubuntu 13.04) and my installed python
is Python 2.7.4.
I tried this script which I expected to produce a file containing aligned
nucleotide sequences. But no error message is shown but it outputs an empty
file (nothing written on the file).

import os
> my_pal2nal = os.path.join(os.getcwd(), 'pal2nal.v14')
> my_prot_file = os.path.join(os.getcwd(), 'pal2nal.v14', 'dnds.aln')
> my_nucl_file = os.path.join(os.getcwd(), 'pal2nal.v14', 'dnds.nuc')
> output_file = '/home/edson/pal2nal.v14/output'
> os.system(my_pal2nal + 'perl pal2nal.pl' + my_prot_file + my_nucl_file +
> ' -output paml' + '>' + output_file + ' -nogap')
>

What perfect way should I proceed and how do I include a script for
'codeml'?

Thanks.

Regards,

Edson.



Edson B. Ishengoma
PhD-Candidate
*School of Life Sciences and Engineering
Nelson Mandela African Institute of Science and Technology
Nelson Mandela Road
P. O. Box 447, Arusha
Tanzania (255)
*
*ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
*

<http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
  Website: www.nm-aist.ac.tz
Skype: edson.ishengoma

*
*
**

From zruan1991 at gmail.com  Fri Jan 17 10:18:22 2014
From: zruan1991 at gmail.com (Zheng Ruan)
Date: Fri, 17 Jan 2014 10:18:22 -0500
Subject: [Biopython] How to run PAL2NAL commandline via python
In-Reply-To: <CAKoVMyn1iLRQMffc5xvPb9HSs8e+YD180Yc20ApP9MjGhjmTFQ@mail.gmail.com>
References: <CAKoVMyn1iLRQMffc5xvPb9HSs8e+YD180Yc20ApP9MjGhjmTFQ@mail.gmail.com>
Message-ID: <CABM7aFpD4tWc0bvfJqLR3rtjjDdKn1A39QHkBrt+kzu1hS8Jxg@mail.gmail.com>

Hey Edson,

There are a couple of issues in your code. You need to make sure the
command called by os.system() is able to run in the shell (my_pal2nal
should not be called; you also missed a space between my_prot_file and
my_nucl_file; the '-nogap' option should be placed before redirecting).

Biopython do have a codeml wrapper. see
http://biopython.org/wiki/PAML#codeml. To run codeml, you also need a tree
file specified. You'd better make sure that you can successfully run codeml
in the command line before including it in your script.

Hope it helps,

Best,
Zheng Ruan


On Fri, Jan 17, 2014 at 2:11 AM, Edson Ishengoma
<ishengomae at nm-aist.ac.tz>wrote:

> Dear all,
>
> I recently was introduced to pal2nal as a convenient tool to convert
> aligned protein residues (from tblastn, for example) back to their original
> nucleotide sequences. My boss suggested I use a python or perl script to
> call the tool and feed the resulting nucleotide alignments to the 'codeml'
> program to calculate Ka, Ks.
>
> I don't know perl, so I would like to know how to do this from python -- a
> python script which includes the way to feed the resulting codon alignments
> to  PAML for "codeml" program to calculate Ka, Ks values.
>
> I tried to check for the pre-existence of  Biopython wrapper for Pal2Nal I
> didnt see one. I am on linux machine (Ubuntu 13.04) and my installed python
> is Python 2.7.4.
> I tried this script which I expected to produce a file containing aligned
> nucleotide sequences. But no error message is shown but it outputs an empty
> file (nothing written on the file).
>
> import os
> > my_pal2nal = os.path.join(os.getcwd(), 'pal2nal.v14')
> > my_prot_file = os.path.join(os.getcwd(), 'pal2nal.v14', 'dnds.aln')
> > my_nucl_file = os.path.join(os.getcwd(), 'pal2nal.v14', 'dnds.nuc')
> > output_file = '/home/edson/pal2nal.v14/output'
> > os.system(my_pal2nal + 'perl pal2nal.pl' + my_prot_file + my_nucl_file +
> > ' -output paml' + '>' + output_file + ' -nogap')
> >
>
> What perfect way should I proceed and how do I include a script for
> 'codeml'?
>
> Thanks.
>
> Regards,
>
> Edson.
>
>
>
> Edson B. Ishengoma
> PhD-Candidate
> *School of Life Sciences and Engineering
> Nelson Mandela African Institute of Science and Technology
> Nelson Mandela Road
> P. O. Box 447, Arusha
> Tanzania (255)
> *
> *ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
> *
>
> <http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
>   Website: www.nm-aist.ac.tz
> Skype: edson.ishengoma
>
> *
> *
> **
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>

From philipp.schiffer at gmail.com  Sun Jan 19 04:36:53 2014
From: philipp.schiffer at gmail.com (Philipp Schiffer)
Date: Sun, 19 Jan 2014 10:36:53 +0100
Subject: [Biopython] GFF parsing: getting features of specific proteins in
	gff
Message-ID: <6AA379FAFB7845079A6E0D300FC1C237@gmail.com>

Hi all and Brad Chapman in particular,

I just started exploring the GFF parser for some Augustus derived gff3 files, but running into trouble when trying to collect information for a specific protein. Ultimately my goal is to get introns and exons for a specific set of genes. Following the wiki I can replicate everything with my data and have adjusted the following piece to my data:

from BCBio import GFF    
in_file = "your_file.gff"    
limit_info = dict( gff_id = ["chr1"],
 gff_source = ["Coding_transcript"])    
in_handle = open(in_file)  
for rec in GFF.parse(in_handle, limit_info=limit_info):  
print rec.features[0] in_handle.close()

For testing on a subset I changed "chr1" to one of my contig IDs and that works. Then I limited to gff_type = ["intron"] and that also works for my data.

However now I'd like not to print all rec.features, but only for a specific gene. Picked the first one "g1.t1", which is on the contig and is displayed as an id in the printout of all features. It is also contained in the "list" that rec.features appears to be, but apparently you can't do something like `if x in list:` with the rec.features, at least I get an error when trying. I looked through the Biopython tutorial to see if there is an attribute to rec.features that I could query for the id, but somehow that didn?t make me any wiser.
I guess this is just me being thick and newbie, but could anybody point me in the right direction maybe?

Thanks

Philipp

From ishengomae at nm-aist.ac.tz  Tue Jan 21 06:42:58 2014
From: ishengomae at nm-aist.ac.tz (Edson Ishengoma)
Date: Tue, 21 Jan 2014 14:42:58 +0300
Subject: [Biopython] Biopython function for operating multiple homologous
 sequences in a single file
Message-ID: <CAKoVMymaWaoFVj7z2j0Sk9GsD+1NUK7vBMMVj9xFv77=Lwz-Nw@mail.gmail.com>

Hi all,

I have a single large file containing many (thousands) coding sequence
pairs according to their homologs as so:

> >ENSBTAT00000048342_species1
> sequences
> >ENSBTAT00000048342_species2
> sequences
> >ENSBTAT00000009085_species1
> sequences
> >ENSBTAT00000009085_species2
> sequences
> >ENSBTAT00000009212_species1
> sequences
> >ENSBTAT00000009212_species2
> sequences
> ......
> ......
> ......
>

Now I want to produce a clustalw alignment for each cds pair. Is there a
way to use the biopython commandline function for clustalw to treat each
gene pair separately for all pairs, run alignment and produce an ouput
(alignments + trees file)?

I appreciate your time and look forward to hear from you,

With regards,

Edson B. Ishengoma
PhD-Candidate
*School of Life Sciences and Engineering
Nelson Mandela African Institute of Science and Technology
Nelson Mandela Road
P. O. Box 447, Arusha
Tanzania (255)
*
*ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
*

<http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
  Website: www.nm-aist.ac.tz
Skype: edson.ishengoma

*
*
**

From mike.thon at gmail.com  Tue Jan 21 11:39:06 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Tue, 21 Jan 2014 17:39:06 +0100
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <96EDC3CA-6DBD-4825-8704-95BF45590211@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
	<AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
	<96EDC3CA-6DBD-4825-8704-95BF45590211@gmail.com>
Message-ID: <29CB27F1-43BE-4FC5-9591-0640CEC31CC1@gmail.com>

Here?s another question.  I have this GenBank formatted feature:

     CDS             order(complement(3448..3635),complement(2617..3256))
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_05457-RA:cds"
                     /label=?CDS"

When I extract the sequence I get this:

(Pdb) str(feat.extract(seq).seq)
'ACCAGTCGGCTCCGGCAAGACAGCTCTGATGCTCGCCCTCTGCCTCGCCCTGCGCGAAAAATACTCCATCGCCGCCGTCACAAACGACATCTTCACCCGTGAGGACGCCGAATTCCTCACCCGCCACAAGGCCCTGCCCGCCCCGCGCATCCGCGCCATCGAGACGGGCGGCTGCCCGCACGCCGCCGTGCGCGAGGACATCTCGGCCAACCTCGCCGCCCTCGAGGACCTCCACCGCGAGTTCGACGCCGATCTGCTCCTCATCGAGTCCGGCGGCGACAACCTGGCCGCCAACTACTCCCGCGAGCTGGCCGATTACATCATCTACGTCATTGACGTCTCGGGAGGCGACAAGATCCCGCGCAAGGGCGGCCCGGGTATCACACAGAGCGACTTGCTGGTTGTGAACAAGACGGATCTGGCCGAGATTGTGGGCGCGGATCTGGGTGTCATGGAGAGGGACGCGCGCAAGATGCGAGAGGGCGGGCCGACTGTGTTTGCGCAGGTGAAGAAGAATGTTGCCGTTGATCACATTGTCAACCTCATGCTTAGCGCGTGGAAGGCGAGTGGTGCCGAGGAGAACCGTAGGGCTGCGGGCGGACCGCGGCCTACAGAGGGCCTTGACAGCCTCAAGGCTTGAATGTCTCACGAGCACTCACACGACGGCCCTCATGGCCACGCGCACTCCCACGAGGGCGGCTTCAATGCCCAGGAGCACGGCCACTCCCACGAGATCCTTGATGGTCCTGGAAGCTATCTCGGCCGCGAGATGCCCATTGTCGAGGGCAGAAACTGGAGCGATCGTGCTTTCACAATTGGTATTGGAGG'

This is supposed to be a CDS which can be translated to a protein coding sequence starting with M and ending with a stop codon.  the above sequence isn?t correct - the exons are in the wrong order.  When I reverse the order of the exons I get the correct order and get a CDS sequence that can be translated:

(Pdb) feat.location.parts.reverse()
(Pdb) str(feat.extract(seq).seq)
'ATGTCTCACGAGCACTCACACGACGGCCCTCATGGCCACGCGCACTCCCACGAGGGCGGCTTCAATGCCCAGGAGCACGGCCACTCCCACGAGATCCTTGATGGTCCTGGAAGCTATCTCGGCCGCGAGATGCCCATTGTCGAGGGCAGAAACTGGAGCGATCGTGCTTTCACAATTGGTATTGGAGGACCAGTCGGCTCCGGCAAGACAGCTCTGATGCTCGCCCTCTGCCTCGCCCTGCGCGAAAAATACTCCATCGCCGCCGTCACAAACGACATCTTCACCCGTGAGGACGCCGAATTCCTCACCCGCCACAAGGCCCTGCCCGCCCCGCGCATCCGCGCCATCGAGACGGGCGGCTGCCCGCACGCCGCCGTGCGCGAGGACATCTCGGCCAACCTCGCCGCCCTCGAGGACCTCCACCGCGAGTTCGACGCCGATCTGCTCCTCATCGAGTCCGGCGGCGACAACCTGGCCGCCAACTACTCCCGCGAGCTGGCCGATTACATCATCTACGTCATTGACGTCTCGGGAGGCGACAAGATCCCGCGCAAGGGCGGCCCGGGTATCACACAGAGCGACTTGCTGGTTGTGAACAAGACGGATCTGGCCGAGATTGTGGGCGCGGATCTGGGTGTCATGGAGAGGGACGCGCGCAAGATGCGAGAGGGCGGGCCGACTGTGTTTGCGCAGGTGAAGAAGAATGTTGCCGTTGATCACATTGTCAACCTCATGCTTAGCGCGTGGAAGGCGAGTGGTGCCGAGGAGAACCGTAGGGCTGCGGGCGGACCGCGGCCTACAGAGGGCCTTGACAGCCTCAAGGCTTGA'
(Pdb) str(feat.extract(seq).seq.translate())
'MSHEHSHDGPHGHAHSHEGGFNAQEHGHSHEILDGPGSYLGREMPIVEGRNWSDRAFTIGIGGPVGSGKTALMLALCLALREKYSIAAVTNDIFTREDAEFLTRHKALPAPRIRAIETGGCPHAAVREDISANLAALEDLHREFDADLLLIESGGDNLAANYSRELADYIIYVIDVSGGDKIPRKGGPGITQSDLLVVNKTDLAEIVGADLGVMERDARKMREGGPTVFAQVKKNVAVDHIVNLMLSAWKASGAEENRRAAGGPRPTEGLDSLKA*'

So my question is, is there something wrong with the file I?m parsing?

On Jan 14, 2014, at 12:22 PM, Heath O'Brien <Heath.OBrien at bristol.ac.uk> wrote:

> Finally a question that I?m confident I can answer?
> 
> Genbank uses one-based numbering and closed intervals while python uses zero-based numbering and half-open intervals, so it?s necessary to convert the coordinates. See https://plus.google.com/115212051037621986145/posts/YTUxbXYZyfi
> 
> You can convert back to one-based coordinates by adding 1 to the start coordinate.
> 
> all good things,
> Heath
> 
> On 14 Jan 2014, at 10:20, Michael Thon <mike.thon at gmail.com> wrote:
> 
>> Hi Peter - Thanks for your help.  Here is another problem.  Here is the block of features in my GenBank file for a gene:
>> 
>>    gene            complement(1..588)
>>                    /Source="maker"
>>                    /ID="CFIO01_14176"
>>                    /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
>>                    -gene-0.30"
>>                    /label="CFIO01_14176"
>>    CDS             order(complement(200..588),complement(1..124))
>>                    /Source="maker"
>>                    /codon_start=1
>>                    /ID="CFIO01_14176-RA:cds"
>>                    /label="CDS"
>>    mRNA            complement(1..588)
>>                    /Source="maker"
>>                    /ID="CFIO01_14176-RA"
>>                    /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
>>                    -gene-0.30-mRNA-1"
>>                    /_AED="0.06"
>>                    /_QI="0|0|0|1|1|1|2|0|171"
>>                    /_eAED="0.06"
>>                    /label="CFIO01_14176-RA"
>> 
>> Now, here is the CDS feature after is was parsed by BioPython:
>> 
>> 
>> (Pdb) feat.location.parts
>> [FeatureLocation(ExactPosition(0), ExactPosition(124), strand=-1), FeatureLocation(ExactPosition(199), ExactPosition(588), strand=-1)]
>> 
>> Note that two positions have changed.  The CDS segments are (complement(200..588),complement(1..124)) but the positions in SeqFeature object are 0..124 and 199..588
>> 
>> I checked some other features too and it looks like BioPython adds 1 to the start of each segment.  For the features on the complementary strand it subtracts 1.  
>> 
>> When I translate the feature into a protein sequence like this: str(feat.extract(seq).seq.translate()) , the sequence is correct so this must not be a bug. so, how to I access the exact values that are in the genbank formatted file?  
>> 
>> On Jan 13, 2014, at 5:18 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> 
>>> On Mon, Jan 13, 2014 at 4:07 PM, Michael Thon <mike.thon at gmail.com> wrote:
>>>> Here are two examples from the GenBank format file (not from GenBank though)
>>>> 
>>>> 
>>>>   CDS             order(6621..6658,6739..6985)
>>>>                   /Source="maker"
>>>>                   /codon_start=1
>>>>                   /ID="CFIO01_14847-RA:cds"
>>>>                   /label=?CDS"
>>>> 
>>>>   CDS             419..2374
>>>>                   /Source="maker"
>>>>                   /codon_start=1
>>>>                   /ID="CFIO01_05899-RA:cds"
>>>>                   /label=?CDS"
>>>> 
>>>> if the feature is a simple feature, then I just need to access its start and end.
>>>> If its a compound feature then I need to iterate over each segment, accessing the start and end.
>>>> 
>>>> What I am doing at the moment is this:
>>>> 
>>>> if feat._sub_features:
>>>>      for sf in feat.sub_features:
>>>>              start = sf.location.start
>>>>              ?
>>>> else:
>>>>      start = feat.location.start
>>>>      ?
>>>> 
>>>> it works, I think.  Is there a better way?
>>> 
>>> Don't do that :) Python variables/methods/etc starting with a single
>>> underscore are by convention private and should not generally be
>>> used. In this case, ._sub_features is an internal detail for the behind
>>> the scenes backwards compatibility for the now deprecated property
>>> .sub_features (don't use that either).
>>> 
>>> Instead use the location object itself directly, it now holds any
>>> sub-location information using a CompoundLocation object.
>>> See the .parts attribute, which gives a list of simple locations.
>>> 
>>> e.g.
>>> 
>>> for part in feat.location.parts:
>>>  start = part.start
>>>  ...
>>> 
>>>> 
>>>> Also, is there an easy way to get the sequence represented by the seqfeature,
>>>> if it is made up of CompoundLocations?  These features are CDSs where each
>>>> sub-feature is an exon.  I need to splice them all together and get the translation.
>>>> 
>>> 
>>> Yes, where `feat` is a SubFeature object use `feat.extract(the_parent_sequence)`
>>> to get the spliced sequence, which you can then translate. See the section
>>> "Sequence described by a feature or location" in the Tutorial,
>>> 
>>> http://biopython.org/DIST/docs/tutorial/Tutorial.html
>>> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>>> 
>>> On reflection, the Tutorial could do with a bit more detail on how to use
>>> a CompoundLocation, but I did try to cover this in the docstrings.
>>> 
>>> Regards,
>>> 
>>> 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  Tue Jan 21 11:52:35 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 21 Jan 2014 16:52:35 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <29CB27F1-43BE-4FC5-9591-0640CEC31CC1@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
	<AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
	<96EDC3CA-6DBD-4825-8704-95BF45590211@gmail.com>
	<29CB27F1-43BE-4FC5-9591-0640CEC31CC1@gmail.com>
Message-ID: <CAKVJ-_6UvMcht638vyGtd1xghxO=D8Wzrnn5QpVw60ZPRF1tqA@mail.gmail.com>

On Tue, Jan 21, 2014 at 4:39 PM, Michael Thon <mike.thon at gmail.com> wrote:

> Here?s another question.  I have this GenBank formatted feature:
>
>      CDS             order(complement(3448..3635),complement(2617..3256))
>                      /Source="maker"
>                      /codon_start=1
>                      /ID="CFIO01_05457-RA:cds"
>                      /label=?CDS"
>
> When I extract the sequence I get this:
>
> (Pdb) str(feat.extract(seq).seq)
> ...
>
> This is supposed to be a CDS which can be translated to a protein coding
> sequence starting with M and ending with a stop codon.  the above sequence
> isn?t correct - the exons are in the wrong order.  When I reverse the order
> of the exons I get the correct order and get a CDS sequence that can be
> translated:
>
> (Pdb) feat.location.parts.reverse()
> (Pdb) str(feat.extract(seq).seq)
> ...
> (Pdb) str(feat.extract(seq).seq.translate())
>
> 'MSHEHSHDGPHGHAHSHEGGFNAQEHGHSHEILDGPGSYLGREMPIVEGRNWSDRAFTIGIGGPVGSGKTALMLALCLALREKYSIAAVTNDIFTREDAEFLTRHKALPAPRIRAIETGGCPHAAVREDISANLAALEDLHREFDADLLLIESGGDNLAANYSRELADYIIYVIDVSGGDKIPRKGGPGITQSDLLVVNKTDLAEIVGADLGVMERDARKMREGGPTVFAQVKKNVAVDHIVNLMLSAWKASGAEENRRAAGGPRPTEGLDSLKA*'
>
> So my question is, is there something wrong with the file I?m parsing?
>

Possibly - the 'order' tag actually means the order of the parts is unknown.
If the order is known, it should be 'join' instead:

join(complement(3448..3635),complement(2617..3256))

What's the accession/URL for the full file this example came from?

Peter


From chapmanb at 50mail.com  Tue Jan 21 20:25:04 2014
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 21 Jan 2014 20:25:04 -0500
Subject: [Biopython] GFF parsing: getting features of specific proteins
	in gff
In-Reply-To: <6AA379FAFB7845079A6E0D300FC1C237@gmail.com>
References: <6AA379FAFB7845079A6E0D300FC1C237@gmail.com>
Message-ID: <86bnz495an.fsf@fastmail.fm>


Philipp;
Thanks for the e-mail about GFF parsing and sorry for the delay in
getting back with you. I've merged your second off-list e-mail with this
and copied back to the mailing list in case other folks have
comments/thoughts to share as well.

> I just started exploring the GFF parser for some Augustus derived gff3
> files, but running into trouble when trying to collect information for
> a specific protein. Ultimately my goal is to get introns and exons for
> a specific set of genes.
[...]
> However now I'd like not to print all rec.features, but only for a
> specific gene.
>
> I found that in principle I can do something like?
> ```for rec in GFF.parse(in_handle, limit_info=limit_info):
>             if 'g1' in rec.features[0].qualifiers:
>                 GFF.write([rec], out_handle)```
>
> However this does not really solve my problem. For once it gives me
> all the genes on a contig if the search string is in
> rec.features[0]. I guess I could somehow just write the first then,
> but what seems more important if a gene I am looking for is in
> rec.features[1] or higher index

To do this you'd want to also loop over the features, so do:

for rec in GFF.parse(in_handle, limit_info=limit_info):
   for feature in rec.features:
      if 'g1' in f.qualifiers:
          GFF.write([rec], out_handle)
          break

This is definitely sub-optimal since it's a brute force loop over all of
the items in the GFF, but would work for what you need.

If speed becomes an issue, Ryan Dale's GFFUtils may be useful:

https://github.com/daler/gffutils
http://pythonhosted.org/gffutils/

It creates a SQLite database based on the GFF, so enables faster query
access by gene than the line-based parser. It doesn't yet integrate with
Biopython (that is on my overdue todo list) but provides a nice Python
API with examples in the documentation.

Hope this helps,
Brad


From p.j.a.cock at googlemail.com  Wed Jan 22 06:19:49 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 22 Jan 2014 11:19:49 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <CAKVJ-_6UvMcht638vyGtd1xghxO=D8Wzrnn5QpVw60ZPRF1tqA@mail.gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
	<AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
	<96EDC3CA-6DBD-4825-8704-95BF45590211@gmail.com>
	<29CB27F1-43BE-4FC5-9591-0640CEC31CC1@gmail.com>
	<CAKVJ-_6UvMcht638vyGtd1xghxO=D8Wzrnn5QpVw60ZPRF1tqA@mail.gmail.com>
Message-ID: <CAKVJ-_7-g4YZBq-Nn0a2RnCfCGondG_=JVbJdvZHs2MxjyHQ7Q@mail.gmail.com>

On Tue, Jan 21, 2014 at 4:52 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Tue, Jan 21, 2014 at 4:39 PM, Michael Thon <mike.thon at gmail.com> wrote:
>>
>> Here?s another question.  I have this GenBank formatted feature:
>>
>>      CDS             order(complement(3448..3635),complement(2617..3256))
>>                      /Source="maker"
>>                      /codon_start=1
>>                      /ID="CFIO01_05457-RA:cds"
>>                      /label=?CDS"
>>
>> When I extract the sequence I get this:
>>
>> (Pdb) str(feat.extract(seq).seq)
>> ...
>>
>>
>> This is supposed to be a CDS which can be translated to a protein coding
>> sequence starting with M and ending with a stop codon.  the above sequence
>> isn?t correct - the exons are in the wrong order.  When I reverse the order
>> of the exons I get the correct order and get a CDS sequence that can be
>> translated:
>>
>> (Pdb) feat.location.parts.reverse()
>> (Pdb) str(feat.extract(seq).seq)
>> ...
>>
>> (Pdb) str(feat.extract(seq).seq.translate())
>>
>> 'MSHEHSHDGPHGHAHSHEGGFNAQEHGHSHEILDGPGSYLGREMPIVEGRNWSDRAFTIGIGGPVGSGKTALMLALCLALREKYSIAAVTNDIFTREDAEFLTRHKALPAPRIRAIETGGCPHAAVREDISANLAALEDLHREFDADLLLIESGGDNLAANYSRELADYIIYVIDVSGGDKIPRKGGPGITQSDLLVVNKTDLAEIVGADLGVMERDARKMREGGPTVFAQVKKNVAVDHIVNLMLSAWKASGAEENRRAAGGPRPTEGLDSLKA*'
>>
>> So my question is, is there something wrong with the file I?m parsing?
>
>
> Possibly - the 'order' tag actually means the order of the parts is unknown.
> If the order is known, it should be 'join' instead:
>
> join(complement(3448..3635),complement(2617..3256))
>
> What's the accession/URL for the full file this example came from?
>
> Peter

Thanks for sending me the file. I don't think Biopython is really at
fault, rather something is going wrong in the production of this
GenBank format file. It appears to be a tricky case of trans-splicing.

