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redmine | 18 Jun 2013 08:06

[Biopython - Bug #3435] (New) Pyhlo.draw_ascii() type error


Issue #3435 has been reported by Giulio Valentino Dalla Riva.

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Bug #3435: Pyhlo.draw_ascii() type error
https://redmine.open-bio.org/issues/3435

Author: Giulio Valentino Dalla Riva
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 

I define a simple tree in a newick format file (the example one in the tutorial 13.1).
I read it using
 <at> tree = Phylo.read("simple.dnd", "newick") <at> 
which works.
When I try to use draw_ascii() to draw it I get a Type error:
 <at> Phylo.draw_ascii(tree) <at> 
produces
 <at> Traceback (most recent call last):
  File "<pyshell#7>", line 1, in <module>
    Phylo.draw_ascii(tree)
  File "C:\Python32\lib\site-packages\Bio\Phylo\_utils.py", line 253, in draw_ascii
    draw_clade(tree.root, 0)
  File "C:\Python32\lib\site-packages\Bio\Phylo\_utils.py", line 239, in draw_clade
    char_matrix[thisrow][col] = '_'
TypeError: list indices must be integers, not float <at>
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Yanbo Ye | 16 Jun 2013 08:39
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Post for the first week

Hi Eric, Mark and Jeet,

I post a blog describing the design idea of tree construction module and
some works for the first week. Here is the link:
http://blog.yeyanbo.com/posts/google-summer-of-code-2.html

Best,
Yanbo
--

-- 

叶彦波

中科院武汉病毒所生物信息学课题组

Yanbo Ye

Bioinformatics Group, Wuhan Institute Of Virology, Chinese Academy of
Sciences

_______________________________________________
Biopython-dev mailing list
Biopython-dev <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython-dev
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Yanbo Ye | 15 Jun 2013 05:38
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Re: Biopython Tutorial Chinese Translation

I've contacted the bioxxx website admin. While he agreed, the copyright is
still a problem. He said they just organized the translation from the
original website and make a pdf version. As the original site is not
accessible anymore, now it is hard to find the original translator. Maybe
we can just write an explanation and wait for him/her to contact us.

On Fri, Jun 14, 2013 at 11:36 PM, Zheng Ruan <zruan1991 <at> gmail.com> wrote:

> Cool. Go ahead!
>
> Zheng Ruan
>
>
> On Fri, Jun 14, 2013 at 11:34 AM, Yanbo Ye <yeyanbo289 <at> gmail.com> wrote:
>
>> Sure. The original site for this translation is not accessible anymore.
>> But I know the bioxxx website admin. We can contact him about the author.
>> 在 2013-6-14 下午11:17，"Zheng Ruan" <zruan1991 <at> gmail.com>写道：
>>
>> Yep, some old chapters do not change much. But the copyright seems to be
>>> a concern. Do we need to contact the original author for such a permission.
>>> I think they will be happy to grant it.
>>>
>>> Thanks,
>>> Zheng Ruan
>>>
>>>
>>> On Fri, Jun 14, 2013 at 10:55 AM, Yanbo Ye <yeyanbo289 <at> gmail.com> wrote:
>>>
>>>> Thanks, Zhen Ruan.
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Zheng Ruan | 15 Jun 2013 05:18
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Codon Alignment GSoC Homepage

Hi all,

Following Peter and Karen's suggestion, I set up my project homepage in
github (http://zruanweb.com/ <http://zruanweb.com/index.html>). I also have
a first four weeks' plan there (http://zruanweb.com/project-timeline.html).
Thanks.

Best,
Ruan
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Zheng Ruan | 14 Jun 2013 16:43
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Fwd: Biopython Tutorial Chinese Translation

There was once a discussion in http://www.bioxxx.cn. You can find relevant
info at http://www.bioxxx.cn/thread-2354-1-1.html. However, this seems not
to be an official translation. I find a copy of it in case you don't have
permission (send you off-list).

Best,
Zheng Ruan

On Fri, Jun 14, 2013 at 7:24 AM, Yanbo Ye <yeyanbo289 <at> gmail.com> wrote:

> Hi everyone,
>
> Here we have some people like to translate the biopython tutorial into
> Chinese, so that more people in China can use biopython for their research
> and contribute to biopython. We noticed there is a LaTeX file for this
> tutorial that we can work on.
>
> Before we start, we want to know what is the right way to do this. Is there
> any previous or ongoing translation project that we can follow?
>
> Thanks,
> Yanbo
> --
>
> 叶彦波
>
> 中科院武汉病毒所生物信息学课题组
>
> Yanbo Ye
>
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Yanbo Ye | 14 Jun 2013 13:24
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Biopython Tutorial Chinese Translation

Hi everyone,

Here we have some people like to translate the biopython tutorial into
Chinese, so that more people in China can use biopython for their research
and contribute to biopython. We noticed there is a LaTeX file for this
tutorial that we can work on.

Before we start, we want to know what is the right way to do this. Is there
any previous or ongoing translation project that we can follow?