However, thinking about this, it might be reasonable for Biopython
to give an error or warning when extracting an "order" location because
this means the order of the sub-parts is not determined (and thus
could be stitched together wrongly - as you have seen).

The following variants of the location string all give the (nonsensical)
sequence you are seeing:

     CDS             order(complement(3448..3635),complement(2617..3256))
     CDS             join(complement(3448..3635),complement(2617..3256))
     CDS             complement(join(3448..3635,2617..3256))

Extracting and translating gives this sequence with multiple in
frame stop codons, but lacking a terminal stop codon. i.e.

TSRLRQDSSDARPLPRPARKILHRRRHKRHLHP*GRR...YWR (ends)

Surprisingly, what I think the annotation is trying to say is that this case
the exons appear to be trans-spliced, rather than being in the typical
order you would expect from the strand. These "work" and give the
protein sequence you wanted,

     CDS             complement(join(2617..3256,3448..3635))
     CDS             join(complement(2617..3256),complement(3448..3635))
     CDS             order(complement(2617..3256),complement(3448..3635))

For GenBank format it would be nice to also add the /trans_splicing
tag as well. I would recommend you (or the team)  go back to the original
annotation to check what was the intended meaning here.

Regards,

Peter


From philipp.schiffer at gmail.com  Wed Jan 22 08:44:52 2014
From: philipp.schiffer at gmail.com (Philipp Schiffer)
Date: Wed, 22 Jan 2014 14:44:52 +0100
Subject: [Biopython] GFF parsing: getting features of specific proteins
 in gff
In-Reply-To: <86bnz495an.fsf@fastmail.fm>
References: <6AA379FAFB7845079A6E0D300FC1C237@gmail.com>
	<86bnz495an.fsf@fastmail.fm>
Message-ID: <45004206D5B843E489D001BFBF47DB0E@googlemail.com>

Hi Brad,  

thanks for coming back to me on this. Works (well of course). Also thanks for the GFFUtils link. I have actually been aware of that, but wanted to figure out my own way (kind off). Well, eh, failed there I guess. But I surely learnt something, which is always the point. Also I wanted to integrate this in a larger script where I get the genes of interest from a clustering output first. Anyway, in the end it might really make sense to use the GFFUtils on lists I prepared first.   

Thanks again

Philipp

--  
Philipp Schiffer
Sent with Sparrow (http://www.sparrowmailapp.com/?sig)


On Wednesday, 22 January 2014 at 02:25, Brad Chapman wrote:

>  
> Philipp;
> Thanks for the e-mail about GFF parsing and sorry for the delay in
> getting back with you. I've merged your second off-list e-mail with this
> and copied back to the mailing list in case other folks have
> comments/thoughts to share as well.
>  
> > I just started exploring the GFF parser for some Augustus derived gff3
> > files, but running into trouble when trying to collect information for
> > a specific protein. Ultimately my goal is to get introns and exons for
> > a specific set of genes.
> >  
>  
> [...]
> > However now I'd like not to print all rec.features, but only for a
> > specific gene.
> >  
> > I found that in principle I can do something like?
> > ```for rec in GFF.parse(in_handle, limit_info=limit_info):
> > if 'g1' in rec.features[0].qualifiers:
> > GFF.write([rec], out_handle)```
> >  
> > However this does not really solve my problem. For once it gives me
> > all the genes on a contig if the search string is in
> > rec.features[0]. I guess I could somehow just write the first then,
> > but what seems more important if a gene I am looking for is in
> > rec.features[1] or higher index
> >  
>  
>  
> To do this you'd want to also loop over the features, so do:
>  
> for rec in GFF.parse(in_handle, limit_info=limit_info):
> for feature in rec.features:
> if 'g1' in f.qualifiers:
> GFF.write([rec], out_handle)
> break
>  
> This is definitely sub-optimal since it's a brute force loop over all of
> the items in the GFF, but would work for what you need.
>  
> If speed becomes an issue, Ryan Dale's GFFUtils may be useful:
>  
> https://github.com/daler/gffutils
> http://pythonhosted.org/gffutils/
>  
> It creates a SQLite database based on the GFF, so enables faster query
> access by gene than the line-based parser. It doesn't yet integrate with
> Biopython (that is on my overdue todo list) but provides a nice Python
> API with examples in the documentation.
>  
> Hope this helps,
> Brad
>  
>  




From alanwilter at gmail.com  Wed Jan 22 11:28:57 2014
From: alanwilter at gmail.com (Alan)
Date: Wed, 22 Jan 2014 16:28:57 +0000
Subject: [Biopython] help with seqxml format
Message-ID: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>

I have an input fasta file (test.fasta), like:

>tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus musculus
GN=Negr1 PE=2 SV=1
MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGA
SKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTP
RTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQ
YLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCE
GAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTT
NASLPLNQSSIPWQVFFMLKVSFLLVCIL

Then I am trying this:

from Bio import SeqIO
from Bio.Alphabet import generic_protein
handle = open("test.fasta")
records = list(SeqIO.parse(handle, "fasta", generic_protein))
aa = records[0]

print aa.format('seqxml')
<?xml version="1.0" encoding="utf-8"?>
<seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
http://www.seqxml.org/0.4/seqxml.xsd">
 <entry id="tr|A0A4W9|A0A4W9_MOUSE">
  <description>growth regulator 1</description>

<AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
 </entry>
</seqXML>

Note above that my SeqIO.parse is not picking all the info in the Fasta
header.

But I want to tweak this to output something more like this:
<seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
http://www.seqxml.org/0.4/seqxml.xsd" source="QfO
http://www.ebi.ac.uk/reference_proteomes/" sourceVersion="2014_04">
 <entry id="A0A4W9" source="UniProtKB">
  <species name="Mus musculus" ncbiTaxID="10090" />
  <description>Neuronal growth regulator 1</description>

 <AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
  <DBRef type="gene" source="GN" id="Negr1" />
  <DBRef type="gene" source="Gene" id="TK0418" />
  <property name="PE" value="2" />
  <property name="SV" value="1" />
 </entry>
</seqXML>

The aa.id, aa.description wouldn't be a problem to update and some info I
have to provide from elsewhere (like ncbiTaxID and species name), but how
to add the details in the <seqXML>, <entry source> or create <species>,
<DBRef> etc.?

Many thanks in advance,

Alan


From p.j.a.cock at googlemail.com  Wed Jan 22 11:53:08 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 22 Jan 2014 16:53:08 +0000
Subject: [Biopython] help with seqxml format
In-Reply-To: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>
References: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>
Message-ID: <CAKVJ-_4ivQkwHUxd0C7w-7qvyyHrYPAjDikY=J7L-ZkF4pLWCA@mail.gmail.com>

On Wed, Jan 22, 2014 at 4:28 PM, Alan <alanwilter at gmail.com> wrote:
> I have an input fasta file (test.fasta), like:
>
>>tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus musculus
> GN=Negr1 PE=2 SV=1
> MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGA
> SKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTP
> RTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQ
> YLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCE
> GAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTT
> NASLPLNQSSIPWQVFFMLKVSFLLVCIL
>
> Then I am trying this:
>
> from Bio import SeqIO
> from Bio.Alphabet import generic_protein
> handle = open("test.fasta")
> records = list(SeqIO.parse(handle, "fasta", generic_protein))
> aa = records[0]
>
> print aa.format('seqxml')
> <?xml version="1.0" encoding="utf-8"?>
> <seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
> http://www.seqxml.org/0.4/seqxml.xsd">
>  <entry id="tr|A0A4W9|A0A4W9_MOUSE">
>   <description>growth regulator 1</description>
>
> <AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
>  </entry>
> </seqXML>
>
> Note above that my SeqIO.parse is not picking all the info in the Fasta
> header.

Odd, what does aa.description give you?

> But I want to tweak this to output something more like this:
> ...
>   <species name="Mus musculus" ncbiTaxID="10090" />
>   <description>Neuronal growth regulator 1</description>
>
> The aa.id, aa.description wouldn't be a problem to update and some info I
> have to provide from elsewhere (like ncbiTaxID and species name), but how
> to add the details in the <seqXML>, <entry source> or create <species>,
> <DBRef> etc.?

Set record.annotations["organism"] and record.annotations["ncbi_taxid"]
to suitable strings, and the list record.dbxref = ["db:identifer", ...].

Also what version of Biopython are you using?

Peter


From hlapp at drycafe.net  Wed Jan 22 14:33:10 2014
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 22 Jan 2014 14:33:10 -0500
Subject: [Biopython] Fwd: Call for Org Admins for OBF's 2014 Google Summer
	of Code participation
References: <AD3B86E4-05E0-4395-ADD8-DAC30DDA87A0@drycafe.net>
Message-ID: <BA38F9AA-11FB-4360-BDE0-548740504AA9@drycafe.net>

FYI, we are extending the deadline for responding to this Saturday, January 25.

Also, in case this wasn't clear from the text, this isn't a pro forma solicitation. There is no plan B. If we don't receive qualified applications by the deadline, OBF will not apply this year as a mentoring organization.

	-hilmar

Begin forwarded message:

From: Hilmar Lapp <hlapp at drycafe.net>
Subject: Call for Org Admins for OBF's 2014 Google Summer of Code participation 
Date: January 14, 2014 6:16:02 PM EST
To: BioPerl List <bioperl-l at lists.open-bio.org>

The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring organization applications from Feb 3 to 14.

OBF participated on behalf of our member projects from 2010-2012, and those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.

To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve. 

An org admin?s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to ?keep it together.? Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org?s mentors. The org admin?s responsibilities include:
	? Representing our online face to GSoC, in particular to GSoC students.
	? Shepherding our mentoring organization application, and submitting it.
	? Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises.
	? Knowing GSoC rules and processes, and making sure ours are consistent with them.
	? Reminding participants of rules, and enforcing them in the event it is necessary.
	? Mediating, and sometimes arbitrating between students and mentors when needed.
	? Ensuring that GSoC timelines are met by everyone.
The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener.

If you are interested in helping us out in this role, please email us (by Jan 21, 2014) a statement at board at open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project?s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects.

We are looking forward to hearing from you!

Hilmar Lapp, OBF President, on behalf of the OBF Board of Directors
[1] http://www.google-melange.com/gsoc/events/google/gsoc2014

-- 
Hilmar Lapp -:- lappland.io




From lthiberiol at gmail.com  Wed Jan 22 14:58:10 2014
From: lthiberiol at gmail.com (Luiz Thiberio Rangel)
Date: Wed, 22 Jan 2014 17:58:10 -0200
Subject: [Biopython] Phylo.draw - coloring node names
Message-ID: <CAA8DvhaNs=cLo3RgzgXzF7JuM02HR0=E-DzMVFE9NP98f2dFSg@mail.gmail.com>

Hey,

   I am trying to quickly edit some trees coloring the node names according
to they taxonomy. I figured out that all I can do is to color the branches (
tree.get_nonterminals()[0].color = 'grey'), not the texts. Is there any way
to color the node names?

thx,

Luiz Thib?rio Rangel


From ishengomae at nm-aist.ac.tz  Thu Jan 23 02:39:12 2014
From: ishengomae at nm-aist.ac.tz (Edson Ishengoma)
Date: Thu, 23 Jan 2014 10:39:12 +0300
Subject: [Biopython] Follow-up about python/biopython code for submitting
	multiple jobs to clustalw
Message-ID: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>

Hi all,

I couldn't get a response about my struggles which I asked few days past, I
presume it was either a poorly submitted question or my approach with what
I want to do is totally out of touch with mainstream bioinformatics. The
thing is I am a newbie to both python programming and bioinformatics but I
believe there are people here who can help, so I will try again with more
background.

The overall goal with what I want to achieve is to perform selection
analyses on multiple species with codeml in PAML. For this the inputs
should be both the sequence alignments and tree files. I already have
sequence file (produced by pal2nal) but I still need a corresponding tree
file.

So what I am challenged with is the fact that my nucleotide alignment file
contain cds of four species at many loci (it is kind of whole genome data)
so I will have to submit the job to a tree producing program per each
alignment - I can use clustalw or Phylip.

Looking at biopython facility, thankfully there is biopython wrapper for
clustalw which I attempted to use for trees, but the fact that my alignment
file contains multiple alignments, I cannot use the code the way it is (the
straight code assumes the file contains a single alignment). So I reasoned
that I can couple this clustalw wrapper with a Dictionary facility to
output the desired results as so:

from Bio import SeqIO
> from Bio.Align.Applications import ClustalwCommandline
>
> def get_ids(record):
>     """"Given a SeqRecord, return the common number shared among sequence
> descriptions.
>             e.g. ">ENSBTAT00000009085_cow or ENSBTAT00000009085_goat or
> ENSBTAT00000009085_sheep
>             " -> "ENSBTAT00000009085"
>             """
>     parts = record.description[:18]
>     return parts
>
> myseq_dict = SeqIO.to_dict(SeqIO.parse("/home/edson/ungulate/infile.fa",
> "fasta"), key_function=get_ids)
> #print myseq_dict.keys()
> cline = ClustalwCommandline("clustalw2", infile="myseq_dict")
> stdout, stderr = clustalw_cline()
>

It turned out this code is a result of my naive (very naive) reasoning and
it is obvious why it cannot work. But I am just putting it here to give you
a clue of what I want to do. I'm sure there is a convenient way to do what
I want to do and I hope this forum will help. I apologize it is a long
email (english is not my first language, at times I'm being wordy to make
myself clear). Any resource will be appreciated.

Thanks.


Edson B. Ishengoma
PhD-Candidate
*School of Life Sciences and Engineering
Nelson Mandela African Institute of Science and Technology
Nelson Mandela Road
P. O. Box 447, Arusha
Tanzania (255)
*
*ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
*

<http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
  Website: www.nm-aist.ac.tz
Skype: edson.ishengoma

*
*
**

From p.j.a.cock at googlemail.com  Thu Jan 23 04:44:35 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 Jan 2014 09:44:35 +0000
Subject: [Biopython] Biopython function for operating multiple
 homologous sequences in a single file
In-Reply-To: <CAKoVMymaWaoFVj7z2j0Sk9GsD+1NUK7vBMMVj9xFv77=Lwz-Nw@mail.gmail.com>
References: <CAKoVMymaWaoFVj7z2j0Sk9GsD+1NUK7vBMMVj9xFv77=Lwz-Nw@mail.gmail.com>
Message-ID: <CAKVJ-_7-Xyw4=-2fOLQzLAgVX067O7YOLag-5PVpPWaL5yyMag@mail.gmail.com>

On Tue, Jan 21, 2014 at 11:42 AM, Edson Ishengoma
<ishengomae at nm-aist.ac.tz> wrote:
> Hi all,
>
> I have a single large file containing many (thousands) coding sequence
> pairs according to their homologs as so:
>
>> >ENSBTAT00000048342_species1
>> sequences
>> >ENSBTAT00000048342_species2
>> sequences
>> >ENSBTAT00000009085_species1
>> sequences
>> >ENSBTAT00000009085_species2
>> sequences
>> >ENSBTAT00000009212_species1
>> sequences
>> >ENSBTAT00000009212_species2
>> sequences
>> ......
>> ......
>> ......
>>
>
> Now I want to produce a clustalw alignment for each cds pair.

Why do you want to do that?

A pairwise alignment tool might be better... like EMBOSS needle or
water depending on if you want global (full sequence) or local
(partial sequence) alignment. In particular, look at needleall which
is for many-against-many pairwise alignments:
http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html

> Is there a
> way to use the biopython commandline function for clustalw to treat each
> gene pair separately for all pairs, run alignment and produce an ouput
> (alignments + trees file)?

If you really want to run lots of pairwise alignment with clustalw, you
would need a big loop over all the pairs, and call clustalw again and
again (once for each pair). I would think something like needleall
would be better.

Also, you shouldn't use the guide tree from clustalw for any serious
analysis, and anyway if you are doing pairwise alignments the trees
will always be a trivial with two sequences.

Regards,

Peter

From p.j.a.cock at googlemail.com  Thu Jan 23 04:57:50 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 Jan 2014 09:57:50 +0000
Subject: [Biopython] Follow-up about python/biopython code for
 submitting multiple jobs to clustalw
In-Reply-To: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>
References: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>
Message-ID: <CAKVJ-_6RMESVxvXXym_JWYw+1Nm=dV8zaoLWUP1JyirQsJTSRA@mail.gmail.com>

On Thu, Jan 23, 2014 at 7:39 AM, Edson Ishengoma
<ishengomae at nm-aist.ac.tz> wrote:
> Hi all,
>
> I couldn't get a response about my struggles which I asked few days past, I
> presume it was either a poorly submitted question or my approach with what I
> want to do is totally out of touch with mainstream bioinformatics. The thing
> is I am a newbie to both python programming and bioinformatics but I believe
> there are people here who can help, so I will try again with more
> background.
>
> The overall goal with what I want to achieve is to perform selection
> analyses on multiple species with codeml in PAML. For this the inputs should
> be both the sequence alignments and tree files. I already have sequence file
> (produced by pal2nal) but I still need a corresponding tree file.
>
> So what I am challenged with is the fact that my nucleotide alignment file
> contain cds of four species at many loci (it is kind of whole genome data)
> so I will have to submit the job to a tree producing program per each
> alignment - I can use clustalw or Phylip.

If you haven't already, try to get some advice from a phylogenetics
specialist about what to do. For example, clustalw is old and superseded.

You have 4 species, and (say) 50 genes/loci from each. One approach
is to make 50 protein alignments (one for each set of four genes),
turn these into 50 codon-aware nucleotide alignments (with pal2nal
or similar, e.g. [1]), then you could use Biopython to combine these
into a single large concatenated alignment (4 rows for the 4 species),
and use that to build a tree.

This may not be the best plan, but one of our students here did
something like this recently (using Biopython in part).

Peter
[1] https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py

From alanwilter at gmail.com  Thu Jan 23 08:40:42 2014
From: alanwilter at gmail.com (Alan)
Date: Thu, 23 Jan 2014 13:40:42 +0000
Subject: [Biopython] help with seqxml format
In-Reply-To: <CAKVJ-_4ivQkwHUxd0C7w-7qvyyHrYPAjDikY=J7L-ZkF4pLWCA@mail.gmail.com>
References: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>
	<CAKVJ-_4ivQkwHUxd0C7w-7qvyyHrYPAjDikY=J7L-ZkF4pLWCA@mail.gmail.com>
Message-ID: <CAEznbz=a5zWwPQzrq4dfobn+BT+idpp9zabtv71Ho45VMVf5BQ@mail.gmail.com>

Thanks Peter,

I am using the latest version 1.63.

I?ve found some mistakes of myself, aa.description is fine:

print aa
ID: tr|A0A4W9|A0A4W9_MOUSE
Name: tr|A0A4W9|A0A4W9_MOUSE
Description: tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus
musculus GN=Negr1 PE=2 SV=1
Number of features: 0
Seq('MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRC...CIL',
ProteinAlphabet())

print aa.format('seqxml')
<?xml version="1.0" encoding="utf-8"?>
<seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
http://www.seqxml.org/0.4/seqxml.xsd">
 <entry id="tr|A0A4W9|A0A4W9_MOUSE">
  <description>tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus
musculus GN=Negr1 PE=2 SV=1</description>

<AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
 </entry>
</seqXML>

aa.id = 'A0A4W9'
aa.description = 'Neuronal growth regulator 1'
aa.annotations = {'PE': '2', 'ncbi_taxid': '10090', 'organism': 'Mus
musculus', 'source': 'UniProtKB', 'SV':'1'}
aa.dbxrefs = ['GN:Negr1']

which gives now:
print aa.format('seqxml')
<?xml version="1.0" encoding="utf-8"?>
<seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
http://www.seqxml.org/0.4/seqxml.xsd">
 <entry source="UniProtKB" id="A0A4W9">
  <species name="Mus musculus" ncbiTaxID="10090"></species>
  <description>Neuronal growth regulator 1</description>

<AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
  <DBRef source="GN" id="Negr1"></DBRef>
  <property name="SV" value="1"></property>
  <property name="PE" value="2"></property>
 </entry>
</seqXML>

This is almost what I want. The only thing I?d like to add is
???source="QfO http://www.ebi.ac.uk/reference_proteomes/"
sourceVersion="2013_04">??? to the <seqXML> tag header. How would I do it
please?

Many thanks again,

Alan



On 22 January 2014 16:53, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Jan 22, 2014 at 4:28 PM, Alan <alanwilter at gmail.com> wrote:
> > I have an input fasta file (test.fasta), like:
> >
> >>tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus musculus
> > GN=Negr1 PE=2 SV=1
> > MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGA
> > SKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTP
> > RTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQ
> > YLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCE
> > GAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTT
> > NASLPLNQSSIPWQVFFMLKVSFLLVCIL
> >
> > Then I am trying this:
> >
> > from Bio import SeqIO
> > from Bio.Alphabet import generic_protein
> > handle = open("test.fasta")
> > records = list(SeqIO.parse(handle, "fasta", generic_protein))
> > aa = records[0]
> >
> > print aa.format('seqxml')
> > <?xml version="1.0" encoding="utf-8"?>
> > <seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> > seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
> > http://www.seqxml.org/0.4/seqxml.xsd">
> >  <entry id="tr|A0A4W9|A0A4W9_MOUSE">
> >   <description>growth regulator 1</description>
> >
> >
> <AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
> >  </entry>
> > </seqXML>
> >
> > Note above that my SeqIO.parse is not picking all the info in the Fasta
> > header.
>
> Odd, what does aa.description give you?
>
> > But I want to tweak this to output something more like this:
> > ...
> >   <species name="Mus musculus" ncbiTaxID="10090" />
> >   <description>Neuronal growth regulator 1</description>
> >
> > The aa.id, aa.description wouldn't be a problem to update and some info
> I
> > have to provide from elsewhere (like ncbiTaxID and species name), but how
> > to add the details in the <seqXML>, <entry source> or create <species>,
> > <DBRef> etc.?
>
> Set record.annotations["organism"] and record.annotations["ncbi_taxid"]
> to suitable strings, and the list record.dbxref = ["db:identifer", ...].
>
> Also what version of Biopython are you using?
>
> Peter
>


From p.j.a.cock at googlemail.com  Thu Jan 23 08:56:08 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 Jan 2014 13:56:08 +0000
Subject: [Biopython] help with seqxml format
In-Reply-To: <CAEznbz=a5zWwPQzrq4dfobn+BT+idpp9zabtv71Ho45VMVf5BQ@mail.gmail.com>
References: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>
	<CAKVJ-_4ivQkwHUxd0C7w-7qvyyHrYPAjDikY=J7L-ZkF4pLWCA@mail.gmail.com>
	<CAEznbz=a5zWwPQzrq4dfobn+BT+idpp9zabtv71Ho45VMVf5BQ@mail.gmail.com>
Message-ID: <CAKVJ-_7ZF1jO6g50YgvgMVfwPCAZcfu0wQd8mUXM9p=yjpfsGA@mail.gmail.com>

On Thu, Jan 23, 2014 at 1:40 PM, Alan <alanwilter at gmail.com> wrote:
> Thanks Peter,
>
> I am using the latest version 1.63.
>
> I?ve found some mistakes of myself, aa.description is fine:
>

Oh good - I was puzzled about that bit.

> This is almost what I want. The only thing I?d like to add is ???source="QfO
> http://www.ebi.ac.uk/reference_proteomes/" sourceVersion="2013_04">??? to
> the <seqXML> tag header. How would I do it please?

Setting record.annotations["sourceVersion"] = "2013_04" should do it.

(I'm assuming the odd QfO bit for the source value was a problem
copying text into the email).

If you are wondering, I've just been reading the source code for
the SeqXmlWriter class to see where it looks for fields:
https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SeqXmlIO.py

It would be nice if someone was to summarise this mapping
in the module's help text (the docstrings).

Regards,

Peter


From alanwilter at gmail.com  Thu Jan 23 09:55:24 2014
From: alanwilter at gmail.com (Alan)
Date: Thu, 23 Jan 2014 14:55:24 +0000
Subject: [Biopython] =?utf-8?b?dHlwbyBlcnJvciDigJxzb3VyY2VfZXJzaW9u4oCd?=
	=?utf-8?q?_=2C_it_should_be_=E2=80=9Csource=5Fversion=22?=
Message-ID: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>

In https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SeqXmlIO.py

    def write_header(self):
        """Write root node with document metadata."""

        SequentialSequenceWriter.write_header(self)

        attrs = {"xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
                 "xsi:noNamespaceSchemaLocation":
"http://www.seqxml.org/0.4/seqxml.xsd",
                 "seqXMLversion": "0.4"}

        if self.source is not None:
            attrs["source"] = self.source
        if self.source_version is not None:
            attrs["sourceVersion"] = self.source_ersion

Alan

From p.j.a.cock at googlemail.com  Thu Jan 23 10:11:07 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 Jan 2014 15:11:07 +0000
Subject: [Biopython]
	=?windows-1252?q?typo_error_=93source=5Fersion=94_=2C?=
	=?windows-1252?q?_it_should_be_=93source=5Fversion=22?=
In-Reply-To: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>
References: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>
Message-ID: <CAKVJ-_7WiNxq9nk=uQv=1rVRUA9pThj8oV=d+_NQMrFf2_1P2A@mail.gmail.com>

On Thu, Jan 23, 2014 at 2:55 PM, Alan <alanwilter at gmail.com> wrote:
> In https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SeqXmlIO.py
>
> ...
>
>             attrs["sourceVersion"] = self.source_ersion
>
>
> Alan

Yes indeed, fixed - thank you:
https://github.com/biopython/biopython/commit/0e23daf8d0d2ad9130479417d77147e794e182be

This highlights that we could do with a few more unit tests on
the annotation side of things in the SeqXML code:
https://github.com/biopython/biopython/blob/master/Tests/test_SeqIO_SeqXML.py

Regards,

Peter

From mike.thon at gmail.com  Thu Jan 23 11:31:50 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Thu, 23 Jan 2014 17:31:50 +0100
Subject: [Biopython] Follow-up about python/biopython code for
	submitting multiple jobs to clustalw
In-Reply-To: <CAKVJ-_6RMESVxvXXym_JWYw+1Nm=dV8zaoLWUP1JyirQsJTSRA@mail.gmail.com>
References: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>
	<CAKVJ-_6RMESVxvXXym_JWYw+1Nm=dV8zaoLWUP1JyirQsJTSRA@mail.gmail.com>
Message-ID: <C4A00153-A1B3-4FE9-95F8-933A4A5C0E4E@gmail.com>

Hi Edson -  It sounds like you have many alignments concatenated together in one file.  You may want to keep each of your loci (a.k.a. orthologous sets of DNA or protein sequences) in a separate file for each family.  I think you will find it easier to do your alignment and tree building operations on them.  For each locus make a protein file in FASTA format and a transcript file in fasta format, each file would have four sequences in it.  then its simple to loop through the contents of a directory and call a command line program on each file.  You may not even need python for all the steps. 


On Jan 23, 2014, at 10:57 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, Jan 23, 2014 at 7:39 AM, Edson Ishengoma
> <ishengomae at nm-aist.ac.tz> wrote:
>> Hi all,
>> 
>> I couldn't get a response about my struggles which I asked few days past, I
>> presume it was either a poorly submitted question or my approach with what I
>> want to do is totally out of touch with mainstream bioinformatics. The thing
>> is I am a newbie to both python programming and bioinformatics but I believe
>> there are people here who can help, so I will try again with more
>> background.
>> 
>> The overall goal with what I want to achieve is to perform selection
>> analyses on multiple species with codeml in PAML. For this the inputs should
>> be both the sequence alignments and tree files. I already have sequence file
>> (produced by pal2nal) but I still need a corresponding tree file.
>> 
>> So what I am challenged with is the fact that my nucleotide alignment file
>> contain cds of four species at many loci (it is kind of whole genome data)
>> so I will have to submit the job to a tree producing program per each
>> alignment - I can use clustalw or Phylip.
> 
> If you haven't already, try to get some advice from a phylogenetics
> specialist about what to do. For example, clustalw is old and superseded.
> 
> You have 4 species, and (say) 50 genes/loci from each. One approach
> is to make 50 protein alignments (one for each set of four genes),
> turn these into 50 codon-aware nucleotide alignments (with pal2nal
> or similar, e.g. [1]), then you could use Biopython to combine these
> into a single large concatenated alignment (4 rows for the 4 species),
> and use that to build a tree.
> 
> This may not be the best plan, but one of our students here did
> something like this recently (using Biopython in part).
> 
> Peter
> [1] https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython



From ishengomae at nm-aist.ac.tz  Thu Jan 23 13:01:47 2014
From: ishengomae at nm-aist.ac.tz (Edson Ishengoma)
Date: Thu, 23 Jan 2014 21:01:47 +0300
Subject: [Biopython] Follow-up about python/biopython code for
 submitting multiple jobs to clustalw
In-Reply-To: <C4A00153-A1B3-4FE9-95F8-933A4A5C0E4E@gmail.com>
References: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>
	<CAKVJ-_6RMESVxvXXym_JWYw+1Nm=dV8zaoLWUP1JyirQsJTSRA@mail.gmail.com>
	<C4A00153-A1B3-4FE9-95F8-933A4A5C0E4E@gmail.com>
Message-ID: <CAKoVMyn+wLnEiWTEzMeoY8W8hMVD5BifFDXLd39YYXWcx+sSBw@mail.gmail.com>

Thanks Michael,
Yes I have many orthologous alignments (about 20,000 thousands genes
--typical of mammalian genomes anyway). Initially I thought of this idea of
having separate files and I hesitated because of computer memory expenses
in writing files. So thanks for reinforcing my thought that it can be a
viable option.

Regards,

Edson B. Ishengoma
PhD-Candidate
*School of Life Sciences and Engineering
Nelson Mandela African Institute of Science and Technology
Nelson Mandela Road
P. O. Box 447, Arusha
Tanzania (255)
*
*ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
*

<http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
  Website: www.nm-aist.ac.tz
Skype: edson.ishengoma

*
*
**


On Thu, Jan 23, 2014 at 7:31 PM, Michael Thon <mike.thon at gmail.com> wrote:

> Hi Edson -  It sounds like you have many alignments concatenated together
> in one file.  You may want to keep each of your loci (a.k.a. orthologous
> sets of DNA or protein sequences) in a separate file for each family.  I
> think you will find it easier to do your alignment and tree building
> operations on them.  For each locus make a protein file in FASTA format and
> a transcript file in fasta format, each file would have four sequences in
> it.  then its simple to loop through the contents of a directory and call a
> command line program on each file.  You may not even need python for all
> the steps.
>
>
> On Jan 23, 2014, at 10:57 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
> On Thu, Jan 23, 2014 at 7:39 AM, Edson Ishengoma
> <ishengomae at nm-aist.ac.tz> wrote:
>
> Hi all,
>
> I couldn't get a response about my struggles which I asked few days past, I
> presume it was either a poorly submitted question or my approach with what
> I
> want to do is totally out of touch with mainstream bioinformatics. The
> thing
> is I am a newbie to both python programming and bioinformatics but I
> believe
> there are people here who can help, so I will try again with more
> background.
>
> The overall goal with what I want to achieve is to perform selection
> analyses on multiple species with codeml in PAML. For this the inputs
> should
> be both the sequence alignments and tree files. I already have sequence
> file
> (produced by pal2nal) but I still need a corresponding tree file.
>
> So what I am challenged with is the fact that my nucleotide alignment file
> contain cds of four species at many loci (it is kind of whole genome data)
> so I will have to submit the job to a tree producing program per each
> alignment - I can use clustalw or Phylip.
>
>
> If you haven't already, try to get some advice from a phylogenetics
> specialist about what to do. For example, clustalw is old and superseded.
>
> You have 4 species, and (say) 50 genes/loci from each. One approach
> is to make 50 protein alignments (one for each set of four genes),
> turn these into 50 codon-aware nucleotide alignments (with pal2nal
> or similar, e.g. [1]), then you could use Biopython to combine these
> into a single large concatenated alignment (4 rows for the 4 species),
> and use that to build a tree.
>
> This may not be the best plan, but one of our students here did
> something like this recently (using Biopython in part).
>
> Peter
> [1]
> https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>
>

From alanwilter at gmail.com  Fri Jan 24 08:50:34 2014
From: alanwilter at gmail.com (Alan)
Date: Fri, 24 Jan 2014 13:50:34 +0000
Subject: [Biopython] =?utf-8?b?dHlwbyBlcnJvciDigJxzb3VyY2VfZXJzaW9u4oCd?=
	=?utf-8?q?_=2C_it_should_be_=E2=80=9Csource=5Fversion=22?=
In-Reply-To: <CAKVJ-_7WiNxq9nk=uQv=1rVRUA9pThj8oV=d+_NQMrFf2_1P2A@mail.gmail.com>
References: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>
	<CAKVJ-_7WiNxq9nk=uQv=1rVRUA9pThj8oV=d+_NQMrFf2_1P2A@mail.gmail.com>
Message-ID: <CAEznbznDeOXP7gowa33vN4k=62FC7FdKoOtWL9ZHs_rqr14+Hg@mail.gmail.com>

Hi Peter,

I cannot promise, but I will try to see how to improve
test_SeqIO_SeqXML.py. Meanwhile, another typo:

        if self.species is not None:
            if not isinstance(species, basestring):

should be:

        if self.species is not None:
            if not isinstance(*self.*species, basestring):



On 23 January 2014 15:11, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, Jan 23, 2014 at 2:55 PM, Alan <alanwilter at gmail.com> wrote:
> > In
> https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SeqXmlIO.py
> >
> > ...
> >
> >             attrs["sourceVersion"] = self.source_ersion
> >
> >
> > Alan
>
> Yes indeed, fixed - thank you:
>
> https://github.com/biopython/biopython/commit/0e23daf8d0d2ad9130479417d77147e794e182be
>
> This highlights that we could do with a few more unit tests on
> the annotation side of things in the SeqXML code:
>
> https://github.com/biopython/biopython/blob/master/Tests/test_SeqIO_SeqXML.py
>
> Regards,
>
> Peter
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588

From p.j.a.cock at googlemail.com  Sun Jan 26 08:18:47 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sun, 26 Jan 2014 13:18:47 +0000
Subject: [Biopython]
	=?windows-1252?q?typo_error_=93source=5Fersion=94_=2C?=
	=?windows-1252?q?_it_should_be_=93source=5Fversion=22?=
In-Reply-To: <CAEznbznDeOXP7gowa33vN4k=62FC7FdKoOtWL9ZHs_rqr14+Hg@mail.gmail.com>
References: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>
	<CAKVJ-_7WiNxq9nk=uQv=1rVRUA9pThj8oV=d+_NQMrFf2_1P2A@mail.gmail.com>
	<CAEznbznDeOXP7gowa33vN4k=62FC7FdKoOtWL9ZHs_rqr14+Hg@mail.gmail.com>
Message-ID: <CAKVJ-_7qBrCrOgFOkF_GoSpYgPEDtDkaJuC=-0R+=07uGR-g2Q@mail.gmail.com>

On Fri, Jan 24, 2014 at 1:50 PM, Alan <alanwilter at gmail.com> wrote:
> Hi Peter,
>
> I cannot promise, but I will try to see how to improve test_SeqIO_SeqXML.py.
> Meanwhile, another typo:
>
>         if self.species is not None:
>             if not isinstance(species, basestring):
>
> should be:
>
>         if self.species is not None:
>             if not isinstance(self.species, basestring):
>

Hi Alan,

That's fixed too now, thanks again:
https://github.com/biopython/biopython/commit/d06e85da15bae355219f1cfb767b93fb02d8130d

And I added a basic test which drew my attention to the fact that the
SeqXML parser was not fully compatible with the precedent set by
the plain text SwissProt and UniProt XML parsers (lists versus strings):
https://github.com/biopython/biopython/commit/91810c8acdd4d407b6820ef62cbf9fa591d9341d
https://github.com/biopython/biopython/commit/50f47b8a7e08be5e22f66be59f0eef23249d05e1

The SeqXML species stuff probably still needs more tests... in
particular chimeric records may cause trouble?

Regards,

Peter

From eyalarian at gmail.com  Tue Jan 28 13:42:44 2014
From: eyalarian at gmail.com (Eyal Arian)
Date: Tue, 28 Jan 2014 10:42:44 -0800
Subject: [Biopython] IMGT/HLA DB Access
Message-ID: <AE1743A2-0D79-408A-9541-350F47182DC2@gmail.com>

Hello,
I would like to access data directly from the imgt/hla database into BioPython: http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/align.cgi

For example, the following doesn't work, but it may give you the idea of what I am trying to do:
>>> import Bio
>>> from Bio import Entrez
>>> Entrez.email = "eyalarian at gmail.com"
>>> handle = Entrez.esearch(db="x-imgt-hla", term="DPB1*01:01:01")
>>> record = Entrez.read(handle) 
Traceback (most recent call last): 
File "<stdin>", line 1, in <module> 
File "Bio/Entrez/__init__.py", line 372, in read 
record = handler.read(handle) 
File "Bio/Entrez/Parser.py", line 187, in read 
self.parser.ParseFile(handle) 
File "Bio/Entrez/Parser.py", line 325, in endElementHandler 
raise RuntimeError(value) 
RuntimeError: Invalid db name specified: x-imgt-hla 

Thanks!
E. Arian

From djwinter at asu.edu  Tue Jan 28 17:00:53 2014
From: djwinter at asu.edu (David Winter)
Date: Tue, 28 Jan 2014 15:00:53 -0700
Subject: [Biopython] IMGT/HLA DB Access
In-Reply-To: <AE1743A2-0D79-408A-9541-350F47182DC2@gmail.com>
References: <AE1743A2-0D79-408A-9541-350F47182DC2@gmail.com>
Message-ID: <CAHYKzYY4trGVj=k=7GhwvSd_=Ceh+J3EJ8BraKWQ2mmODMsyXQ@mail.gmail.com>

Hi Eyal,

The Entrez module is specifically for the NCBI's entrez databases (the
likes of the nucleotide, refseq and pubmed), and won't work for others.

If the mgt/hla database has an API (a quick search around the site doesn't
find one) it might be possible to write your own code to access the
database programatically, but I don't think there in anything in Biopython
that will help you with actually querying the database or fetching records
from it.

David


On Tue, Jan 28, 2014 at 11:42 AM, Eyal Arian <eyalarian at gmail.com> wrote:

> Hello,
> I would like to access data directly from the imgt/hla database into
> BioPython: http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/align.cgi
>
> For example, the following doesn't work, but it may give you the idea of
> what I am trying to do:
> >>> import Bio
> >>> from Bio import Entrez
> >>> Entrez.email = "eyalarian at gmail.com"
> >>> handle = Entrez.esearch(db="x-imgt-hla", term="DPB1*01:01:01")
> >>> record = Entrez.read(handle)
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "Bio/Entrez/__init__.py", line 372, in read
> record = handler.read(handle)
> File "Bio/Entrez/Parser.py", line 187, in read
> self.parser.ParseFile(handle)
> File "Bio/Entrez/Parser.py", line 325, in endElementHandler
> raise RuntimeError(value)
> RuntimeError: Invalid db name specified: x-imgt-hla
>
> Thanks!
> E. Arian
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
David Winter
Postdoctoral Research Associate
Center for Evolutionary Medicine and Informatics
The Biodesign Institute
Arizona State University

ph: +1 480 519 5113
w: www.david-winter.info
lab: http://cartwrig.ht/lab/
blog: sciblogs.co.nz/the-atavism

From jordan.r.willis at Vanderbilt.Edu  Tue Jan 28 17:22:20 2014
From: jordan.r.willis at Vanderbilt.Edu (Willis, Jordan R)
Date: Tue, 28 Jan 2014 22:22:20 +0000
Subject: [Biopython] IMGT/HLA DB Access
In-Reply-To: <CAHYKzYY4trGVj=k=7GhwvSd_=Ceh+J3EJ8BraKWQ2mmODMsyXQ@mail.gmail.com>
References: <AE1743A2-0D79-408A-9541-350F47182DC2@gmail.com>
	<CAHYKzYY4trGVj=k=7GhwvSd_=Ceh+J3EJ8BraKWQ2mmODMsyXQ@mail.gmail.com>
Message-ID: <AC7D5B64FC829E429B0C96F7E3EE5AAD6A69E547@ITS-HCWNEM108.ds.vanderbilt.edu>

Hi Eyal,

The imgt database is not that dynamic to be honest. Will one download not suffice? You can get all the accession numbers from this table.

http://www.imgt.org/IMGTrepertoireMH/index.php?section=LocusGenes&repertoire=RepresentativeGenes#notes

I have been trying to get an IMGT api for years now. Unfortunately, you are just better off creating your own tools from scratch.



On Jan 28, 2014, at 4:00 PM, David Winter <djwinter at asu.edu<mailto:djwinter at asu.edu>> wrote:

Hi Eyal,

The Entrez module is specifically for the NCBI's entrez databases (the
likes of the nucleotide, refseq and pubmed), and won't work for others.

If the mgt/hla database has an API (a quick search around the site doesn't
find one) it might be possible to write your own code to access the
database programatically, but I don't think there in anything in Biopython
that will help you with actually querying the database or fetching records
from it.

David


On Tue, Jan 28, 2014 at 11:42 AM, Eyal Arian <eyalarian at gmail.com<mailto:eyalarian at gmail.com>> wrote:

Hello,
I would like to access data directly from the imgt/hla database into
BioPython: http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/align.cgi

For example, the following doesn't work, but it may give you the idea of
what I am trying to do:
import Bio
from Bio import Entrez
Entrez.email = "eyalarian at gmail.com<mailto:eyalarian at gmail.com>"
handle = Entrez.esearch(db="x-imgt-hla", term="DPB1*01:01:01")
record = Entrez.read(handle)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "Bio/Entrez/__init__.py", line 372, in read
record = handler.read(handle)
File "Bio/Entrez/Parser.py", line 187, in read
self.parser.ParseFile(handle)
File "Bio/Entrez/Parser.py", line 325, in endElementHandler
raise RuntimeError(value)
RuntimeError: Invalid db name specified: x-imgt-hla

Thanks!
E. Arian
_______________________________________________
Biopython mailing list  -  Biopython at lists.open-bio.org<mailto:Biopython at lists.open-bio.org>
http://lists.open-bio.org/mailman/listinfo/biopython




--
David Winter
Postdoctoral Research Associate
Center for Evolutionary Medicine and Informatics
The Biodesign Institute
Arizona State University

ph: +1 480 519 5113
w: www.david-winter.info<http://www.david-winter.info>
lab: http://cartwrig.ht/lab/
blog: sciblogs.co.nz/the-atavism<http://sciblogs.co.nz/the-atavism>
_______________________________________________
Biopython mailing list  -  Biopython at lists.open-bio.org<mailto:Biopython at lists.open-bio.org>
http://lists.open-bio.org/mailman/listinfo/biopython




From vivekraiiitkgp at gmail.com  Wed Jan 29 04:38:13 2014
From: vivekraiiitkgp at gmail.com (Vivek Rai)
Date: Wed, 29 Jan 2014 15:08:13 +0530
Subject: [Biopython] Where to start contributing in BioPython
Message-ID: <CAGetqtX+m6Eacczg7KjCRfZ4jjyBVZuc4wrSf+c0UA9WvAgvAQ@mail.gmail.com>

Hi everyone,

I am looking for opportunities to contribute into development of BioPython.
However, I could not find a suitable page which guides me in appropriate
direction. I may not be capable enough to start working directly into the
core modules. Therefore, I would request you all to suggest me how shall I
proceed to get introduced with the workings of BioPython, explore code and
may be start with fixing few smaller open bugs.

Secondly, the ideas or suggestions page for GSoC 2014 doesn't seems to be
active. If someone is having any idea about that, please let me know.

Thanks,

-- 
*Vivek Rai*
*Sophomore Undergraduate*

From p.j.a.cock at googlemail.com  Wed Jan 29 04:55:41 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jan 2014 09:55:41 +0000
Subject: [Biopython] Where to start contributing in BioPython
In-Reply-To: <CAGetqtX+m6Eacczg7KjCRfZ4jjyBVZuc4wrSf+c0UA9WvAgvAQ@mail.gmail.com>
References: <CAGetqtX+m6Eacczg7KjCRfZ4jjyBVZuc4wrSf+c0UA9WvAgvAQ@mail.gmail.com>
Message-ID: <CAKVJ-_768ij6c+faCzoTUV1dh5rZeM+XP-sYB948-v17NTFHTA@mail.gmail.com>

On Wed, Jan 29, 2014 at 9:38 AM, Vivek Rai <vivekraiiitkgp at gmail.com> wrote:
> Hi everyone,
>
> I am looking for opportunities to contribute into development of BioPython.
> However, I could not find a suitable page which guides me in appropriate
> direction. I may not be capable enough to start working directly into the
> core modules. Therefore, I would request you all to suggest me how shall I
> proceed to get introduced with the workings of BioPython, explore code and
> may be start with fixing few smaller open bugs.

Hi Vivek,

Are you doing any bioinformatics in your studies or work? Which general
area - for example sequences, alignments, phylogenetics, HMM, gene
expression, ... - that would be a good way to narrow your focus.

On the more technical side, do you know C or have an interest in
cross-platform development?

> Secondly, the ideas or suggestions page for GSoC 2014 doesn't seems to be
> active. If someone is having any idea about that, please let me know.

We (the OBF) should be making a formal announcement soon, but we
do intend to apply to be a Google Summer of Code mentoring organisation
again this year, and we should start brain-storming and discussing some
more possible project ideas on the biopython-dev mailing list.

Thanks for you interest,

Peter

From j.connolly at sheffield.ac.uk  Wed Jan 29 09:43:28 2014
From: j.connolly at sheffield.ac.uk (John Connolly)
Date: Wed, 29 Jan 2014 14:43:28 +0000
Subject: [Biopython] Problem running blastp
Message-ID: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>

Hi,

I am very new to Biopython and python, so please excuse me if this is a
very basic question.

I have installed Blast+, which runs fine from the command line. I have also
used Biopython to produce a program that parses xml output, which works
fine.

My problem is that I would like to run a local blast from within a python
program, tacked on to the start of my parsing program.

I have used the program in the tutorial:

from Bio.Blast.Applications import NcbiblastpCommandline

cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
remote=True)

cline
NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB', outfmt=5,
remote=True)
print(cline)
blastp -query seqs.txt -db NADB -outfmt 5 -remote
stdout, stderr = cline()

I don't expect any output, but I get the following:

  File "test.py", line 8
    blastp -query seqs.txt -db NADB -outfmt 5 -remote
                     ^
SyntaxError: invalid syntax


I appreciate any help you could give.

From p.j.a.cock at googlemail.com  Wed Jan 29 10:16:16 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jan 2014 15:16:16 +0000
Subject: [Biopython] Problem running blastp
In-Reply-To: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>
References: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>
Message-ID: <CAKVJ-_4+voJUR2k-_Wd70ueUBd05qg4Ev=LyeOYNPbudDjaESg@mail.gmail.com>

On Wed, Jan 29, 2014 at 2:43 PM, John Connolly
<j.connolly at sheffield.ac.uk> wrote:
> Hi,
>
> I am very new to Biopython and python, so please excuse me if this is a
> very basic question.
>
> I have installed Blast+, which runs fine from the command line. I have also
> used Biopython to produce a program that parses xml output, which works
> fine.
>
> My problem is that I would like to run a local blast from within a python
> program, tacked on to the start of my parsing program.
>
> I have used the program in the tutorial:
>
> from Bio.Blast.Applications import NcbiblastpCommandline
>
> cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
> remote=True)
>
> cline
> NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB', outfmt=5,
> remote=True)
> print(cline)
> blastp -query seqs.txt -db NADB -outfmt 5 -remote
> stdout, stderr = cline()
>
> I don't expect any output, but I get the following:
>
>   File "test.py", line 8
>     blastp -query seqs.txt -db NADB -outfmt 5 -remote
>                      ^
> SyntaxError: invalid syntax
>
>
> I appreciate any help you could give.