Thanks,
Yanbo
--

-- 

叶彦波

中科院武汉病毒所生物信息学课题组

Yanbo Ye

Bioinformatics Group, Wuhan Institute Of Virology, Chinese Academy of
Sciences

_______________________________________________
Biopython-dev mailing list
Biopython-dev <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython-dev
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John Berrisford | 13 Jun 2013 21:01
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changing PDB file chains

Hi

I'm trying to use biopython to update a PDB file.

I'm trying to update the chain ID of a series of waters in a PDB file. I
have the original chain ID, new chain ID and water residue number in an
mmcif file which I parse using a separate parser. Then for each water I have
in the mmcif file I want to update the chain ID from the cif file. 

I then want to write out the updated water line (to test it works) or write
out the updated PDB file.

Is this possible with biopython?

Regards

John
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Yanbo Ye | 6 Jun 2013 17:58
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GSOC Project Introduction

Hi everyone,

I'm Yanbo Ye. I'm happy that I was accepted by NESCent for this year's GSOC
and that I can contribute to Biopython through this project. I will work on
two phylogenetic modules of the Phylo package: tree construction and
consensus tree searching. To share my project progress, as Peter Cock
suggested, I have setup a blog <http://blog.yeyanbo.com/> on github.
Here<http://blog.yeyanbo.com/posts/google-summer-of-code-1.html>is my
first introduction post.

Cheers,

Yanbo

--

-- 

叶彦波

中科院武汉病毒所生物信息学课题组

Yanbo Ye

Bioinformatics Group, Wuhan Institute Of Virology, Chinese Academy of
Sciences

_______________________________________________
Biopython-dev mailing list
Biopython-dev <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython-dev
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redmine | 5 Jun 2013 05:31

[Biopython - Bug #3434] (New) PDB.PDBParser


Issue #3434 has been reported by Mirslaw Syzdek.

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Bug #3434: PDB.PDBParser 
https://redmine.open-bio.org/issues/3434

Author: Mirslaw Syzdek
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 

Two months ago I downloaded a pdb file from NCBI (Database: Structure, Name: 1EZQ). With this file the
following code works fine:

 <at> parser = PDB.PDBParser()
struct = parser.get_structure('1EZQ.pdb', '1EZQ.pdb')
ppb = PDB.PPBuilder()
peptides = ppb.build_peptides(struct) <at> 

Few days ago I downloaded the pdb file one more time. For the new file above code stopped working. The
PDBParser is throwing an error. The error is cause by different column separation (see the line 423 in the
attached files).  

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Dave Clements | 4 Jun 2013 21:29
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GCC2013 Regular Registration Closes June 14

Hello all,

This is the final
registration<http://wiki.galaxyproject.org/Events/GCC2013/Register>
reminder for
the 2013 Galaxy Community Conference
(GCC2013<http://wiki.galaxyproject.org/Events/GCC2013>),
being held in Oslo, 30 June through July 2. GCC2013 is a great opportunity
to share best practices and network with other researchers who are also
facing the challenges of data-intensive biology.

Registration <http://wiki.galaxyproject.org/Events/GCC2013/Register> closes
June 14*, ten days from today.  Register
now<http://wiki.galaxyproject.org/Events/GCC2013/Register> and
guarantee your spot in the Training Day
sessions<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> you
want to take.*  *Registration is still a bargain with the full 3-day
registration starting at ~ €165 for post-docs and students (or just €55 per
day).

The program <http://wiki.galaxyproject.org/Events/GCC2013/Program> features

15 Training Day
sessions<http://wiki.galaxyproject.org/Events/GCC2013/Program#Day_0:_Training_Day.2C_30_June>
in
5 tracks on 12 different topics,
25 Talks<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Talk_Abstracts>
on
topics ranging from
Reproducibility<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FAbstracts.2FTalks.A1_July:_Session_1:_Reproducible_science>
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Peter Cock | 4 Jun 2013 19:29
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Alphabet bug in Bio.Motif and Bio.motifs

Hi Bartek,

I'm hoping you or Michiel can investigate this issue,
http://www.biostars.org/p/73500/

I believe Ivan has correctly diagnosed a Biopython issue in the alphabet
handling of the motif class on this BioStars question, and he's given a
workaround. The problem code looks like this:

        if self.alphabet!=IUPAC.unambiguous_dna:
            raise ValueError("Wrong alphabet! Use only with DNA motifs")

First, assuming the test is really for just IUPAC unambiguous DNA,
the error message is misleading - it sounds like using generic_dna
or IUPAC ambiguous DNA would be acceptable but it isn't.

The core problem here is that IUPAC.unambiguous_dna is just
one instance of the IUPACUnambiguousDNA() class, and other
instances should be equally acceptable but will fail the equality.

I have sometimes wondered if we could and should make some of
the Alphabet objects into singletons (only one instance allowed),
which might be one way to solve this issue.

Alternatively, perhaps all we need is to here is see if the alphabet
is DNA and which letter set it uses? Is that the key point for the matrix
calculations etc? e.g.

from Bio.Alphabet import _get_base_alphabet, DNAAlphabet
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