This is not a Python command:

blastp -query seqs.txt -db NADB -outfmt 5 -remote

I think you've got a line of sample output inside your Python script,
try reducing it to just these four lines:

from Bio.Blast.Applications import NcbiblastpCommandline
cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
remote=True)
print(cline) # optionally print out what it will run...
stdout, stderr = cline() # run the BLAST

Regards,

Peter

From j.connolly at sheffield.ac.uk  Wed Jan 29 11:26:53 2014
From: j.connolly at sheffield.ac.uk (John Connolly)
Date: Wed, 29 Jan 2014 16:26:53 +0000
Subject: [Biopython] Problem running blastp
In-Reply-To: <CAKVJ-_4+voJUR2k-_Wd70ueUBd05qg4Ev=LyeOYNPbudDjaESg@mail.gmail.com>
References: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>
	<CAKVJ-_4+voJUR2k-_Wd70ueUBd05qg4Ev=LyeOYNPbudDjaESg@mail.gmail.com>
Message-ID: <CAFV3WFv29nUHg7kRtW0=k0yJ_j5m0PPXNPaS7zrE3oS+XrRZKg@mail.gmail.com>

Hi Peter,

Thank you for your reply.

I realised that the line you mentioned was unnecessary after I'd sent the
message, but I didn't know how to update the mailing list. Sorry about that.

Here's the program after I've modified it a little:

"from Bio.Blast.Applications import NcbiblastpCommandline

cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5)

cline
NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB', outfmt=5)
print(cline)
#blastp -query seqs.txt -db NADB -outfmt 5 -remote
stdout, stderr = cline()"

It runs fine, but I thought I knew how to assign the results of the blast
to a file_handle, which I could then parse. I thought that the results
would be in cline(). I know how to get the results to a file, but I would
like to parse them in the same program (I have a parsing program that does
exactly what I need).



On 29 January 2014 15:16, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Jan 29, 2014 at 2:43 PM, John Connolly
> <j.connolly at sheffield.ac.uk> wrote:
> > Hi,
> >
> > I am very new to Biopython and python, so please excuse me if this is a
> > very basic question.
> >
> > I have installed Blast+, which runs fine from the command line. I have
> also
> > used Biopython to produce a program that parses xml output, which works
> > fine.
> >
> > My problem is that I would like to run a local blast from within a python
> > program, tacked on to the start of my parsing program.
> >
> > I have used the program in the tutorial:
> >
> > from Bio.Blast.Applications import NcbiblastpCommandline
> >
> > cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
> > remote=True)
> >
> > cline
> > NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB',
> outfmt=5,
> > remote=True)
> > print(cline)
> > blastp -query seqs.txt -db NADB -outfmt 5 -remote
> > stdout, stderr = cline()
> >
> > I don't expect any output, but I get the following:
> >
> >   File "test.py", line 8
> >     blastp -query seqs.txt -db NADB -outfmt 5 -remote
> >                      ^
> > SyntaxError: invalid syntax
> >
> >
> > I appreciate any help you could give.
>
> This is not a Python command:
>
> blastp -query seqs.txt -db NADB -outfmt 5 -remote
>
> I think you've got a line of sample output inside your Python script,
> try reducing it to just these four lines:
>
> from Bio.Blast.Applications import NcbiblastpCommandline
> cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
> remote=True)
> print(cline) # optionally print out what it will run...
> stdout, stderr = cline() # run the BLAST
>
> Regards,
>
> Peter
>

From p.j.a.cock at googlemail.com  Wed Jan 29 11:33:11 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jan 2014 16:33:11 +0000
Subject: [Biopython] Problem running blastp
In-Reply-To: <CAFV3WFv29nUHg7kRtW0=k0yJ_j5m0PPXNPaS7zrE3oS+XrRZKg@mail.gmail.com>
References: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>
	<CAKVJ-_4+voJUR2k-_Wd70ueUBd05qg4Ev=LyeOYNPbudDjaESg@mail.gmail.com>
	<CAFV3WFv29nUHg7kRtW0=k0yJ_j5m0PPXNPaS7zrE3oS+XrRZKg@mail.gmail.com>
Message-ID: <CAKVJ-_7+VNz3V2bRU1+PszNfJbR=8LXW+HXc5hEGNg2-i8jAkA@mail.gmail.com>

On Wed, Jan 29, 2014 at 4:26 PM, John Connolly
<j.connolly at sheffield.ac.uk> wrote:
> Hi Peter,
>
> Thank you for your reply.
>
> I realised that the line you mentioned was unnecessary after I'd sent the
> message, but I didn't know how to update the mailing list. Sorry about that.
>
> Here's the program after I've modified it a little:
>
> "from Bio.Blast.Applications import NcbiblastpCommandline
>
> cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5)
>
> cline
> NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB', outfmt=5)
> print(cline)
> #blastp -query seqs.txt -db NADB -outfmt 5 -remote
> stdout, stderr = cline()"
>
> It runs fine, but I thought I knew how to assign the results of the blast to
> a file_handle, which I could then parse. I thought that the results would be
> in cline(). I know how to get the results to a file, but I would like to
> parse them in the same program (I have a parsing program that does exactly
> what I need).

As written, BLAST's output will be sent to stdout (default behaviour),
and therefore captured as a (potentially large) string. You could turn
this into a handle with StringIO:

from io import StringIO
handle = StringIO(stdout)

Don't use this StringIO approach for large output - it will waste
a lot of memory.

What I would normally do is ask BLAST to save the output to
a file, and open the file for reading to get a handle.

This also means you can separate running BLAST (usually slow)
and processing the output (usually fast, but I find I often need
to adjust the code so I'd want to repeat this bit many times while
working on the code - without having to rerun BLAST each time).

Peter

From eric.talevich at gmail.com  Wed Jan 29 16:29:02 2014
From: eric.talevich at gmail.com (Eric Talevich)
Date: Wed, 29 Jan 2014 13:29:02 -0800
Subject: [Biopython] Google Summer of Code 2014 - Call for project ideas
Message-ID: <CAMC681ktJLOjcS746YB3MwCb534rZvfk87p-HGVdyt3Le=Y2RQ@mail.gmail.com>

Hi folks,

Google Summer of Code is on again for 2014, and the Open Bioinformatics
Foundation (OBF) is once again applying as a mentoring organization.
Participating in GSoC as an organization is very competitive, and we will
need your help in gathering a good set of ideas and potential mentors for
Biopython's role in GSoC this year.

If you have an idea for a Summer of Code project, please post your idea
here on the Biopython mailing list for discussion and start an outline on
this wiki page:
http://biopython.org/wiki/Google_Summer_of_Code

We also welcome ideas that fit with OBF's mission but are not part of a
single Bio* project, or span multiple projects -- these ideas can be posted
on the OBF wiki and discussed on the OBF mailing list:
http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Here's to another fun and productive Summer of Code!

Cheers,
Eric & Raoul

From p.j.a.cock at googlemail.com  Fri Jan 31 05:55:55 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 31 Jan 2014 10:55:55 +0000
Subject: [Biopython] Google Summer of Code 2014 - Call for project ideas
In-Reply-To: <CAMC681ktJLOjcS746YB3MwCb534rZvfk87p-HGVdyt3Le=Y2RQ@mail.gmail.com>
References: <CAMC681ktJLOjcS746YB3MwCb534rZvfk87p-HGVdyt3Le=Y2RQ@mail.gmail.com>
Message-ID: <CAKVJ-_7wV2JD2=Lbjem1WDW6e=eO=W6x4KOHxJh0zuVyNrsrVw@mail.gmail.com>

On Wed, Jan 29, 2014 at 9:29 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> Hi folks,
>
> Google Summer of Code is on again for 2014, and the Open Bioinformatics
> Foundation (OBF) is once again applying as a mentoring organization.
> Participating in GSoC as an organization is very competitive, and we will
> need your help in gathering a good set of ideas and potential mentors for
> Biopython's role in GSoC this year.
>
> If you have an idea for a Summer of Code project, please post your idea
> here on the Biopython mailing list for discussion and start an outline on
> this wiki page:
> http://biopython.org/wiki/Google_Summer_of_Code
>
> We also welcome ideas that fit with OBF's mission but are not part of a
> single Bio* project, or span multiple projects -- these ideas can be posted
> on the OBF wiki and discussed on the OBF mailing list:
> http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>
> Here's to another fun and productive Summer of Code!
>
> Cheers,
> Eric & Raoul

Thanks Eric & Raoul,

Remember that the ideas don't have to come from potential mentors -
if as a student there is something you'd particularly like to work on
please ask, and perhaps we can find a suitable (Biopython) mentor.

Regards,

Peter

From darkarcanis at mail.ru  Sun Jan 12 14:04:59 2014
From: darkarcanis at mail.ru (Evgeniy Alekseev)
Date: Sun, 12 Jan 2014 18:04:59 +0400
Subject: [Biopython] Biopython packages in Archlinux
Message-ID: <1427507.T7rLfSDXj6@arcanis>

Hello everyone,

First, thank you for developing this useful module.

I'm one of Archlinux Trusted User [1]. Today I moved packages python-biopython 
and python2-biopython which provide biopython module in Archlinux from user 
repository (AUR) into official ([community]) [2] and will maintain it.

I want ask someone, who can do it, to edit wiki page [3] and add something 
like that:
-----------------wiki text------------------------
Archlinux
Biopython is avaible in an official repository. The package named python-
biopython (for python3) or python2-biopython (for python2) and they can be 
installed using pacman:
   pacman -S python-biopython
or
   pacman -S python2-biopython
-----------------wiki text------------------------

Thank you!

Also if you have an additional request feel free to contact me and ask it.

Links:
[1] https://wiki.archlinux.org/index.php/Trusted%20Users
[2] https://www.archlinux.org/packages/biopython
[3] http://biopython.org/wiki/Download
-- 
? ?????????, ?.????????.
Sincerely yours, E.Alekseev.

e-mail: darkarcanis at mail.ru
ICQ: 407-398-235
Jabber: arcanis at jabber.ru
-------------- next part --------------
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From eric.talevich at gmail.com  Mon Jan 13 02:43:54 2014
From: eric.talevich at gmail.com (Eric Talevich)
Date: Sun, 12 Jan 2014 18:43:54 -0800
Subject: [Biopython] Biopython packages in Archlinux
In-Reply-To: <1427507.T7rLfSDXj6@arcanis>
References: <1427507.T7rLfSDXj6@arcanis>
Message-ID: <CAMC681=KFeKr1JaFXfvTniEJiFZZnJnouiu3WvD9jBatRxkWaw@mail.gmail.com>

On Sun, Jan 12, 2014 at 6:04 AM, Evgeniy Alekseev <darkarcanis at mail.ru>wrote:

> Hello everyone,
>
> First, thank you for developing this useful module.
>
> I'm one of Archlinux Trusted User [1]. Today I moved packages
> python-biopython
> and python2-biopython which provide biopython module in Archlinux from user
> repository (AUR) into official ([community]) [2] and will maintain it.
>
> I want ask someone, who can do it, to edit wiki page [3] and add something
> like that:
> -----------------wiki text------------------------
> Archlinux
> Biopython is avaible in an official repository. The package named python-
> biopython (for python3) or python2-biopython (for python2) and they can be
> installed using pacman:
>    pacman -S python-biopython
> or
>    pacman -S python2-biopython
> -----------------wiki text------------------------
>
> Thank you!
>
> Also if you have an additional request feel free to contact me and ask it.
>
> Links:
> [1] https://wiki.archlinux.org/index.php/Trusted%20Users
> [2] https://www.archlinux.org/packages/biopython
> [3] http://biopython.org/wiki/Download
> --
> ? ?????????, ?.????????.
> Sincerely yours, E.Alekseev.
>

Thanks for creating these packages, Evgeniy. I've added an edited version
of your notes to the wiki here:
http://biopython.org/wiki/Download#Archlinux

Cheers,
Eric



From mike.thon at gmail.com  Mon Jan 13 15:09:41 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Mon, 13 Jan 2014 16:09:41 +0100
Subject: [Biopython] iterating over FeatureLocation
Message-ID: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>

I need to iterate over all the features of a sequence, and then iterate over the locations/sublocations in each feature.  I?m not sure how to work with the sublocations though:

I need to do something like this:

for feat in seq.features:
	for loc in feat.locations:
		start = loc.start
		?

which does not work but maybe shows what I need to do.  Can anyone help me out?


From p.j.a.cock at googlemail.com  Mon Jan 13 15:38:54 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 13 Jan 2014 15:38:54 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
Message-ID: <CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>

On Mon, Jan 13, 2014 at 3:09 PM, Michael Thon <mike.thon at gmail.com> wrote:
> I need to iterate over all the features of a sequence, and then
> iterate over the locations/sublocations in each feature.  I?m not
> sure how to work with the sublocations though:
>
> I need to do something like this:
>
> for feat in seq.features:
>         for loc in feat.locations:
>                 start = loc.start
>                 ?
>
> which does not work but maybe shows what I need to do.
> Can anyone help me out?

Are you talking about join locations? Could you give an example
(e.g. link to a GenBank file) and what you want to look at?

Peter

P.S. This changed a bit back in Biopython 1.62 with the introduction
of the CompoundLocation object.



From mike.thon at gmail.com  Mon Jan 13 16:07:45 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Mon, 13 Jan 2014 17:07:45 +0100
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
Message-ID: <D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>

Here are two examples from the GenBank format file (not from GenBank though)


     CDS             order(6621..6658,6739..6985)
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_14847-RA:cds"
                     /label=?CDS"

     CDS             419..2374
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_05899-RA:cds"
                     /label=?CDS"

if the feature is a simple feature, then I just need to access its start and end.  If its a compound feature then I need to iterate over each segment, accessing the start and end.

What I am doing at the moment is this:

if feat._sub_features:
	for sf in feat.sub_features:
		start = sf.location.start
		?
else:
	start = feat.location.start
	?

it works, I think.  Is there a better way?

Also, is there an easy way to get the sequence represented by the seqfeature, if it is made up of CompoundLocations?  These features are CDSs where each sub-feature is an exon.  I need to splice them all together and get the translation.

Thanks

On Jan 13, 2014, at 4:38 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Jan 13, 2014 at 3:09 PM, Michael Thon <mike.thon at gmail.com> wrote:
>> I need to iterate over all the features of a sequence, and then
>> iterate over the locations/sublocations in each feature.  I?m not
>> sure how to work with the sublocations though:
>> 
>> I need to do something like this:
>> 
>> for feat in seq.features:
>>        for loc in feat.locations:
>>                start = loc.start
>>                ?
>> 
>> which does not work but maybe shows what I need to do.
>> Can anyone help me out?
> 
> Are you talking about join locations? Could you give an example
> (e.g. link to a GenBank file) and what you want to look at?
> 
> Peter
> 
> P.S. This changed a bit back in Biopython 1.62 with the introduction
> of the CompoundLocation object.




From p.j.a.cock at googlemail.com  Mon Jan 13 16:18:01 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 13 Jan 2014 16:18:01 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
Message-ID: <CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>

On Mon, Jan 13, 2014 at 4:07 PM, Michael Thon <mike.thon at gmail.com> wrote:
> Here are two examples from the GenBank format file (not from GenBank though)
>
>
>      CDS             order(6621..6658,6739..6985)
>                      /Source="maker"
>                      /codon_start=1
>                      /ID="CFIO01_14847-RA:cds"
>                      /label=?CDS"
>
>      CDS             419..2374
>                      /Source="maker"
>                      /codon_start=1
>                      /ID="CFIO01_05899-RA:cds"
>                      /label=?CDS"
>
> if the feature is a simple feature, then I just need to access its start and end.
> If its a compound feature then I need to iterate over each segment, accessing the start and end.
>
> What I am doing at the moment is this:
>
> if feat._sub_features:
>         for sf in feat.sub_features:
>                 start = sf.location.start
>                 ?
> else:
>         start = feat.location.start
>         ?
>
> it works, I think.  Is there a better way?

Don't do that :) Python variables/methods/etc starting with a single
underscore are by convention private and should not generally be
used. In this case, ._sub_features is an internal detail for the behind
the scenes backwards compatibility for the now deprecated property
.sub_features (don't use that either).

Instead use the location object itself directly, it now holds any
sub-location information using a CompoundLocation object.
See the .parts attribute, which gives a list of simple locations.

e.g.

for part in feat.location.parts:
    start = part.start
    ...

>
> Also, is there an easy way to get the sequence represented by the seqfeature,
> if it is made up of CompoundLocations?  These features are CDSs where each
> sub-feature is an exon.  I need to splice them all together and get the translation.
>

Yes, where `feat` is a SubFeature object use `feat.extract(the_parent_sequence)`
to get the spliced sequence, which you can then translate. See the section
"Sequence described by a feature or location" in the Tutorial,

http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

On reflection, the Tutorial could do with a bit more detail on how to use
a CompoundLocation, but I did try to cover this in the docstrings.

Regards,

Peter



From jere_2001 at ig.com.br  Tue Jan 14 03:04:42 2014
From: jere_2001 at ig.com.br (Jeremias Ponciano da Silva)
Date: Tue, 14 Jan 2014 01:04:42 -0200
Subject: [Biopython] Monte Carlo Simulation
Message-ID: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>

Hi people!
I'm doing a Monte Carlo Simulation, must take a DNA sequence and this
sequence can randomize N times, and with these seguencias plot on a Normal
chart monte carlo simulation, one would have any suggestions?

-- 
*Jeremias Ponciano*


From mike.thon at gmail.com  Tue Jan 14 10:20:00 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Tue, 14 Jan 2014 11:20:00 +0100
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
Message-ID: <AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>

Hi Peter - Thanks for your help.  Here is another problem.  Here is the block of features in my GenBank file for a gene:

     gene            complement(1..588)
                     /Source="maker"
                     /ID="CFIO01_14176"
                     /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
                     -gene-0.30"
                     /label="CFIO01_14176"
     CDS             order(complement(200..588),complement(1..124))
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_14176-RA:cds"
                     /label="CDS"
     mRNA            complement(1..588)
                     /Source="maker"
                     /ID="CFIO01_14176-RA"
                     /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
                     -gene-0.30-mRNA-1"
                     /_AED="0.06"
                     /_QI="0|0|0|1|1|1|2|0|171"
                     /_eAED="0.06"
                     /label="CFIO01_14176-RA"
 
Now, here is the CDS feature after is was parsed by BioPython:

                    
(Pdb) feat.location.parts
[FeatureLocation(ExactPosition(0), ExactPosition(124), strand=-1), FeatureLocation(ExactPosition(199), ExactPosition(588), strand=-1)]

Note that two positions have changed.  The CDS segments are (complement(200..588),complement(1..124)) but the positions in SeqFeature object are 0..124 and 199..588

I checked some other features too and it looks like BioPython adds 1 to the start of each segment.  For the features on the complementary strand it subtracts 1.  

When I translate the feature into a protein sequence like this: str(feat.extract(seq).seq.translate()) , the sequence is correct so this must not be a bug. so, how to I access the exact values that are in the genbank formatted file?  

On Jan 13, 2014, at 5:18 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Jan 13, 2014 at 4:07 PM, Michael Thon <mike.thon at gmail.com> wrote:
>> Here are two examples from the GenBank format file (not from GenBank though)
>> 
>> 
>>     CDS             order(6621..6658,6739..6985)
>>                     /Source="maker"
>>                     /codon_start=1
>>                     /ID="CFIO01_14847-RA:cds"
>>                     /label=?CDS"
>> 
>>     CDS             419..2374
>>                     /Source="maker"
>>                     /codon_start=1
>>                     /ID="CFIO01_05899-RA:cds"
>>                     /label=?CDS"
>> 
>> if the feature is a simple feature, then I just need to access its start and end.
>> If its a compound feature then I need to iterate over each segment, accessing the start and end.
>> 
>> What I am doing at the moment is this:
>> 
>> if feat._sub_features:
>>        for sf in feat.sub_features:
>>                start = sf.location.start
>>                ?
>> else:
>>        start = feat.location.start
>>        ?
>> 
>> it works, I think.  Is there a better way?
> 
> Don't do that :) Python variables/methods/etc starting with a single
> underscore are by convention private and should not generally be
> used. In this case, ._sub_features is an internal detail for the behind
> the scenes backwards compatibility for the now deprecated property
> .sub_features (don't use that either).
> 
> Instead use the location object itself directly, it now holds any
> sub-location information using a CompoundLocation object.
> See the .parts attribute, which gives a list of simple locations.
> 
> e.g.
> 
> for part in feat.location.parts:
>    start = part.start
>    ...
> 
>> 
>> Also, is there an easy way to get the sequence represented by the seqfeature,
>> if it is made up of CompoundLocations?  These features are CDSs where each
>> sub-feature is an exon.  I need to splice them all together and get the translation.
>> 
> 
> Yes, where `feat` is a SubFeature object use `feat.extract(the_parent_sequence)`
> to get the spliced sequence, which you can then translate. See the section
> "Sequence described by a feature or location" in the Tutorial,
> 
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
> 
> On reflection, the Tutorial could do with a bit more detail on how to use
> a CompoundLocation, but I did try to cover this in the docstrings.
> 
> Regards,
> 
> Peter




From mike.thon at gmail.com  Tue Jan 14 10:25:56 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Tue, 14 Jan 2014 11:25:56 +0100
Subject: [Biopython] Monte Carlo Simulation
In-Reply-To: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>
References: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>
Message-ID: <F31ABAEC-5C0B-49CD-8DE8-E8D1A3C06CB0@gmail.com>

Check out:
http://stackoverflow.com/questions/976882/shuffling-a-list-of-objects-in-python

Something like this should work:

from random import shuffle

x = ?GCAT?
s = list(x)
shuffle(s)


On Jan 14, 2014, at 4:04 AM, Jeremias Ponciano da Silva <jere_2001 at ig.com.br> wrote:

> Hi people!
> I'm doing a Monte Carlo Simulation, must take a DNA sequence and this
> sequence can randomize N times, and with these seguencias plot on a Normal
> chart monte carlo simulation, one would have any suggestions?
> 
> -- 
> *Jeremias Ponciano*
> _______________________________________________
> 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  Tue Jan 14 11:18:12 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 14 Jan 2014 11:18:12 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
	<AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
Message-ID: <CAKVJ-_7m4JQtnQj=jMa=Yyy4RQHW2SmrQkxbMyzOucWwT-3vHw@mail.gmail.com>

On Tue, Jan 14, 2014 at 10:20 AM, Michael Thon <mike.thon at gmail.com> wrote:
> Hi Peter - Thanks for your help.  Here is another problem.  Here is the
> block of features in my GenBank file for a gene:
>
>      gene            complement(1..588)
>                      /Source="maker"
>                      /ID="CFIO01_14176"
>
> /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
>                      -gene-0.30"
>                      /label="CFIO01_14176"
>      CDS             order(complement(200..588),complement(1..124))
>                      /Source="maker"
>                      /codon_start=1
>                      /ID="CFIO01_14176-RA:cds"
>                      /label="CDS"
>      mRNA            complement(1..588)
>                      /Source="maker"
>                      /ID="CFIO01_14176-RA"
>
> /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
>                      -gene-0.30-mRNA-1"
>                      /_AED="0.06"
>                      /_QI="0|0|0|1|1|1|2|0|171"
>                      /_eAED="0.06"
>                      /label="CFIO01_14176-RA"
>
> Now, here is the CDS feature after is was parsed by BioPython:
>
>
> (Pdb) feat.location.parts
> [FeatureLocation(ExactPosition(0), ExactPosition(124), strand=-1),
> FeatureLocation(ExactPosition(199), ExactPosition(588), strand=-1)]
>
> Note that two positions have changed.  The CDS segments are
> (complement(200..588),complement(1..124)) but the positions in SeqFeature
> object are 0..124 and 199..588
>
> I checked some other features too and it looks like BioPython adds 1 to the
> start of each segment.  For the features on the complementary strand it
> subtracts 1.

Not quite, no.

The Biopython SeqFeature location system uses Python counting as
in string slicing etc. This means that effectively all the start coordinates
you see are one less than the start coordinates in GenBank/EMBL
format files.

> When I translate the feature into a protein sequence like this:
> str(feat.extract(seq).seq.translate()) , the sequence is correct so this
> must not be a bug. so, how to I access the exact values that are in the
> genbank formatted file?

You must convert back from Python counting to GenBank/EMBL counting,

location.start + 1
location.end

However, for many things the Python counting is more natural once
you are used to it ;)

Peter


From jere_2001 at ig.com.br  Tue Jan 14 18:57:16 2014
From: jere_2001 at ig.com.br (Jeremias Ponciano da Silva)
Date: Tue, 14 Jan 2014 16:57:16 -0200
Subject: [Biopython] Monte Carlo Simulation
In-Reply-To: <F31ABAEC-5C0B-49CD-8DE8-E8D1A3C06CB0@gmail.com>
References: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>
	<F31ABAEC-5C0B-49CD-8DE8-E8D1A3C06CB0@gmail.com>
Message-ID: <CADtZUJ7aMiDWcx1jOQ6zRbJNtgbhT+p+whOfs8JX6yB4bgs1=w@mail.gmail.com>

Hi guys!
Thanks for the replies.
I can do randomization, even my biggest problem is how to make a plot of
Monte Carlo with the data I already have.


2014/1/14 Michael Thon <mike.thon at gmail.com>

> Check out:
>
> http://stackoverflow.com/questions/976882/shuffling-a-list-of-objects-in-python
>
> Something like this should work:
>
> from random import shuffle
>
> x = ?GCAT?
> s = list(x)
> shuffle(s)
>
>
> On Jan 14, 2014, at 4:04 AM, Jeremias Ponciano da Silva <
> jere_2001 at ig.com.br> wrote:
>
> > Hi people!
> > I'm doing a Monte Carlo Simulation, must take a DNA sequence and this
> > sequence can randomize N times, and with these seguencias plot on a
> Normal
> > chart monte carlo simulation, one would have any suggestions?
> >
> > --
> > *Jeremias Ponciano*
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
>
>


-- 
*Jeremias Ponciano*



From jere_2001 at ig.com.br  Tue Jan 14 19:41:24 2014
From: jere_2001 at ig.com.br (Jeremias Ponciano da Silva)
Date: Tue, 14 Jan 2014 17:41:24 -0200
Subject: [Biopython] Monte Carlo Simulation
In-Reply-To: <CADWfS5pux5+Qe7CmeKw5kdVYj==cz+HBaeS_N+xT0-UBFPHptg@mail.gmail.com>
References: <CADtZUJ7yA6xD4EH5Xfd_K681xAOj_9qVWNhuKc=BcPB=Tu64-Q@mail.gmail.com>
	<F31ABAEC-5C0B-49CD-8DE8-E8D1A3C06CB0@gmail.com>
	<CADtZUJ7aMiDWcx1jOQ6zRbJNtgbhT+p+whOfs8JX6yB4bgs1=w@mail.gmail.com>
	<CADWfS5pux5+Qe7CmeKw5kdVYj==cz+HBaeS_N+xT0-UBFPHptg@mail.gmail.com>
Message-ID: <CADtZUJ5631fGFx2k_6dk9NSmEjyg-tU-r7V7U61JRw6kyWZRHQ@mail.gmail.com>

Thanks Jared for the reply.
Seek a similarity of DNA, for example with the blast, getting this similar
sequence, eg 70%, I got to take this sequence, and do a test to see if it
is significant or not, making the randomization of this sample obtained, I
thought to do with Monte Carlo test to see if this within the normal 95% or
beyond 5%, which is what I seek.


2014/1/14 Jared Adolf-Bryfogle <jadolfbr at gmail.com>

> I think the distribution of your simulation will always be random - No
> monte carlo.  I'm not sure the problem your trying to solve.  If you want a
> monte carlo - based design algorithm on a structure, then you can try
> Rosetta:  https://www.rosettacommons.org/ (but I'm not sure if it does
> DNA design).
>
> Do you mean the combinations of sequences you get out?  Basically in
> either of these cases, the more times you choose a sequence, the more you
> sample the sequence space - however - your distribution will always be
> random, in that some sequences are not preferred.  Monte carlo is useful
> when you have a very large space to sample from, some constraints (such as
> a design algorithm and a dna structure), and you want to sample the range
> of possibilities.  In your case, you have no constraints, so,
> unfortunately, the result has no meaning...
>
> I would go back and see if Monte Carlo is what you really want?
>
>
> Jared Adolf-Bryfogle
> PhD Candidate
> Lab of Dr. Roland Dunbrack
> FCCC/DrexelMed
>
>
>
>
> On Tue, Jan 14, 2014 at 1:57 PM, Jeremias Ponciano da Silva <
> jere_2001 at ig.com.br> wrote:
>
>> Hi guys!
>> Thanks for the replies.
>> I can do randomization, even my biggest problem is how to make a plot of
>> Monte Carlo with the data I already have.
>>
>>
>> 2014/1/14 Michael Thon <mike.thon at gmail.com>
>>
>> > Check out:
>> >
>> >
>> http://stackoverflow.com/questions/976882/shuffling-a-list-of-objects-in-python
>> >
>> > Something like this should work:
>> >
>> > from random import shuffle
>> >
>> > x = ?GCAT?
>> > s = list(x)
>> > shuffle(s)
>> >
>> >
>> > On Jan 14, 2014, at 4:04 AM, Jeremias Ponciano da Silva <
>> > jere_2001 at ig.com.br> wrote:
>> >
>> > > Hi people!
>> > > I'm doing a Monte Carlo Simulation, must take a DNA sequence and this
>> > > sequence can randomize N times, and with these seguencias plot on a
>> > Normal
>> > > chart monte carlo simulation, one would have any suggestions?
>> > >
>> > > --
>> > > *Jeremias Ponciano*
>> > > _______________________________________________
>> > > Biopython mailing list  -  Biopython at lists.open-bio.org
>> > > http://lists.open-bio.org/mailman/listinfo/biopython
>> >
>> >
>>
>>
>> --
>> *Jeremias Ponciano*
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>


-- 
*Jeremias Ponciano*



From debruinjj at gmail.com  Thu Jan 16 11:48:47 2014
From: debruinjj at gmail.com (Jurgens de Bruin)
Date: Thu, 16 Jan 2014 13:48:47 +0200
Subject: [Biopython] Bio.PDB.PDBParser() Superimposer()
Message-ID: <CAMrqo6zww=ftqVOUCbYn=A3JUtnYWC3aciiCd2eJVfOccYXR-A@mail.gmail.com>

Hi,

I am trying to calculate the RMS for two pdb files but the proteins differ
in length. Currently I want to exclude the leading/trailing parts of the
longer sequence but I am having difficulty figuring out how I will be able
to do this.

Any help would be appreciated.


-- 
Regards/Groete/Mit freundlichen Gr??en/recuerdos/meilleures salutations/
distinti saluti/siong/du? y?/??????

Jurgens de Bruin



From anaryin at gmail.com  Thu Jan 16 11:59:43 2014
From: anaryin at gmail.com (=?UTF-8?Q?Jo=C3=A3o_Rodrigues?=)
Date: Thu, 16 Jan 2014 12:59:43 +0100
Subject: [Biopython] Bio.PDB.PDBParser() Superimposer()
In-Reply-To: <CAMrqo6zww=ftqVOUCbYn=A3JUtnYWC3aciiCd2eJVfOccYXR-A@mail.gmail.com>
References: <CAMrqo6zww=ftqVOUCbYn=A3JUtnYWC3aciiCd2eJVfOccYXR-A@mail.gmail.com>
Message-ID: <CAJ9sUYN01JGb+TxKPVRt8PGaXXjgD33_TRLxycAWwxNfkVws7A@mail.gmail.com>

Hi Jurgens,

When you pass the two sequences to the Superimposer I guess you can trim
the sequence to that which you want (pass a list of residues that is sliced
to those that you want to include). The only requirement would be that both
have the same number of atoms.

If this doesn't make much sense I can give an example with code.

Cheers,

Jo?o


2014/1/16 Jurgens de Bruin <debruinjj at gmail.com>

> Hi,
>
> I am trying to calculate the RMS for two pdb files but the proteins differ
> in length. Currently I want to exclude the leading/trailing parts of the
> longer sequence but I am having difficulty figuring out how I will be able
> to do this.
>
> Any help would be appreciated.
>
>
> --
> Regards/Groete/Mit freundlichen Gr??en/recuerdos/meilleures salutations/
> distinti saluti/siong/du? y?/??????
>
> Jurgens de Bruin
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



From debruinjj at gmail.com  Thu Jan 16 12:18:28 2014
From: debruinjj at gmail.com (Jurgens de Bruin)
Date: Thu, 16 Jan 2014 14:18:28 +0200
Subject: [Biopython] Bio.PDB.PDBParser() Superimposer()
In-Reply-To: <CAJ9sUYN01JGb+TxKPVRt8PGaXXjgD33_TRLxycAWwxNfkVws7A@mail.gmail.com>
References: <CAMrqo6zww=ftqVOUCbYn=A3JUtnYWC3aciiCd2eJVfOccYXR-A@mail.gmail.com>
	<CAJ9sUYN01JGb+TxKPVRt8PGaXXjgD33_TRLxycAWwxNfkVws7A@mail.gmail.com>
Message-ID: <CAMrqo6zSgOZFWJ3ZSBtEOTTGRbch6dShw4gtUpYBD7ZpxjEVvA@mail.gmail.com>

Hi Jo?o Rodrigues,

Thanks for the reply much appreciated, this does make sense but I would
greatly appreciate examples with some code.

Thanks


On 16 January 2014 13:59, Jo?o Rodrigues <anaryin at gmail.com> wrote:

> Hi Jurgens,
>
> When you pass the two sequences to the Superimposer I guess you can trim
> the sequence to that which you want (pass a list of residues that is sliced
> to those that you want to include). The only requirement would be that both
> have the same number of atoms.
>
> If this doesn't make much sense I can give an example with code.
>
> Cheers,
>
> Jo?o
>
>
> 2014/1/16 Jurgens de Bruin <debruinjj at gmail.com>
>
>> Hi,
>>
>> I am trying to calculate the RMS for two pdb files but the proteins differ
>> in length. Currently I want to exclude the leading/trailing parts of the
>> longer sequence but I am having difficulty figuring out how I will be able
>> to do this.
>>
>> Any help would be appreciated.
>>
>>
>> --
>> Regards/Groete/Mit freundlichen Gr??en/recuerdos/meilleures salutations/
>> distinti saluti/siong/du? y?/??????
>>
>> Jurgens de Bruin
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>


-- 
Regards/Groete/Mit freundlichen Gr??en/recuerdos/meilleures salutations/
distinti saluti/siong/du? y?/??????

Jurgens de Bruin



From ishengomae at nm-aist.ac.tz  Fri Jan 17 07:11:41 2014
From: ishengomae at nm-aist.ac.tz (Edson Ishengoma)
Date: Fri, 17 Jan 2014 10:11:41 +0300
Subject: [Biopython] How to run PAL2NAL commandline via python
Message-ID: <CAKoVMyn1iLRQMffc5xvPb9HSs8e+YD180Yc20ApP9MjGhjmTFQ@mail.gmail.com>

Dear all,

I recently was introduced to pal2nal as a convenient tool to convert
aligned protein residues (from tblastn, for example) back to their original
nucleotide sequences. My boss suggested I use a python or perl script to
call the tool and feed the resulting nucleotide alignments to the 'codeml'
program to calculate Ka, Ks.

I don't know perl, so I would like to know how to do this from python -- a
python script which includes the way to feed the resulting codon alignments
to  PAML for "codeml" program to calculate Ka, Ks values.

I tried to check for the pre-existence of  Biopython wrapper for Pal2Nal I
didnt see one. I am on linux machine (Ubuntu 13.04) and my installed python
is Python 2.7.4.
I tried this script which I expected to produce a file containing aligned
nucleotide sequences. But no error message is shown but it outputs an empty
file (nothing written on the file).

import os
> my_pal2nal = os.path.join(os.getcwd(), 'pal2nal.v14')
> my_prot_file = os.path.join(os.getcwd(), 'pal2nal.v14', 'dnds.aln')
> my_nucl_file = os.path.join(os.getcwd(), 'pal2nal.v14', 'dnds.nuc')
> output_file = '/home/edson/pal2nal.v14/output'
> os.system(my_pal2nal + 'perl pal2nal.pl' + my_prot_file + my_nucl_file +
> ' -output paml' + '>' + output_file + ' -nogap')
>

What perfect way should I proceed and how do I include a script for
'codeml'?

Thanks.

Regards,

Edson.



Edson B. Ishengoma
PhD-Candidate
*School of Life Sciences and Engineering
Nelson Mandela African Institute of Science and Technology
Nelson Mandela Road
P. O. Box 447, Arusha
Tanzania (255)
*
*ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
*

<http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
  Website: www.nm-aist.ac.tz
Skype: edson.ishengoma

*
*
**


From zruan1991 at gmail.com  Fri Jan 17 15:18:22 2014
From: zruan1991 at gmail.com (Zheng Ruan)
Date: Fri, 17 Jan 2014 10:18:22 -0500
Subject: [Biopython] How to run PAL2NAL commandline via python
In-Reply-To: <CAKoVMyn1iLRQMffc5xvPb9HSs8e+YD180Yc20ApP9MjGhjmTFQ@mail.gmail.com>
References: <CAKoVMyn1iLRQMffc5xvPb9HSs8e+YD180Yc20ApP9MjGhjmTFQ@mail.gmail.com>
Message-ID: <CABM7aFpD4tWc0bvfJqLR3rtjjDdKn1A39QHkBrt+kzu1hS8Jxg@mail.gmail.com>

Hey Edson,

There are a couple of issues in your code. You need to make sure the
command called by os.system() is able to run in the shell (my_pal2nal
should not be called; you also missed a space between my_prot_file and
my_nucl_file; the '-nogap' option should be placed before redirecting).

Biopython do have a codeml wrapper. see
http://biopython.org/wiki/PAML#codeml. To run codeml, you also need a tree
file specified. You'd better make sure that you can successfully run codeml
in the command line before including it in your script.

Hope it helps,

Best,
Zheng Ruan


On Fri, Jan 17, 2014 at 2:11 AM, Edson Ishengoma
<ishengomae at nm-aist.ac.tz>wrote:

> Dear all,
>
> I recently was introduced to pal2nal as a convenient tool to convert
> aligned protein residues (from tblastn, for example) back to their original
> nucleotide sequences. My boss suggested I use a python or perl script to
> call the tool and feed the resulting nucleotide alignments to the 'codeml'
> program to calculate Ka, Ks.
>
> I don't know perl, so I would like to know how to do this from python -- a
> python script which includes the way to feed the resulting codon alignments
> to  PAML for "codeml" program to calculate Ka, Ks values.
>
> I tried to check for the pre-existence of  Biopython wrapper for Pal2Nal I
> didnt see one. I am on linux machine (Ubuntu 13.04) and my installed python
> is Python 2.7.4.
> I tried this script which I expected to produce a file containing aligned
> nucleotide sequences. But no error message is shown but it outputs an empty
> file (nothing written on the file).
>
> import os
> > my_pal2nal = os.path.join(os.getcwd(), 'pal2nal.v14')
> > my_prot_file = os.path.join(os.getcwd(), 'pal2nal.v14', 'dnds.aln')
> > my_nucl_file = os.path.join(os.getcwd(), 'pal2nal.v14', 'dnds.nuc')
> > output_file = '/home/edson/pal2nal.v14/output'
> > os.system(my_pal2nal + 'perl pal2nal.pl' + my_prot_file + my_nucl_file +
> > ' -output paml' + '>' + output_file + ' -nogap')
> >
>
> What perfect way should I proceed and how do I include a script for
> 'codeml'?
>
> Thanks.
>
> Regards,
>
> Edson.
>
>
>
> Edson B. Ishengoma
> PhD-Candidate
> *School of Life Sciences and Engineering
> Nelson Mandela African Institute of Science and Technology
> Nelson Mandela Road
> P. O. Box 447, Arusha
> Tanzania (255)
> *
> *ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
> *
>
> <http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
>   Website: www.nm-aist.ac.tz
> Skype: edson.ishengoma
>
> *
> *
> **
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>


From philipp.schiffer at gmail.com  Sun Jan 19 09:36:53 2014
From: philipp.schiffer at gmail.com (Philipp Schiffer)
Date: Sun, 19 Jan 2014 10:36:53 +0100
Subject: [Biopython] GFF parsing: getting features of specific proteins in
	gff
Message-ID: <6AA379FAFB7845079A6E0D300FC1C237@gmail.com>

Hi all and Brad Chapman in particular,

I just started exploring the GFF parser for some Augustus derived gff3 files, but running into trouble when trying to collect information for a specific protein. Ultimately my goal is to get introns and exons for a specific set of genes. Following the wiki I can replicate everything with my data and have adjusted the following piece to my data:

from BCBio import GFF    
in_file = "your_file.gff"    
limit_info = dict( gff_id = ["chr1"],
 gff_source = ["Coding_transcript"])    
in_handle = open(in_file)  
for rec in GFF.parse(in_handle, limit_info=limit_info):  
print rec.features[0] in_handle.close()

For testing on a subset I changed "chr1" to one of my contig IDs and that works. Then I limited to gff_type = ["intron"] and that also works for my data.

However now I'd like not to print all rec.features, but only for a specific gene. Picked the first one "g1.t1", which is on the contig and is displayed as an id in the printout of all features. It is also contained in the "list" that rec.features appears to be, but apparently you can't do something like `if x in list:` with the rec.features, at least I get an error when trying. I looked through the Biopython tutorial to see if there is an attribute to rec.features that I could query for the id, but somehow that didn?t make me any wiser.
I guess this is just me being thick and newbie, but could anybody point me in the right direction maybe?

Thanks

Philipp


From ishengomae at nm-aist.ac.tz  Tue Jan 21 11:42:58 2014
From: ishengomae at nm-aist.ac.tz (Edson Ishengoma)
Date: Tue, 21 Jan 2014 14:42:58 +0300
Subject: [Biopython] Biopython function for operating multiple homologous
 sequences in a single file
Message-ID: <CAKoVMymaWaoFVj7z2j0Sk9GsD+1NUK7vBMMVj9xFv77=Lwz-Nw@mail.gmail.com>

Hi all,

I have a single large file containing many (thousands) coding sequence
pairs according to their homologs as so:

> >ENSBTAT00000048342_species1
> sequences
> >ENSBTAT00000048342_species2
> sequences
> >ENSBTAT00000009085_species1
> sequences
> >ENSBTAT00000009085_species2
> sequences
> >ENSBTAT00000009212_species1
> sequences
> >ENSBTAT00000009212_species2
> sequences
> ......
> ......
> ......
>

Now I want to produce a clustalw alignment for each cds pair. Is there a
way to use the biopython commandline function for clustalw to treat each
gene pair separately for all pairs, run alignment and produce an ouput
(alignments + trees file)?

I appreciate your time and look forward to hear from you,

With regards,

Edson B. Ishengoma
PhD-Candidate
*School of Life Sciences and Engineering
Nelson Mandela African Institute of Science and Technology
Nelson Mandela Road
P. O. Box 447, Arusha
Tanzania (255)
*
*ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
*

<http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
  Website: www.nm-aist.ac.tz
Skype: edson.ishengoma

*
*
**


From mike.thon at gmail.com  Tue Jan 21 16:39:06 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Tue, 21 Jan 2014 17:39:06 +0100
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <96EDC3CA-6DBD-4825-8704-95BF45590211@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
	<AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
	<96EDC3CA-6DBD-4825-8704-95BF45590211@gmail.com>
Message-ID: <29CB27F1-43BE-4FC5-9591-0640CEC31CC1@gmail.com>

Here?s another question.  I have this GenBank formatted feature:

     CDS             order(complement(3448..3635),complement(2617..3256))
                     /Source="maker"
                     /codon_start=1
                     /ID="CFIO01_05457-RA:cds"
                     /label=?CDS"

When I extract the sequence I get this:

(Pdb) str(feat.extract(seq).seq)
'ACCAGTCGGCTCCGGCAAGACAGCTCTGATGCTCGCCCTCTGCCTCGCCCTGCGCGAAAAATACTCCATCGCCGCCGTCACAAACGACATCTTCACCCGTGAGGACGCCGAATTCCTCACCCGCCACAAGGCCCTGCCCGCCCCGCGCATCCGCGCCATCGAGACGGGCGGCTGCCCGCACGCCGCCGTGCGCGAGGACATCTCGGCCAACCTCGCCGCCCTCGAGGACCTCCACCGCGAGTTCGACGCCGATCTGCTCCTCATCGAGTCCGGCGGCGACAACCTGGCCGCCAACTACTCCCGCGAGCTGGCCGATTACATCATCTACGTCATTGACGTCTCGGGAGGCGACAAGATCCCGCGCAAGGGCGGCCCGGGTATCACACAGAGCGACTTGCTGGTTGTGAACAAGACGGATCTGGCCGAGATTGTGGGCGCGGATCTGGGTGTCATGGAGAGGGACGCGCGCAAGATGCGAGAGGGCGGGCCGACTGTGTTTGCGCAGGTGAAGAAGAATGTTGCCGTTGATCACATTGTCAACCTCATGCTTAGCGCGTGGAAGGCGAGTGGTGCCGAGGAGAACCGTAGGGCTGCGGGCGGACCGCGGCCTACAGAGGGCCTTGACAGCCTCAAGGCTTGAATGTCTCACGAGCACTCACACGACGGCCCTCATGGCCACGCGCACTCCCACGAGGGCGGCTTCAATGCCCAGGAGCACGGCCACTCCCACGAGATCCTTGATGGTCCTGGAAGCTATCTCGGCCGCGAGATGCCCATTGTCGAGGGCAGAAACTGGAGCGATCGTGCTTTCACAATTGGTATTGGAGG'

This is supposed to be a CDS which can be translated to a protein coding sequence starting with M and ending with a stop codon.  the above sequence isn?t correct - the exons are in the wrong order.  When I reverse the order of the exons I get the correct order and get a CDS sequence that can be translated:

(Pdb) feat.location.parts.reverse()
(Pdb) str(feat.extract(seq).seq)
'ATGTCTCACGAGCACTCACACGACGGCCCTCATGGCCACGCGCACTCCCACGAGGGCGGCTTCAATGCCCAGGAGCACGGCCACTCCCACGAGATCCTTGATGGTCCTGGAAGCTATCTCGGCCGCGAGATGCCCATTGTCGAGGGCAGAAACTGGAGCGATCGTGCTTTCACAATTGGTATTGGAGGACCAGTCGGCTCCGGCAAGACAGCTCTGATGCTCGCCCTCTGCCTCGCCCTGCGCGAAAAATACTCCATCGCCGCCGTCACAAACGACATCTTCACCCGTGAGGACGCCGAATTCCTCACCCGCCACAAGGCCCTGCCCGCCCCGCGCATCCGCGCCATCGAGACGGGCGGCTGCCCGCACGCCGCCGTGCGCGAGGACATCTCGGCCAACCTCGCCGCCCTCGAGGACCTCCACCGCGAGTTCGACGCCGATCTGCTCCTCATCGAGTCCGGCGGCGACAACCTGGCCGCCAACTACTCCCGCGAGCTGGCCGATTACATCATCTACGTCATTGACGTCTCGGGAGGCGACAAGATCCCGCGCAAGGGCGGCCCGGGTATCACACAGAGCGACTTGCTGGTTGTGAACAAGACGGATCTGGCCGAGATTGTGGGCGCGGATCTGGGTGTCATGGAGAGGGACGCGCGCAAGATGCGAGAGGGCGGGCCGACTGTGTTTGCGCAGGTGAAGAAGAATGTTGCCGTTGATCACATTGTCAACCTCATGCTTAGCGCGTGGAAGGCGAGTGGTGCCGAGGAGAACCGTAGGGCTGCGGGCGGACCGCGGCCTACAGAGGGCCTTGACAGCCTCAAGGCTTGA'
(Pdb) str(feat.extract(seq).seq.translate())
'MSHEHSHDGPHGHAHSHEGGFNAQEHGHSHEILDGPGSYLGREMPIVEGRNWSDRAFTIGIGGPVGSGKTALMLALCLALREKYSIAAVTNDIFTREDAEFLTRHKALPAPRIRAIETGGCPHAAVREDISANLAALEDLHREFDADLLLIESGGDNLAANYSRELADYIIYVIDVSGGDKIPRKGGPGITQSDLLVVNKTDLAEIVGADLGVMERDARKMREGGPTVFAQVKKNVAVDHIVNLMLSAWKASGAEENRRAAGGPRPTEGLDSLKA*'

So my question is, is there something wrong with the file I?m parsing?

On Jan 14, 2014, at 12:22 PM, Heath O'Brien <Heath.OBrien at bristol.ac.uk> wrote:

> Finally a question that I?m confident I can answer?
> 
> Genbank uses one-based numbering and closed intervals while python uses zero-based numbering and half-open intervals, so it?s necessary to convert the coordinates. See https://plus.google.com/115212051037621986145/posts/YTUxbXYZyfi
> 
> You can convert back to one-based coordinates by adding 1 to the start coordinate.
> 
> all good things,
> Heath
> 
> On 14 Jan 2014, at 10:20, Michael Thon <mike.thon at gmail.com> wrote:
> 
>> Hi Peter - Thanks for your help.  Here is another problem.  Here is the block of features in my GenBank file for a gene:
>> 
>>    gene            complement(1..588)
>>                    /Source="maker"
>>                    /ID="CFIO01_14176"
>>                    /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
>>                    -gene-0.30"
>>                    /label="CFIO01_14176"
>>    CDS             order(complement(200..588),complement(1..124))
>>                    /Source="maker"
>>                    /codon_start=1
>>                    /ID="CFIO01_14176-RA:cds"
>>                    /label="CDS"
>>    mRNA            complement(1..588)
>>                    /Source="maker"
>>                    /ID="CFIO01_14176-RA"
>>                    /Alias="maker-NODE_118_length_29757_cov_21.340693-augustus
>>                    -gene-0.30-mRNA-1"
>>                    /_AED="0.06"
>>                    /_QI="0|0|0|1|1|1|2|0|171"
>>                    /_eAED="0.06"
>>                    /label="CFIO01_14176-RA"
>> 
>> Now, here is the CDS feature after is was parsed by BioPython:
>> 
>> 
>> (Pdb) feat.location.parts
>> [FeatureLocation(ExactPosition(0), ExactPosition(124), strand=-1), FeatureLocation(ExactPosition(199), ExactPosition(588), strand=-1)]
>> 
>> Note that two positions have changed.  The CDS segments are (complement(200..588),complement(1..124)) but the positions in SeqFeature object are 0..124 and 199..588
>> 
>> I checked some other features too and it looks like BioPython adds 1 to the start of each segment.  For the features on the complementary strand it subtracts 1.  
>> 
>> When I translate the feature into a protein sequence like this: str(feat.extract(seq).seq.translate()) , the sequence is correct so this must not be a bug. so, how to I access the exact values that are in the genbank formatted file?  
>> 
>> On Jan 13, 2014, at 5:18 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> 
>>> On Mon, Jan 13, 2014 at 4:07 PM, Michael Thon <mike.thon at gmail.com> wrote:
>>>> Here are two examples from the GenBank format file (not from GenBank though)
>>>> 
>>>> 
>>>>   CDS             order(6621..6658,6739..6985)
>>>>                   /Source="maker"
>>>>                   /codon_start=1
>>>>                   /ID="CFIO01_14847-RA:cds"
>>>>                   /label=?CDS"
>>>> 
>>>>   CDS             419..2374
>>>>                   /Source="maker"
>>>>                   /codon_start=1
>>>>                   /ID="CFIO01_05899-RA:cds"
>>>>                   /label=?CDS"
>>>> 
>>>> if the feature is a simple feature, then I just need to access its start and end.
>>>> If its a compound feature then I need to iterate over each segment, accessing the start and end.
>>>> 
>>>> What I am doing at the moment is this:
>>>> 
>>>> if feat._sub_features:
>>>>      for sf in feat.sub_features:
>>>>              start = sf.location.start
>>>>              ?
>>>> else:
>>>>      start = feat.location.start
>>>>      ?
>>>> 
>>>> it works, I think.  Is there a better way?
>>> 
>>> Don't do that :) Python variables/methods/etc starting with a single
>>> underscore are by convention private and should not generally be
>>> used. In this case, ._sub_features is an internal detail for the behind
>>> the scenes backwards compatibility for the now deprecated property
>>> .sub_features (don't use that either).
>>> 
>>> Instead use the location object itself directly, it now holds any
>>> sub-location information using a CompoundLocation object.
>>> See the .parts attribute, which gives a list of simple locations.
>>> 
>>> e.g.
>>> 
>>> for part in feat.location.parts:
>>>  start = part.start
>>>  ...
>>> 
>>>> 
>>>> Also, is there an easy way to get the sequence represented by the seqfeature,
>>>> if it is made up of CompoundLocations?  These features are CDSs where each
>>>> sub-feature is an exon.  I need to splice them all together and get the translation.
>>>> 
>>> 
>>> Yes, where `feat` is a SubFeature object use `feat.extract(the_parent_sequence)`
>>> to get the spliced sequence, which you can then translate. See the section
>>> "Sequence described by a feature or location" in the Tutorial,
>>> 
>>> http://biopython.org/DIST/docs/tutorial/Tutorial.html
>>> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>>> 
>>> On reflection, the Tutorial could do with a bit more detail on how to use
>>> a CompoundLocation, but I did try to cover this in the docstrings.
>>> 
>>> Regards,
>>> 
>>> 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  Tue Jan 21 16:52:35 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Tue, 21 Jan 2014 16:52:35 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <29CB27F1-43BE-4FC5-9591-0640CEC31CC1@gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
	<AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
	<96EDC3CA-6DBD-4825-8704-95BF45590211@gmail.com>
	<29CB27F1-43BE-4FC5-9591-0640CEC31CC1@gmail.com>
Message-ID: <CAKVJ-_6UvMcht638vyGtd1xghxO=D8Wzrnn5QpVw60ZPRF1tqA@mail.gmail.com>

On Tue, Jan 21, 2014 at 4:39 PM, Michael Thon <mike.thon at gmail.com> wrote:

> Here?s another question.  I have this GenBank formatted feature:
>
>      CDS             order(complement(3448..3635),complement(2617..3256))
>                      /Source="maker"
>                      /codon_start=1
>                      /ID="CFIO01_05457-RA:cds"
>                      /label=?CDS"
>
> When I extract the sequence I get this:
>
> (Pdb) str(feat.extract(seq).seq)
> ...
>
> This is supposed to be a CDS which can be translated to a protein coding
> sequence starting with M and ending with a stop codon.  the above sequence
> isn?t correct - the exons are in the wrong order.  When I reverse the order
> of the exons I get the correct order and get a CDS sequence that can be
> translated:
>
> (Pdb) feat.location.parts.reverse()
> (Pdb) str(feat.extract(seq).seq)
> ...
> (Pdb) str(feat.extract(seq).seq.translate())
>
> 'MSHEHSHDGPHGHAHSHEGGFNAQEHGHSHEILDGPGSYLGREMPIVEGRNWSDRAFTIGIGGPVGSGKTALMLALCLALREKYSIAAVTNDIFTREDAEFLTRHKALPAPRIRAIETGGCPHAAVREDISANLAALEDLHREFDADLLLIESGGDNLAANYSRELADYIIYVIDVSGGDKIPRKGGPGITQSDLLVVNKTDLAEIVGADLGVMERDARKMREGGPTVFAQVKKNVAVDHIVNLMLSAWKASGAEENRRAAGGPRPTEGLDSLKA*'
>
> So my question is, is there something wrong with the file I?m parsing?
>

Possibly - the 'order' tag actually means the order of the parts is unknown.
If the order is known, it should be 'join' instead:

join(complement(3448..3635),complement(2617..3256))

What's the accession/URL for the full file this example came from?

Peter



From chapmanb at 50mail.com  Wed Jan 22 01:25:04 2014
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 21 Jan 2014 20:25:04 -0500
Subject: [Biopython] GFF parsing: getting features of specific proteins
	in gff
In-Reply-To: <6AA379FAFB7845079A6E0D300FC1C237@gmail.com>
References: <6AA379FAFB7845079A6E0D300FC1C237@gmail.com>
Message-ID: <86bnz495an.fsf@fastmail.fm>


Philipp;
Thanks for the e-mail about GFF parsing and sorry for the delay in
getting back with you. I've merged your second off-list e-mail with this
and copied back to the mailing list in case other folks have
comments/thoughts to share as well.

> I just started exploring the GFF parser for some Augustus derived gff3
> files, but running into trouble when trying to collect information for
> a specific protein. Ultimately my goal is to get introns and exons for
> a specific set of genes.
[...]
> However now I'd like not to print all rec.features, but only for a
> specific gene.
>
> I found that in principle I can do something like?
> ```for rec in GFF.parse(in_handle, limit_info=limit_info):
>             if 'g1' in rec.features[0].qualifiers:
>                 GFF.write([rec], out_handle)```
>
> However this does not really solve my problem. For once it gives me
> all the genes on a contig if the search string is in
> rec.features[0]. I guess I could somehow just write the first then,
> but what seems more important if a gene I am looking for is in
> rec.features[1] or higher index

To do this you'd want to also loop over the features, so do:

for rec in GFF.parse(in_handle, limit_info=limit_info):
   for feature in rec.features:
      if 'g1' in f.qualifiers:
          GFF.write([rec], out_handle)
          break

This is definitely sub-optimal since it's a brute force loop over all of
the items in the GFF, but would work for what you need.

If speed becomes an issue, Ryan Dale's GFFUtils may be useful:

https://github.com/daler/gffutils
http://pythonhosted.org/gffutils/

It creates a SQLite database based on the GFF, so enables faster query
access by gene than the line-based parser. It doesn't yet integrate with
Biopython (that is on my overdue todo list) but provides a nice Python
API with examples in the documentation.

Hope this helps,
Brad



From p.j.a.cock at googlemail.com  Wed Jan 22 11:19:49 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 22 Jan 2014 11:19:49 +0000
Subject: [Biopython] iterating over FeatureLocation
In-Reply-To: <CAKVJ-_6UvMcht638vyGtd1xghxO=D8Wzrnn5QpVw60ZPRF1tqA@mail.gmail.com>
References: <8FAA127C-0169-4FF1-A273-D1E641F972B8@gmail.com>
	<CAKVJ-_5g_hfPrgwc=veZscT9c7ycrBuu_E8J289SQzN=pAzVmQ@mail.gmail.com>
	<D5CD2A67-8BFC-48AB-9D78-E274B44D0E7A@gmail.com>
	<CAKVJ-_7b-1NgxVdGCwGJ1+gpYRX=0zvRbvpw7oWyqPGmx2Ex+Q@mail.gmail.com>
	<AABAB704-58E6-4DD0-AD27-41DBF9FD798D@gmail.com>
	<96EDC3CA-6DBD-4825-8704-95BF45590211@gmail.com>
	<29CB27F1-43BE-4FC5-9591-0640CEC31CC1@gmail.com>
	<CAKVJ-_6UvMcht638vyGtd1xghxO=D8Wzrnn5QpVw60ZPRF1tqA@mail.gmail.com>
Message-ID: <CAKVJ-_7-g4YZBq-Nn0a2RnCfCGondG_=JVbJdvZHs2MxjyHQ7Q@mail.gmail.com>

On Tue, Jan 21, 2014 at 4:52 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Tue, Jan 21, 2014 at 4:39 PM, Michael Thon <mike.thon at gmail.com> wrote:
>>
>> Here?s another question.  I have this GenBank formatted feature:
>>
>>      CDS             order(complement(3448..3635),complement(2617..3256))
>>                      /Source="maker"
>>                      /codon_start=1
>>                      /ID="CFIO01_05457-RA:cds"
>>                      /label=?CDS"
>>
>> When I extract the sequence I get this:
>>
>> (Pdb) str(feat.extract(seq).seq)
>> ...
>>
>>
>> This is supposed to be a CDS which can be translated to a protein coding
>> sequence starting with M and ending with a stop codon.  the above sequence
>> isn?t correct - the exons are in the wrong order.  When I reverse the order
>> of the exons I get the correct order and get a CDS sequence that can be
>> translated:
>>
>> (Pdb) feat.location.parts.reverse()
>> (Pdb) str(feat.extract(seq).seq)
>> ...
>>
>> (Pdb) str(feat.extract(seq).seq.translate())
>>
>> 'MSHEHSHDGPHGHAHSHEGGFNAQEHGHSHEILDGPGSYLGREMPIVEGRNWSDRAFTIGIGGPVGSGKTALMLALCLALREKYSIAAVTNDIFTREDAEFLTRHKALPAPRIRAIETGGCPHAAVREDISANLAALEDLHREFDADLLLIESGGDNLAANYSRELADYIIYVIDVSGGDKIPRKGGPGITQSDLLVVNKTDLAEIVGADLGVMERDARKMREGGPTVFAQVKKNVAVDHIVNLMLSAWKASGAEENRRAAGGPRPTEGLDSLKA*'
>>
>> So my question is, is there something wrong with the file I?m parsing?
>
>
> Possibly - the 'order' tag actually means the order of the parts is unknown.
> If the order is known, it should be 'join' instead:
>
> join(complement(3448..3635),complement(2617..3256))
>
> What's the accession/URL for the full file this example came from?
>
> Peter

Thanks for sending me the file. I don't think Biopython is really at
fault, rather something is going wrong in the production of this
GenBank format file. It appears to be a tricky case of trans-splicing.

However, thinking about this, it might be reasonable for Biopython
to give an error or warning when extracting an "order" location because
this means the order of the sub-parts is not determined (and thus
could be stitched together wrongly - as you have seen).

The following variants of the location string all give the (nonsensical)
sequence you are seeing:

     CDS             order(complement(3448..3635),complement(2617..3256))
     CDS             join(complement(3448..3635),complement(2617..3256))
     CDS             complement(join(3448..3635,2617..3256))

Extracting and translating gives this sequence with multiple in
frame stop codons, but lacking a terminal stop codon. i.e.

TSRLRQDSSDARPLPRPARKILHRRRHKRHLHP*GRR...YWR (ends)

Surprisingly, what I think the annotation is trying to say is that this case
the exons appear to be trans-spliced, rather than being in the typical
order you would expect from the strand. These "work" and give the
protein sequence you wanted,

     CDS             complement(join(2617..3256,3448..3635))
     CDS             join(complement(2617..3256),complement(3448..3635))
     CDS             order(complement(2617..3256),complement(3448..3635))

For GenBank format it would be nice to also add the /trans_splicing
tag as well. I would recommend you (or the team)  go back to the original
annotation to check what was the intended meaning here.

Regards,

Peter



From philipp.schiffer at gmail.com  Wed Jan 22 13:44:52 2014
From: philipp.schiffer at gmail.com (Philipp Schiffer)
Date: Wed, 22 Jan 2014 14:44:52 +0100
Subject: [Biopython] GFF parsing: getting features of specific proteins
 in gff
In-Reply-To: <86bnz495an.fsf@fastmail.fm>
References: <6AA379FAFB7845079A6E0D300FC1C237@gmail.com>
	<86bnz495an.fsf@fastmail.fm>
Message-ID: <45004206D5B843E489D001BFBF47DB0E@googlemail.com>

Hi Brad,  

thanks for coming back to me on this. Works (well of course). Also thanks for the GFFUtils link. I have actually been aware of that, but wanted to figure out my own way (kind off). Well, eh, failed there I guess. But I surely learnt something, which is always the point. Also I wanted to integrate this in a larger script where I get the genes of interest from a clustering output first. Anyway, in the end it might really make sense to use the GFFUtils on lists I prepared first.   

Thanks again

Philipp

--  
Philipp Schiffer
Sent with Sparrow (http://www.sparrowmailapp.com/?sig)


On Wednesday, 22 January 2014 at 02:25, Brad Chapman wrote:

>  
> Philipp;
> Thanks for the e-mail about GFF parsing and sorry for the delay in
> getting back with you. I've merged your second off-list e-mail with this
> and copied back to the mailing list in case other folks have
> comments/thoughts to share as well.
>  
> > I just started exploring the GFF parser for some Augustus derived gff3
> > files, but running into trouble when trying to collect information for
> > a specific protein. Ultimately my goal is to get introns and exons for
> > a specific set of genes.
> >  
>  
> [...]
> > However now I'd like not to print all rec.features, but only for a
> > specific gene.
> >  
> > I found that in principle I can do something like?
> > ```for rec in GFF.parse(in_handle, limit_info=limit_info):
> > if 'g1' in rec.features[0].qualifiers:
> > GFF.write([rec], out_handle)```
> >  
> > However this does not really solve my problem. For once it gives me
> > all the genes on a contig if the search string is in
> > rec.features[0]. I guess I could somehow just write the first then,
> > but what seems more important if a gene I am looking for is in
> > rec.features[1] or higher index
> >  
>  
>  
> To do this you'd want to also loop over the features, so do:
>  
> for rec in GFF.parse(in_handle, limit_info=limit_info):
> for feature in rec.features:
> if 'g1' in f.qualifiers:
> GFF.write([rec], out_handle)
> break
>  
> This is definitely sub-optimal since it's a brute force loop over all of
> the items in the GFF, but would work for what you need.
>  
> If speed becomes an issue, Ryan Dale's GFFUtils may be useful:
>  
> https://github.com/daler/gffutils
> http://pythonhosted.org/gffutils/
>  
> It creates a SQLite database based on the GFF, so enables faster query
> access by gene than the line-based parser. It doesn't yet integrate with
> Biopython (that is on my overdue todo list) but provides a nice Python
> API with examples in the documentation.
>  
> Hope this helps,
> Brad
>  
>  





From alanwilter at gmail.com  Wed Jan 22 16:28:57 2014
From: alanwilter at gmail.com (Alan)
Date: Wed, 22 Jan 2014 16:28:57 +0000
Subject: [Biopython] help with seqxml format
Message-ID: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>

I have an input fasta file (test.fasta), like:

>tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus musculus
GN=Negr1 PE=2 SV=1
MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGA
SKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTP
RTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQ
YLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCE
GAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTT
NASLPLNQSSIPWQVFFMLKVSFLLVCIL

Then I am trying this:

from Bio import SeqIO
from Bio.Alphabet import generic_protein
handle = open("test.fasta")
records = list(SeqIO.parse(handle, "fasta", generic_protein))
aa = records[0]

print aa.format('seqxml')
<?xml version="1.0" encoding="utf-8"?>
<seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
http://www.seqxml.org/0.4/seqxml.xsd">
 <entry id="tr|A0A4W9|A0A4W9_MOUSE">
  <description>growth regulator 1</description>

<AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
 </entry>
</seqXML>

Note above that my SeqIO.parse is not picking all the info in the Fasta
header.

But I want to tweak this to output something more like this:
<seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
http://www.seqxml.org/0.4/seqxml.xsd" source="QfO
http://www.ebi.ac.uk/reference_proteomes/" sourceVersion="2014_04">
 <entry id="A0A4W9" source="UniProtKB">
  <species name="Mus musculus" ncbiTaxID="10090" />
  <description>Neuronal growth regulator 1</description>

 <AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
  <DBRef type="gene" source="GN" id="Negr1" />
  <DBRef type="gene" source="Gene" id="TK0418" />
  <property name="PE" value="2" />
  <property name="SV" value="1" />
 </entry>
</seqXML>

The aa.id, aa.description wouldn't be a problem to update and some info I
have to provide from elsewhere (like ncbiTaxID and species name), but how
to add the details in the <seqXML>, <entry source> or create <species>,
<DBRef> etc.?

Many thanks in advance,

Alan



From p.j.a.cock at googlemail.com  Wed Jan 22 16:53:08 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 22 Jan 2014 16:53:08 +0000
Subject: [Biopython] help with seqxml format
In-Reply-To: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>
References: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>
Message-ID: <CAKVJ-_4ivQkwHUxd0C7w-7qvyyHrYPAjDikY=J7L-ZkF4pLWCA@mail.gmail.com>

On Wed, Jan 22, 2014 at 4:28 PM, Alan <alanwilter at gmail.com> wrote:
> I have an input fasta file (test.fasta), like:
>
>>tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus musculus
> GN=Negr1 PE=2 SV=1
> MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGA
> SKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTP
> RTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQ
> YLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCE
> GAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTT
> NASLPLNQSSIPWQVFFMLKVSFLLVCIL
>
> Then I am trying this:
>
> from Bio import SeqIO
> from Bio.Alphabet import generic_protein
> handle = open("test.fasta")
> records = list(SeqIO.parse(handle, "fasta", generic_protein))
> aa = records[0]
>
> print aa.format('seqxml')
> <?xml version="1.0" encoding="utf-8"?>
> <seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
> http://www.seqxml.org/0.4/seqxml.xsd">
>  <entry id="tr|A0A4W9|A0A4W9_MOUSE">
>   <description>growth regulator 1</description>
>
> <AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
>  </entry>
> </seqXML>
>
> Note above that my SeqIO.parse is not picking all the info in the Fasta
> header.

Odd, what does aa.description give you?

> But I want to tweak this to output something more like this:
> ...
>   <species name="Mus musculus" ncbiTaxID="10090" />
>   <description>Neuronal growth regulator 1</description>
>
> The aa.id, aa.description wouldn't be a problem to update and some info I
> have to provide from elsewhere (like ncbiTaxID and species name), but how
> to add the details in the <seqXML>, <entry source> or create <species>,
> <DBRef> etc.?

Set record.annotations["organism"] and record.annotations["ncbi_taxid"]
to suitable strings, and the list record.dbxref = ["db:identifer", ...].

Also what version of Biopython are you using?

Peter



From hlapp at drycafe.net  Wed Jan 22 19:33:10 2014
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 22 Jan 2014 14:33:10 -0500
Subject: [Biopython] Fwd: Call for Org Admins for OBF's 2014 Google Summer
	of Code participation
References: <AD3B86E4-05E0-4395-ADD8-DAC30DDA87A0@drycafe.net>
Message-ID: <BA38F9AA-11FB-4360-BDE0-548740504AA9@drycafe.net>

FYI, we are extending the deadline for responding to this Saturday, January 25.

Also, in case this wasn't clear from the text, this isn't a pro forma solicitation. There is no plan B. If we don't receive qualified applications by the deadline, OBF will not apply this year as a mentoring organization.

	-hilmar

Begin forwarded message:

From: Hilmar Lapp <hlapp at drycafe.net>
Subject: Call for Org Admins for OBF's 2014 Google Summer of Code participation 
Date: January 14, 2014 6:16:02 PM EST
To: BioPerl List <bioperl-l at lists.open-bio.org>

The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring organization applications from Feb 3 to 14.

OBF participated on behalf of our member projects from 2010-2012, and those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.

To participate this year, we have to designate 2-3 people as primary and backup organization administrators. This is an important role, and we are looking for people from our community to step forward to serve. 

An org admin?s role is in many ways that of a cat herder. The whole team of mentors and admins creates the experience for the students, but it falls on the admin to ?keep it together.? Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions) of its mentors or community, and it falls on the org admin to carry that accountability through to the org?s mentors. The org admin?s responsibilities include:
	? Representing our online face to GSoC, in particular to GSoC students.
	? Shepherding our mentoring organization application, and submitting it.
	? Working out processes and rules for mentors as well as students that promote transparency, fairness, and protect from late-in-the-game surprises.
	? Knowing GSoC rules and processes, and making sure ours are consistent with them.
	? Reminding participants of rules, and enforcing them in the event it is necessary.
	? Mediating, and sometimes arbitrating between students and mentors when needed.
	? Ensuring that GSoC timelines are met by everyone.
The person we are looking for will genuinely care about the well-being of our communities, is well organized, stays calm in email storms, communicates clearly, has good people skills, and generally is known as a good listener.

If you are interested in helping us out in this role, please email us (by Jan 21, 2014) a statement at board at open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC participation is. You need not be a developer or programmer to respond, but for now we do require that you have been active in some capacity in at least one of our project?s communities. Please include in your email a brief summary of such activities even if you are a core developer for one of our projects.

We are looking forward to hearing from you!

Hilmar Lapp, OBF President, on behalf of the OBF Board of Directors
[1] http://www.google-melange.com/gsoc/events/google/gsoc2014

-- 
Hilmar Lapp -:- lappland.io





From lthiberiol at gmail.com  Wed Jan 22 19:58:10 2014
From: lthiberiol at gmail.com (Luiz Thiberio Rangel)
Date: Wed, 22 Jan 2014 17:58:10 -0200
Subject: [Biopython] Phylo.draw - coloring node names
Message-ID: <CAA8DvhaNs=cLo3RgzgXzF7JuM02HR0=E-DzMVFE9NP98f2dFSg@mail.gmail.com>

Hey,

   I am trying to quickly edit some trees coloring the node names according
to they taxonomy. I figured out that all I can do is to color the branches (
tree.get_nonterminals()[0].color = 'grey'), not the texts. Is there any way
to color the node names?

thx,

Luiz Thib?rio Rangel



From ishengomae at nm-aist.ac.tz  Thu Jan 23 07:39:12 2014
From: ishengomae at nm-aist.ac.tz (Edson Ishengoma)
Date: Thu, 23 Jan 2014 10:39:12 +0300
Subject: [Biopython] Follow-up about python/biopython code for submitting
	multiple jobs to clustalw
Message-ID: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>

Hi all,

I couldn't get a response about my struggles which I asked few days past, I
presume it was either a poorly submitted question or my approach with what
I want to do is totally out of touch with mainstream bioinformatics. The
thing is I am a newbie to both python programming and bioinformatics but I
believe there are people here who can help, so I will try again with more
background.

The overall goal with what I want to achieve is to perform selection
analyses on multiple species with codeml in PAML. For this the inputs
should be both the sequence alignments and tree files. I already have
sequence file (produced by pal2nal) but I still need a corresponding tree
file.

So what I am challenged with is the fact that my nucleotide alignment file
contain cds of four species at many loci (it is kind of whole genome data)
so I will have to submit the job to a tree producing program per each
alignment - I can use clustalw or Phylip.

Looking at biopython facility, thankfully there is biopython wrapper for
clustalw which I attempted to use for trees, but the fact that my alignment
file contains multiple alignments, I cannot use the code the way it is (the
straight code assumes the file contains a single alignment). So I reasoned
that I can couple this clustalw wrapper with a Dictionary facility to
output the desired results as so:

from Bio import SeqIO
> from Bio.Align.Applications import ClustalwCommandline
>
> def get_ids(record):
>     """"Given a SeqRecord, return the common number shared among sequence
> descriptions.
>             e.g. ">ENSBTAT00000009085_cow or ENSBTAT00000009085_goat or
> ENSBTAT00000009085_sheep
>             " -> "ENSBTAT00000009085"
>             """
>     parts = record.description[:18]
>     return parts
>
> myseq_dict = SeqIO.to_dict(SeqIO.parse("/home/edson/ungulate/infile.fa",
> "fasta"), key_function=get_ids)
> #print myseq_dict.keys()
> cline = ClustalwCommandline("clustalw2", infile="myseq_dict")
> stdout, stderr = clustalw_cline()
>

It turned out this code is a result of my naive (very naive) reasoning and
it is obvious why it cannot work. But I am just putting it here to give you
a clue of what I want to do. I'm sure there is a convenient way to do what
I want to do and I hope this forum will help. I apologize it is a long
email (english is not my first language, at times I'm being wordy to make
myself clear). Any resource will be appreciated.

Thanks.


Edson B. Ishengoma
PhD-Candidate
*School of Life Sciences and Engineering
Nelson Mandela African Institute of Science and Technology
Nelson Mandela Road
P. O. Box 447, Arusha
Tanzania (255)
*
*ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
*

<http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
  Website: www.nm-aist.ac.tz
Skype: edson.ishengoma

*
*
**


From p.j.a.cock at googlemail.com  Thu Jan 23 09:44:35 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 Jan 2014 09:44:35 +0000
Subject: [Biopython] Biopython function for operating multiple
 homologous sequences in a single file
In-Reply-To: <CAKoVMymaWaoFVj7z2j0Sk9GsD+1NUK7vBMMVj9xFv77=Lwz-Nw@mail.gmail.com>
References: <CAKoVMymaWaoFVj7z2j0Sk9GsD+1NUK7vBMMVj9xFv77=Lwz-Nw@mail.gmail.com>
Message-ID: <CAKVJ-_7-Xyw4=-2fOLQzLAgVX067O7YOLag-5PVpPWaL5yyMag@mail.gmail.com>

On Tue, Jan 21, 2014 at 11:42 AM, Edson Ishengoma
<ishengomae at nm-aist.ac.tz> wrote:
> Hi all,
>
> I have a single large file containing many (thousands) coding sequence
> pairs according to their homologs as so:
>
>> >ENSBTAT00000048342_species1
>> sequences
>> >ENSBTAT00000048342_species2
>> sequences
>> >ENSBTAT00000009085_species1
>> sequences
>> >ENSBTAT00000009085_species2
>> sequences
>> >ENSBTAT00000009212_species1
>> sequences
>> >ENSBTAT00000009212_species2
>> sequences
>> ......
>> ......
>> ......
>>
>
> Now I want to produce a clustalw alignment for each cds pair.

Why do you want to do that?

A pairwise alignment tool might be better... like EMBOSS needle or
water depending on if you want global (full sequence) or local
(partial sequence) alignment. In particular, look at needleall which
is for many-against-many pairwise alignments:
http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html

> Is there a
> way to use the biopython commandline function for clustalw to treat each
> gene pair separately for all pairs, run alignment and produce an ouput
> (alignments + trees file)?

If you really want to run lots of pairwise alignment with clustalw, you
would need a big loop over all the pairs, and call clustalw again and
again (once for each pair). I would think something like needleall
would be better.

Also, you shouldn't use the guide tree from clustalw for any serious
analysis, and anyway if you are doing pairwise alignments the trees
will always be a trivial with two sequences.

Regards,

Peter


From p.j.a.cock at googlemail.com  Thu Jan 23 09:57:50 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 Jan 2014 09:57:50 +0000
Subject: [Biopython] Follow-up about python/biopython code for
 submitting multiple jobs to clustalw
In-Reply-To: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>
References: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>
Message-ID: <CAKVJ-_6RMESVxvXXym_JWYw+1Nm=dV8zaoLWUP1JyirQsJTSRA@mail.gmail.com>

On Thu, Jan 23, 2014 at 7:39 AM, Edson Ishengoma
<ishengomae at nm-aist.ac.tz> wrote:
> Hi all,
>
> I couldn't get a response about my struggles which I asked few days past, I
> presume it was either a poorly submitted question or my approach with what I
> want to do is totally out of touch with mainstream bioinformatics. The thing
> is I am a newbie to both python programming and bioinformatics but I believe
> there are people here who can help, so I will try again with more
> background.
>
> The overall goal with what I want to achieve is to perform selection
> analyses on multiple species with codeml in PAML. For this the inputs should
> be both the sequence alignments and tree files. I already have sequence file
> (produced by pal2nal) but I still need a corresponding tree file.
>
> So what I am challenged with is the fact that my nucleotide alignment file
> contain cds of four species at many loci (it is kind of whole genome data)
> so I will have to submit the job to a tree producing program per each
> alignment - I can use clustalw or Phylip.

If you haven't already, try to get some advice from a phylogenetics
specialist about what to do. For example, clustalw is old and superseded.

You have 4 species, and (say) 50 genes/loci from each. One approach
is to make 50 protein alignments (one for each set of four genes),
turn these into 50 codon-aware nucleotide alignments (with pal2nal
or similar, e.g. [1]), then you could use Biopython to combine these
into a single large concatenated alignment (4 rows for the 4 species),
and use that to build a tree.

This may not be the best plan, but one of our students here did
something like this recently (using Biopython in part).

Peter
[1] https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py


From alanwilter at gmail.com  Thu Jan 23 13:40:42 2014
From: alanwilter at gmail.com (Alan)
Date: Thu, 23 Jan 2014 13:40:42 +0000
Subject: [Biopython] help with seqxml format
In-Reply-To: <CAKVJ-_4ivQkwHUxd0C7w-7qvyyHrYPAjDikY=J7L-ZkF4pLWCA@mail.gmail.com>
References: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>
	<CAKVJ-_4ivQkwHUxd0C7w-7qvyyHrYPAjDikY=J7L-ZkF4pLWCA@mail.gmail.com>
Message-ID: <CAEznbz=a5zWwPQzrq4dfobn+BT+idpp9zabtv71Ho45VMVf5BQ@mail.gmail.com>

Thanks Peter,

I am using the latest version 1.63.

I?ve found some mistakes of myself, aa.description is fine:

print aa
ID: tr|A0A4W9|A0A4W9_MOUSE
Name: tr|A0A4W9|A0A4W9_MOUSE
Description: tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus
musculus GN=Negr1 PE=2 SV=1
Number of features: 0
Seq('MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRC...CIL',
ProteinAlphabet())

print aa.format('seqxml')
<?xml version="1.0" encoding="utf-8"?>
<seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
http://www.seqxml.org/0.4/seqxml.xsd">
 <entry id="tr|A0A4W9|A0A4W9_MOUSE">
  <description>tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus
musculus GN=Negr1 PE=2 SV=1</description>

<AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
 </entry>
</seqXML>

aa.id = 'A0A4W9'
aa.description = 'Neuronal growth regulator 1'
aa.annotations = {'PE': '2', 'ncbi_taxid': '10090', 'organism': 'Mus
musculus', 'source': 'UniProtKB', 'SV':'1'}
aa.dbxrefs = ['GN:Negr1']

which gives now:
print aa.format('seqxml')
<?xml version="1.0" encoding="utf-8"?>
<seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
http://www.seqxml.org/0.4/seqxml.xsd">
 <entry source="UniProtKB" id="A0A4W9">
  <species name="Mus musculus" ncbiTaxID="10090"></species>
  <description>Neuronal growth regulator 1</description>

<AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
  <DBRef source="GN" id="Negr1"></DBRef>
  <property name="SV" value="1"></property>
  <property name="PE" value="2"></property>
 </entry>
</seqXML>

This is almost what I want. The only thing I?d like to add is
???source="QfO http://www.ebi.ac.uk/reference_proteomes/"
sourceVersion="2013_04">??? to the <seqXML> tag header. How would I do it
please?

Many thanks again,

Alan



On 22 January 2014 16:53, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Jan 22, 2014 at 4:28 PM, Alan <alanwilter at gmail.com> wrote:
> > I have an input fasta file (test.fasta), like:
> >
> >>tr|A0A4W9|A0A4W9_MOUSE Neuronal growth regulator 1 OS=Mus musculus
> > GN=Negr1 PE=2 SV=1
> > MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGA
> > SKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTP
> > RTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQ
> > YLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCE
> > GAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTT
> > NASLPLNQSSIPWQVFFMLKVSFLLVCIL
> >
> > Then I am trying this:
> >
> > from Bio import SeqIO
> > from Bio.Alphabet import generic_protein
> > handle = open("test.fasta")
> > records = list(SeqIO.parse(handle, "fasta", generic_protein))
> > aa = records[0]
> >
> > print aa.format('seqxml')
> > <?xml version="1.0" encoding="utf-8"?>
> > <seqXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> > seqXMLversion="0.4" xsi:noNamespaceSchemaLocation="
> > http://www.seqxml.org/0.4/seqxml.xsd">
> >  <entry id="tr|A0A4W9|A0A4W9_MOUSE">
> >   <description>growth regulator 1</description>
> >
> >
> <AAseq>MVLLAQGACCSNQWLAAVLLSLCSCLPAGQSVDFPWAAVDNMLVRKGDTAVLRCYLEDGASKGAWLNRSSIIFAGGDKWSVDPRVSISTLNKRDYSLQIQNVDVTDDGPYTCSVQTQHTPRTMQVHLTVQVPPKIYDISNDMTINEGTNVTLTCLATGKPEPVISWRHISPSAKPFENGQYLDIYGITRDQAGEYECSAENDVSFPDVKKVRVIVNFAPTIQEIKSGTVTPGRSGLIRCEGAGVPPPAFEWYKGEKRLFNGQQGIIIQNFSTRSILTVTNVTQEHFGNYTCVAANKLGTTNASLPLNQSSIPWQVFFMLKVSFLLVCIL</AAseq>
> >  </entry>
> > </seqXML>
> >
> > Note above that my SeqIO.parse is not picking all the info in the Fasta
> > header.
>
> Odd, what does aa.description give you?
>
> > But I want to tweak this to output something more like this:
> > ...
> >   <species name="Mus musculus" ncbiTaxID="10090" />
> >   <description>Neuronal growth regulator 1</description>
> >
> > The aa.id, aa.description wouldn't be a problem to update and some info
> I
> > have to provide from elsewhere (like ncbiTaxID and species name), but how
> > to add the details in the <seqXML>, <entry source> or create <species>,
> > <DBRef> etc.?
>
> Set record.annotations["organism"] and record.annotations["ncbi_taxid"]
> to suitable strings, and the list record.dbxref = ["db:identifer", ...].
>
> Also what version of Biopython are you using?
>
> Peter
>



From p.j.a.cock at googlemail.com  Thu Jan 23 13:56:08 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 Jan 2014 13:56:08 +0000
Subject: [Biopython] help with seqxml format
In-Reply-To: <CAEznbz=a5zWwPQzrq4dfobn+BT+idpp9zabtv71Ho45VMVf5BQ@mail.gmail.com>
References: <CAEznbzkbWyEZv-rqhU4AMohGLhOMjKpUzpWejsQDq7qLHtot=w@mail.gmail.com>
	<CAKVJ-_4ivQkwHUxd0C7w-7qvyyHrYPAjDikY=J7L-ZkF4pLWCA@mail.gmail.com>
	<CAEznbz=a5zWwPQzrq4dfobn+BT+idpp9zabtv71Ho45VMVf5BQ@mail.gmail.com>
Message-ID: <CAKVJ-_7ZF1jO6g50YgvgMVfwPCAZcfu0wQd8mUXM9p=yjpfsGA@mail.gmail.com>

On Thu, Jan 23, 2014 at 1:40 PM, Alan <alanwilter at gmail.com> wrote:
> Thanks Peter,
>
> I am using the latest version 1.63.
>
> I?ve found some mistakes of myself, aa.description is fine:
>

Oh good - I was puzzled about that bit.

> This is almost what I want. The only thing I?d like to add is ???source="QfO
> http://www.ebi.ac.uk/reference_proteomes/" sourceVersion="2013_04">??? to
> the <seqXML> tag header. How would I do it please?

Setting record.annotations["sourceVersion"] = "2013_04" should do it.

(I'm assuming the odd QfO bit for the source value was a problem
copying text into the email).

If you are wondering, I've just been reading the source code for
the SeqXmlWriter class to see where it looks for fields:
https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SeqXmlIO.py

It would be nice if someone was to summarise this mapping
in the module's help text (the docstrings).

Regards,

Peter



From alanwilter at gmail.com  Thu Jan 23 14:55:24 2014
From: alanwilter at gmail.com (Alan)
Date: Thu, 23 Jan 2014 14:55:24 +0000
Subject: [Biopython] =?utf-8?b?dHlwbyBlcnJvciDigJxzb3VyY2VfZXJzaW9u4oCd?=
	=?utf-8?q?_=2C_it_should_be_=E2=80=9Csource=5Fversion=22?=
Message-ID: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>

In https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SeqXmlIO.py

    def write_header(self):
        """Write root node with document metadata."""

        SequentialSequenceWriter.write_header(self)

        attrs = {"xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
                 "xsi:noNamespaceSchemaLocation":
"http://www.seqxml.org/0.4/seqxml.xsd",
                 "seqXMLversion": "0.4"}

        if self.source is not None:
            attrs["source"] = self.source
        if self.source_version is not None:
            attrs["sourceVersion"] = self.source_ersion

Alan


From p.j.a.cock at googlemail.com  Thu Jan 23 15:11:07 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 23 Jan 2014 15:11:07 +0000
Subject: [Biopython]
	=?windows-1252?q?typo_error_=93source=5Fersion=94_=2C?=
	=?windows-1252?q?_it_should_be_=93source=5Fversion=22?=
In-Reply-To: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>
References: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>
Message-ID: <CAKVJ-_7WiNxq9nk=uQv=1rVRUA9pThj8oV=d+_NQMrFf2_1P2A@mail.gmail.com>

On Thu, Jan 23, 2014 at 2:55 PM, Alan <alanwilter at gmail.com> wrote:
> In https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SeqXmlIO.py
>
> ...
>
>             attrs["sourceVersion"] = self.source_ersion
>
>
> Alan

Yes indeed, fixed - thank you:
https://github.com/biopython/biopython/commit/0e23daf8d0d2ad9130479417d77147e794e182be

This highlights that we could do with a few more unit tests on
the annotation side of things in the SeqXML code:
https://github.com/biopython/biopython/blob/master/Tests/test_SeqIO_SeqXML.py

Regards,

Peter


From mike.thon at gmail.com  Thu Jan 23 16:31:50 2014
From: mike.thon at gmail.com (Michael Thon)
Date: Thu, 23 Jan 2014 17:31:50 +0100
Subject: [Biopython] Follow-up about python/biopython code for
	submitting multiple jobs to clustalw
In-Reply-To: <CAKVJ-_6RMESVxvXXym_JWYw+1Nm=dV8zaoLWUP1JyirQsJTSRA@mail.gmail.com>
References: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>
	<CAKVJ-_6RMESVxvXXym_JWYw+1Nm=dV8zaoLWUP1JyirQsJTSRA@mail.gmail.com>
Message-ID: <C4A00153-A1B3-4FE9-95F8-933A4A5C0E4E@gmail.com>

Hi Edson -  It sounds like you have many alignments concatenated together in one file.  You may want to keep each of your loci (a.k.a. orthologous sets of DNA or protein sequences) in a separate file for each family.  I think you will find it easier to do your alignment and tree building operations on them.  For each locus make a protein file in FASTA format and a transcript file in fasta format, each file would have four sequences in it.  then its simple to loop through the contents of a directory and call a command line program on each file.  You may not even need python for all the steps. 


On Jan 23, 2014, at 10:57 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, Jan 23, 2014 at 7:39 AM, Edson Ishengoma
> <ishengomae at nm-aist.ac.tz> wrote:
>> Hi all,
>> 
>> I couldn't get a response about my struggles which I asked few days past, I
>> presume it was either a poorly submitted question or my approach with what I
>> want to do is totally out of touch with mainstream bioinformatics. The thing
>> is I am a newbie to both python programming and bioinformatics but I believe
>> there are people here who can help, so I will try again with more
>> background.
>> 
>> The overall goal with what I want to achieve is to perform selection
>> analyses on multiple species with codeml in PAML. For this the inputs should
>> be both the sequence alignments and tree files. I already have sequence file
>> (produced by pal2nal) but I still need a corresponding tree file.
>> 
>> So what I am challenged with is the fact that my nucleotide alignment file
>> contain cds of four species at many loci (it is kind of whole genome data)
>> so I will have to submit the job to a tree producing program per each
>> alignment - I can use clustalw or Phylip.
> 
> If you haven't already, try to get some advice from a phylogenetics
> specialist about what to do. For example, clustalw is old and superseded.
> 
> You have 4 species, and (say) 50 genes/loci from each. One approach
> is to make 50 protein alignments (one for each set of four genes),
> turn these into 50 codon-aware nucleotide alignments (with pal2nal
> or similar, e.g. [1]), then you could use Biopython to combine these
> into a single large concatenated alignment (4 rows for the 4 species),
> and use that to build a tree.
> 
> This may not be the best plan, but one of our students here did
> something like this recently (using Biopython in part).
> 
> Peter
> [1] https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython




From ishengomae at nm-aist.ac.tz  Thu Jan 23 18:01:47 2014
From: ishengomae at nm-aist.ac.tz (Edson Ishengoma)
Date: Thu, 23 Jan 2014 21:01:47 +0300
Subject: [Biopython] Follow-up about python/biopython code for
 submitting multiple jobs to clustalw
In-Reply-To: <C4A00153-A1B3-4FE9-95F8-933A4A5C0E4E@gmail.com>
References: <CAKoVMy=xKSyGap4M9tsC1kKXWVR9rK1t21T4NtXAed-jSZLffA@mail.gmail.com>
	<CAKVJ-_6RMESVxvXXym_JWYw+1Nm=dV8zaoLWUP1JyirQsJTSRA@mail.gmail.com>
	<C4A00153-A1B3-4FE9-95F8-933A4A5C0E4E@gmail.com>
Message-ID: <CAKoVMyn+wLnEiWTEzMeoY8W8hMVD5BifFDXLd39YYXWcx+sSBw@mail.gmail.com>

Thanks Michael,
Yes I have many orthologous alignments (about 20,000 thousands genes
--typical of mammalian genomes anyway). Initially I thought of this idea of
having separate files and I hesitated because of computer memory expenses
in writing files. So thanks for reinforcing my thought that it can be a
viable option.

Regards,

Edson B. Ishengoma
PhD-Candidate
*School of Life Sciences and Engineering
Nelson Mandela African Institute of Science and Technology
Nelson Mandela Road
P. O. Box 447, Arusha
Tanzania (255)
*
*ishengomae at nm-aist.ac.tz  *ebarongo82 at yahoo.co.uk
*

<http://www.nm-aist.ac.tz/>Mobile: +255 762 348 037, +255 714 789 360,
  Website: www.nm-aist.ac.tz
Skype: edson.ishengoma

*
*
**


On Thu, Jan 23, 2014 at 7:31 PM, Michael Thon <mike.thon at gmail.com> wrote:

> Hi Edson -  It sounds like you have many alignments concatenated together
> in one file.  You may want to keep each of your loci (a.k.a. orthologous
> sets of DNA or protein sequences) in a separate file for each family.  I
> think you will find it easier to do your alignment and tree building
> operations on them.  For each locus make a protein file in FASTA format and
> a transcript file in fasta format, each file would have four sequences in
> it.  then its simple to loop through the contents of a directory and call a
> command line program on each file.  You may not even need python for all
> the steps.
>
>
> On Jan 23, 2014, at 10:57 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
> On Thu, Jan 23, 2014 at 7:39 AM, Edson Ishengoma
> <ishengomae at nm-aist.ac.tz> wrote:
>
> Hi all,
>
> I couldn't get a response about my struggles which I asked few days past, I
> presume it was either a poorly submitted question or my approach with what
> I
> want to do is totally out of touch with mainstream bioinformatics. The
> thing
> is I am a newbie to both python programming and bioinformatics but I
> believe
> there are people here who can help, so I will try again with more
> background.
>
> The overall goal with what I want to achieve is to perform selection
> analyses on multiple species with codeml in PAML. For this the inputs
> should
> be both the sequence alignments and tree files. I already have sequence
> file
> (produced by pal2nal) but I still need a corresponding tree file.
>
> So what I am challenged with is the fact that my nucleotide alignment file
> contain cds of four species at many loci (it is kind of whole genome data)
> so I will have to submit the job to a tree producing program per each
> alignment - I can use clustalw or Phylip.
>
>
> If you haven't already, try to get some advice from a phylogenetics
> specialist about what to do. For example, clustalw is old and superseded.
>
> You have 4 species, and (say) 50 genes/loci from each. One approach
> is to make 50 protein alignments (one for each set of four genes),
> turn these into 50 codon-aware nucleotide alignments (with pal2nal
> or similar, e.g. [1]), then you could use Biopython to combine these
> into a single large concatenated alignment (4 rows for the 4 species),
> and use that to build a tree.
>
> This may not be the best plan, but one of our students here did
> something like this recently (using Biopython in part).
>
> Peter
> [1]
> https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>
>


From alanwilter at gmail.com  Fri Jan 24 13:50:34 2014
From: alanwilter at gmail.com (Alan)
Date: Fri, 24 Jan 2014 13:50:34 +0000
Subject: [Biopython] =?utf-8?b?dHlwbyBlcnJvciDigJxzb3VyY2VfZXJzaW9u4oCd?=
	=?utf-8?q?_=2C_it_should_be_=E2=80=9Csource=5Fversion=22?=
In-Reply-To: <CAKVJ-_7WiNxq9nk=uQv=1rVRUA9pThj8oV=d+_NQMrFf2_1P2A@mail.gmail.com>
References: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>
	<CAKVJ-_7WiNxq9nk=uQv=1rVRUA9pThj8oV=d+_NQMrFf2_1P2A@mail.gmail.com>
Message-ID: <CAEznbznDeOXP7gowa33vN4k=62FC7FdKoOtWL9ZHs_rqr14+Hg@mail.gmail.com>

Hi Peter,

I cannot promise, but I will try to see how to improve
test_SeqIO_SeqXML.py. Meanwhile, another typo:

        if self.species is not None:
            if not isinstance(species, basestring):

should be:

        if self.species is not None:
            if not isinstance(*self.*species, basestring):



On 23 January 2014 15:11, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, Jan 23, 2014 at 2:55 PM, Alan <alanwilter at gmail.com> wrote:
> > In
> https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SeqXmlIO.py
> >
> > ...
> >
> >             attrs["sourceVersion"] = self.source_ersion
> >
> >
> > Alan
>
> Yes indeed, fixed - thank you:
>
> https://github.com/biopython/biopython/commit/0e23daf8d0d2ad9130479417d77147e794e182be
>
> This highlights that we could do with a few more unit tests on
> the annotation side of things in the SeqXML code:
>
> https://github.com/biopython/biopython/blob/master/Tests/test_SeqIO_SeqXML.py
>
> Regards,
>
> Peter
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588


From p.j.a.cock at googlemail.com  Sun Jan 26 13:18:47 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sun, 26 Jan 2014 13:18:47 +0000
Subject: [Biopython]
	=?windows-1252?q?typo_error_=93source=5Fersion=94_=2C?=
	=?windows-1252?q?_it_should_be_=93source=5Fversion=22?=
In-Reply-To: <CAEznbznDeOXP7gowa33vN4k=62FC7FdKoOtWL9ZHs_rqr14+Hg@mail.gmail.com>
References: <CAEznbzkdD80mW2vtPEUN5QP4L6y=Wjd+wnzVmdFXaAT5og1Y6g@mail.gmail.com>
	<CAKVJ-_7WiNxq9nk=uQv=1rVRUA9pThj8oV=d+_NQMrFf2_1P2A@mail.gmail.com>
	<CAEznbznDeOXP7gowa33vN4k=62FC7FdKoOtWL9ZHs_rqr14+Hg@mail.gmail.com>
Message-ID: <CAKVJ-_7qBrCrOgFOkF_GoSpYgPEDtDkaJuC=-0R+=07uGR-g2Q@mail.gmail.com>

On Fri, Jan 24, 2014 at 1:50 PM, Alan <alanwilter at gmail.com> wrote:
> Hi Peter,
>
> I cannot promise, but I will try to see how to improve test_SeqIO_SeqXML.py.
> Meanwhile, another typo:
>
>         if self.species is not None:
>             if not isinstance(species, basestring):
>
> should be:
>
>         if self.species is not None:
>             if not isinstance(self.species, basestring):
>

Hi Alan,

That's fixed too now, thanks again:
https://github.com/biopython/biopython/commit/d06e85da15bae355219f1cfb767b93fb02d8130d

And I added a basic test which drew my attention to the fact that the
SeqXML parser was not fully compatible with the precedent set by
the plain text SwissProt and UniProt XML parsers (lists versus strings):
https://github.com/biopython/biopython/commit/91810c8acdd4d407b6820ef62cbf9fa591d9341d
https://github.com/biopython/biopython/commit/50f47b8a7e08be5e22f66be59f0eef23249d05e1

The SeqXML species stuff probably still needs more tests... in
particular chimeric records may cause trouble?

Regards,

Peter


From eyalarian at gmail.com  Tue Jan 28 18:42:44 2014
From: eyalarian at gmail.com (Eyal Arian)
Date: Tue, 28 Jan 2014 10:42:44 -0800
Subject: [Biopython] IMGT/HLA DB Access
Message-ID: <AE1743A2-0D79-408A-9541-350F47182DC2@gmail.com>

Hello,
I would like to access data directly from the imgt/hla database into BioPython: http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/align.cgi

For example, the following doesn't work, but it may give you the idea of what I am trying to do:
>>> import Bio
>>> from Bio import Entrez
>>> Entrez.email = "eyalarian at gmail.com"
>>> handle = Entrez.esearch(db="x-imgt-hla", term="DPB1*01:01:01")
>>> record = Entrez.read(handle) 
Traceback (most recent call last): 
File "<stdin>", line 1, in <module> 
File "Bio/Entrez/__init__.py", line 372, in read 
record = handler.read(handle) 
File "Bio/Entrez/Parser.py", line 187, in read 
self.parser.ParseFile(handle) 
File "Bio/Entrez/Parser.py", line 325, in endElementHandler 
raise RuntimeError(value) 
RuntimeError: Invalid db name specified: x-imgt-hla 

Thanks!
E. Arian


From djwinter at asu.edu  Tue Jan 28 22:00:53 2014
From: djwinter at asu.edu (David Winter)
Date: Tue, 28 Jan 2014 15:00:53 -0700
Subject: [Biopython] IMGT/HLA DB Access
In-Reply-To: <AE1743A2-0D79-408A-9541-350F47182DC2@gmail.com>
References: <AE1743A2-0D79-408A-9541-350F47182DC2@gmail.com>
Message-ID: <CAHYKzYY4trGVj=k=7GhwvSd_=Ceh+J3EJ8BraKWQ2mmODMsyXQ@mail.gmail.com>

Hi Eyal,

The Entrez module is specifically for the NCBI's entrez databases (the
likes of the nucleotide, refseq and pubmed), and won't work for others.

If the mgt/hla database has an API (a quick search around the site doesn't
find one) it might be possible to write your own code to access the
database programatically, but I don't think there in anything in Biopython
that will help you with actually querying the database or fetching records
from it.

David


On Tue, Jan 28, 2014 at 11:42 AM, Eyal Arian <eyalarian at gmail.com> wrote:

> Hello,
> I would like to access data directly from the imgt/hla database into
> BioPython: http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/align.cgi
>
> For example, the following doesn't work, but it may give you the idea of
> what I am trying to do:
> >>> import Bio
> >>> from Bio import Entrez
> >>> Entrez.email = "eyalarian at gmail.com"
> >>> handle = Entrez.esearch(db="x-imgt-hla", term="DPB1*01:01:01")
> >>> record = Entrez.read(handle)
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "Bio/Entrez/__init__.py", line 372, in read
> record = handler.read(handle)
> File "Bio/Entrez/Parser.py", line 187, in read
> self.parser.ParseFile(handle)
> File "Bio/Entrez/Parser.py", line 325, in endElementHandler
> raise RuntimeError(value)
> RuntimeError: Invalid db name specified: x-imgt-hla
>
> Thanks!
> E. Arian
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
David Winter
Postdoctoral Research Associate
Center for Evolutionary Medicine and Informatics
The Biodesign Institute
Arizona State University

ph: +1 480 519 5113
w: www.david-winter.info
lab: http://cartwrig.ht/lab/
blog: sciblogs.co.nz/the-atavism


From jordan.r.willis at Vanderbilt.Edu  Tue Jan 28 22:22:20 2014
From: jordan.r.willis at Vanderbilt.Edu (Willis, Jordan R)
Date: Tue, 28 Jan 2014 22:22:20 +0000
Subject: [Biopython] IMGT/HLA DB Access
In-Reply-To: <CAHYKzYY4trGVj=k=7GhwvSd_=Ceh+J3EJ8BraKWQ2mmODMsyXQ@mail.gmail.com>
References: <AE1743A2-0D79-408A-9541-350F47182DC2@gmail.com>
	<CAHYKzYY4trGVj=k=7GhwvSd_=Ceh+J3EJ8BraKWQ2mmODMsyXQ@mail.gmail.com>
Message-ID: <AC7D5B64FC829E429B0C96F7E3EE5AAD6A69E547@ITS-HCWNEM108.ds.vanderbilt.edu>

Hi Eyal,

The imgt database is not that dynamic to be honest. Will one download not suffice? You can get all the accession numbers from this table.

http://www.imgt.org/IMGTrepertoireMH/index.php?section=LocusGenes&repertoire=RepresentativeGenes#notes

I have been trying to get an IMGT api for years now. Unfortunately, you are just better off creating your own tools from scratch.



On Jan 28, 2014, at 4:00 PM, David Winter <djwinter at asu.edu<mailto:djwinter at asu.edu>> wrote:

Hi Eyal,

The Entrez module is specifically for the NCBI's entrez databases (the
likes of the nucleotide, refseq and pubmed), and won't work for others.

If the mgt/hla database has an API (a quick search around the site doesn't
find one) it might be possible to write your own code to access the
database programatically, but I don't think there in anything in Biopython
that will help you with actually querying the database or fetching records
from it.

David


On Tue, Jan 28, 2014 at 11:42 AM, Eyal Arian <eyalarian at gmail.com<mailto:eyalarian at gmail.com>> wrote:

Hello,
I would like to access data directly from the imgt/hla database into
BioPython: http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/align.cgi

For example, the following doesn't work, but it may give you the idea of
what I am trying to do:
import Bio
from Bio import Entrez
Entrez.email = "eyalarian at gmail.com<mailto:eyalarian at gmail.com>"
handle = Entrez.esearch(db="x-imgt-hla", term="DPB1*01:01:01")
record = Entrez.read(handle)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "Bio/Entrez/__init__.py", line 372, in read
record = handler.read(handle)
File "Bio/Entrez/Parser.py", line 187, in read
self.parser.ParseFile(handle)
File "Bio/Entrez/Parser.py", line 325, in endElementHandler
raise RuntimeError(value)
RuntimeError: Invalid db name specified: x-imgt-hla

Thanks!
E. Arian
_______________________________________________
Biopython mailing list  -  Biopython at lists.open-bio.org<mailto:Biopython at lists.open-bio.org>
http://lists.open-bio.org/mailman/listinfo/biopython




--
David Winter
Postdoctoral Research Associate
Center for Evolutionary Medicine and Informatics
The Biodesign Institute
Arizona State University

ph: +1 480 519 5113
w: www.david-winter.info<http://www.david-winter.info>
lab: http://cartwrig.ht/lab/
blog: sciblogs.co.nz/the-atavism<http://sciblogs.co.nz/the-atavism>
_______________________________________________
Biopython mailing list  -  Biopython at lists.open-bio.org<mailto:Biopython at lists.open-bio.org>
http://lists.open-bio.org/mailman/listinfo/biopython





From vivekraiiitkgp at gmail.com  Wed Jan 29 09:38:13 2014
From: vivekraiiitkgp at gmail.com (Vivek Rai)
Date: Wed, 29 Jan 2014 15:08:13 +0530
Subject: [Biopython] Where to start contributing in BioPython
Message-ID: <CAGetqtX+m6Eacczg7KjCRfZ4jjyBVZuc4wrSf+c0UA9WvAgvAQ@mail.gmail.com>

Hi everyone,

I am looking for opportunities to contribute into development of BioPython.
However, I could not find a suitable page which guides me in appropriate
direction. I may not be capable enough to start working directly into the
core modules. Therefore, I would request you all to suggest me how shall I
proceed to get introduced with the workings of BioPython, explore code and
may be start with fixing few smaller open bugs.

Secondly, the ideas or suggestions page for GSoC 2014 doesn't seems to be
active. If someone is having any idea about that, please let me know.

Thanks,

-- 
*Vivek Rai*
*Sophomore Undergraduate*


From p.j.a.cock at googlemail.com  Wed Jan 29 09:55:41 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jan 2014 09:55:41 +0000
Subject: [Biopython] Where to start contributing in BioPython
In-Reply-To: <CAGetqtX+m6Eacczg7KjCRfZ4jjyBVZuc4wrSf+c0UA9WvAgvAQ@mail.gmail.com>
References: <CAGetqtX+m6Eacczg7KjCRfZ4jjyBVZuc4wrSf+c0UA9WvAgvAQ@mail.gmail.com>
Message-ID: <CAKVJ-_768ij6c+faCzoTUV1dh5rZeM+XP-sYB948-v17NTFHTA@mail.gmail.com>

On Wed, Jan 29, 2014 at 9:38 AM, Vivek Rai <vivekraiiitkgp at gmail.com> wrote:
> Hi everyone,
>
> I am looking for opportunities to contribute into development of BioPython.
> However, I could not find a suitable page which guides me in appropriate
> direction. I may not be capable enough to start working directly into the
> core modules. Therefore, I would request you all to suggest me how shall I
> proceed to get introduced with the workings of BioPython, explore code and
> may be start with fixing few smaller open bugs.

Hi Vivek,

Are you doing any bioinformatics in your studies or work? Which general
area - for example sequences, alignments, phylogenetics, HMM, gene
expression, ... - that would be a good way to narrow your focus.

On the more technical side, do you know C or have an interest in
cross-platform development?

> Secondly, the ideas or suggestions page for GSoC 2014 doesn't seems to be
> active. If someone is having any idea about that, please let me know.

We (the OBF) should be making a formal announcement soon, but we
do intend to apply to be a Google Summer of Code mentoring organisation
again this year, and we should start brain-storming and discussing some
more possible project ideas on the biopython-dev mailing list.

Thanks for you interest,

Peter


From j.connolly at sheffield.ac.uk  Wed Jan 29 14:43:28 2014
From: j.connolly at sheffield.ac.uk (John Connolly)
Date: Wed, 29 Jan 2014 14:43:28 +0000
Subject: [Biopython] Problem running blastp
Message-ID: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>

Hi,

I am very new to Biopython and python, so please excuse me if this is a
very basic question.

I have installed Blast+, which runs fine from the command line. I have also
used Biopython to produce a program that parses xml output, which works
fine.

My problem is that I would like to run a local blast from within a python
program, tacked on to the start of my parsing program.

I have used the program in the tutorial:

from Bio.Blast.Applications import NcbiblastpCommandline

cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
remote=True)

cline
NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB', outfmt=5,
remote=True)
print(cline)
blastp -query seqs.txt -db NADB -outfmt 5 -remote
stdout, stderr = cline()

I don't expect any output, but I get the following:

  File "test.py", line 8
    blastp -query seqs.txt -db NADB -outfmt 5 -remote
                     ^
SyntaxError: invalid syntax


I appreciate any help you could give.


From p.j.a.cock at googlemail.com  Wed Jan 29 15:16:16 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jan 2014 15:16:16 +0000
Subject: [Biopython] Problem running blastp
In-Reply-To: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>
References: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>
Message-ID: <CAKVJ-_4+voJUR2k-_Wd70ueUBd05qg4Ev=LyeOYNPbudDjaESg@mail.gmail.com>

On Wed, Jan 29, 2014 at 2:43 PM, John Connolly
<j.connolly at sheffield.ac.uk> wrote:
> Hi,
>
> I am very new to Biopython and python, so please excuse me if this is a
> very basic question.
>
> I have installed Blast+, which runs fine from the command line. I have also
> used Biopython to produce a program that parses xml output, which works
> fine.
>
> My problem is that I would like to run a local blast from within a python
> program, tacked on to the start of my parsing program.
>
> I have used the program in the tutorial:
>
> from Bio.Blast.Applications import NcbiblastpCommandline
>
> cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
> remote=True)
>
> cline
> NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB', outfmt=5,
> remote=True)
> print(cline)
> blastp -query seqs.txt -db NADB -outfmt 5 -remote
> stdout, stderr = cline()
>
> I don't expect any output, but I get the following:
>
>   File "test.py", line 8
>     blastp -query seqs.txt -db NADB -outfmt 5 -remote
>                      ^
> SyntaxError: invalid syntax
>
>
> I appreciate any help you could give.

This is not a Python command:

blastp -query seqs.txt -db NADB -outfmt 5 -remote

I think you've got a line of sample output inside your Python script,
try reducing it to just these four lines:

from Bio.Blast.Applications import NcbiblastpCommandline
cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
remote=True)
print(cline) # optionally print out what it will run...
stdout, stderr = cline() # run the BLAST

Regards,

Peter


From j.connolly at sheffield.ac.uk  Wed Jan 29 16:26:53 2014
From: j.connolly at sheffield.ac.uk (John Connolly)
Date: Wed, 29 Jan 2014 16:26:53 +0000
Subject: [Biopython] Problem running blastp
In-Reply-To: <CAKVJ-_4+voJUR2k-_Wd70ueUBd05qg4Ev=LyeOYNPbudDjaESg@mail.gmail.com>
References: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>
	<CAKVJ-_4+voJUR2k-_Wd70ueUBd05qg4Ev=LyeOYNPbudDjaESg@mail.gmail.com>
Message-ID: <CAFV3WFv29nUHg7kRtW0=k0yJ_j5m0PPXNPaS7zrE3oS+XrRZKg@mail.gmail.com>

Hi Peter,

Thank you for your reply.

I realised that the line you mentioned was unnecessary after I'd sent the
message, but I didn't know how to update the mailing list. Sorry about that.

Here's the program after I've modified it a little:

"from Bio.Blast.Applications import NcbiblastpCommandline

cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5)

cline
NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB', outfmt=5)
print(cline)
#blastp -query seqs.txt -db NADB -outfmt 5 -remote
stdout, stderr = cline()"

It runs fine, but I thought I knew how to assign the results of the blast
to a file_handle, which I could then parse. I thought that the results
would be in cline(). I know how to get the results to a file, but I would
like to parse them in the same program (I have a parsing program that does
exactly what I need).



On 29 January 2014 15:16, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Jan 29, 2014 at 2:43 PM, John Connolly
> <j.connolly at sheffield.ac.uk> wrote:
> > Hi,
> >
> > I am very new to Biopython and python, so please excuse me if this is a
> > very basic question.
> >
> > I have installed Blast+, which runs fine from the command line. I have
> also
> > used Biopython to produce a program that parses xml output, which works
> > fine.
> >
> > My problem is that I would like to run a local blast from within a python
> > program, tacked on to the start of my parsing program.
> >
> > I have used the program in the tutorial:
> >
> > from Bio.Blast.Applications import NcbiblastpCommandline
> >
> > cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
> > remote=True)
> >
> > cline
> > NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB',
> outfmt=5,
> > remote=True)
> > print(cline)
> > blastp -query seqs.txt -db NADB -outfmt 5 -remote
> > stdout, stderr = cline()
> >
> > I don't expect any output, but I get the following:
> >
> >   File "test.py", line 8
> >     blastp -query seqs.txt -db NADB -outfmt 5 -remote
> >                      ^
> > SyntaxError: invalid syntax
> >
> >
> > I appreciate any help you could give.
>
> This is not a Python command:
>
> blastp -query seqs.txt -db NADB -outfmt 5 -remote
>
> I think you've got a line of sample output inside your Python script,
> try reducing it to just these four lines:
>
> from Bio.Blast.Applications import NcbiblastpCommandline
> cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5,
> remote=True)
> print(cline) # optionally print out what it will run...
> stdout, stderr = cline() # run the BLAST
>
> Regards,
>
> Peter
>


From p.j.a.cock at googlemail.com  Wed Jan 29 16:33:11 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 Jan 2014 16:33:11 +0000
Subject: [Biopython] Problem running blastp
In-Reply-To: <CAFV3WFv29nUHg7kRtW0=k0yJ_j5m0PPXNPaS7zrE3oS+XrRZKg@mail.gmail.com>
References: <CAFV3WFuAZArp0WUoFtQZs5WtSmHXJsH0ng-x9uOy=ChbCeMgGg@mail.gmail.com>
	<CAKVJ-_4+voJUR2k-_Wd70ueUBd05qg4Ev=LyeOYNPbudDjaESg@mail.gmail.com>
	<CAFV3WFv29nUHg7kRtW0=k0yJ_j5m0PPXNPaS7zrE3oS+XrRZKg@mail.gmail.com>
Message-ID: <CAKVJ-_7+VNz3V2bRU1+PszNfJbR=8LXW+HXc5hEGNg2-i8jAkA@mail.gmail.com>

On Wed, Jan 29, 2014 at 4:26 PM, John Connolly
<j.connolly at sheffield.ac.uk> wrote:
> Hi Peter,
>
> Thank you for your reply.
>
> I realised that the line you mentioned was unnecessary after I'd sent the
> message, but I didn't know how to update the mailing list. Sorry about that.
>
> Here's the program after I've modified it a little:
>
> "from Bio.Blast.Applications import NcbiblastpCommandline
>
> cline = NcbiblastpCommandline(query="seqs.txt", db="NADB", outfmt=5)
>
> cline
> NcbiblastpCommandline(cmd='blastp', query='seqs.txt', db='NADB', outfmt=5)
> print(cline)
> #blastp -query seqs.txt -db NADB -outfmt 5 -remote
> stdout, stderr = cline()"
>
> It runs fine, but I thought I knew how to assign the results of the blast to
> a file_handle, which I could then parse. I thought that the results would be
> in cline(). I know how to get the results to a file, but I would like to
> parse them in the same program (I have a parsing program that does exactly
> what I need).

As written, BLAST's output will be sent to stdout (default behaviour),
and therefore captured as a (potentially large) string. You could turn
this into a handle with StringIO:

from io import StringIO
handle = StringIO(stdout)

Don't use this StringIO approach for large output - it will waste
a lot of memory.

What I would normally do is ask BLAST to save the output to
a file, and open the file for reading to get a handle.

This also means you can separate running BLAST (usually slow)
and processing the output (usually fast, but I find I often need
to adjust the code so I'd want to repeat this bit many times while
working on the code - without having to rerun BLAST each time).

Peter


From eric.talevich at gmail.com  Wed Jan 29 21:29:02 2014
From: eric.talevich at gmail.com (Eric Talevich)
Date: Wed, 29 Jan 2014 13:29:02 -0800
Subject: [Biopython] Google Summer of Code 2014 - Call for project ideas
Message-ID: <CAMC681ktJLOjcS746YB3MwCb534rZvfk87p-HGVdyt3Le=Y2RQ@mail.gmail.com>

Hi folks,

Google Summer of Code is on again for 2014, and the Open Bioinformatics
Foundation (OBF) is once again applying as a mentoring organization.
Participating in GSoC as an organization is very competitive, and we will
need your help in gathering a good set of ideas and potential mentors for
Biopython's role in GSoC this year.

If you have an idea for a Summer of Code project, please post your idea
here on the Biopython mailing list for discussion and start an outline on
this wiki page:
http://biopython.org/wiki/Google_Summer_of_Code

We also welcome ideas that fit with OBF's mission but are not part of a
single Bio* project, or span multiple projects -- these ideas can be posted
on the OBF wiki and discussed on the OBF mailing list:
http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Here's to another fun and productive Summer of Code!

Cheers,
Eric & Raoul


From p.j.a.cock at googlemail.com  Fri Jan 31 10:55:55 2014
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 31 Jan 2014 10:55:55 +0000
Subject: [Biopython] Google Summer of Code 2014 - Call for project ideas
In-Reply-To: <CAMC681ktJLOjcS746YB3MwCb534rZvfk87p-HGVdyt3Le=Y2RQ@mail.gmail.com>
References: <CAMC681ktJLOjcS746YB3MwCb534rZvfk87p-HGVdyt3Le=Y2RQ@mail.gmail.com>
Message-ID: <CAKVJ-_7wV2JD2=Lbjem1WDW6e=eO=W6x4KOHxJh0zuVyNrsrVw@mail.gmail.com>

On Wed, Jan 29, 2014 at 9:29 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> Hi folks,
>
> Google Summer of Code is on again for 2014, and the Open Bioinformatics
> Foundation (OBF) is once again applying as a mentoring organization.
> Participating in GSoC as an organization is very competitive, and we will
> need your help in gathering a good set of ideas and potential mentors for
> Biopython's role in GSoC this year.
>
> If you have an idea for a Summer of Code project, please post your idea
> here on the Biopython mailing list for discussion and start an outline on
> this wiki page:
> http://biopython.org/wiki/Google_Summer_of_Code
>
> We also welcome ideas that fit with OBF's mission but are not part of a
> single Bio* project, or span multiple projects -- these ideas can be posted
> on the OBF wiki and discussed on the OBF mailing list:
> http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas
> http://lists.open-bio.org/mailman/listinfo/open-bio-l
>
> Here's to another fun and productive Summer of Code!
>
> Cheers,
> Eric & Raoul

Thanks Eric & Raoul,

Remember that the ideas don't have to come from potential mentors -
if as a student there is something you'd particularly like to work on
please ask, and perhaps we can find a suitable (Biopython) mentor.

Regards,

Peter