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Paul.Czodrowski | 3 May 2011 12:56
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[Biopython] installation as non-administrator


Dear folks,

I'm struggling around with the biopython installation.
As non-administrator, the manual states the following:
http://biopython.org/DIST/docs/install/Installation.html#htoc30

However, the setup.py (version 1.57) does not contain any entry "
include_dirs=["Bio/Cluster", "your_dir/include/python"]
", but rather only "Bio" entries.

(See attached file: setup.py)

Or do I oversee anything?

Regards,
Paul

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Peter Cock | 3 May 2011 13:31
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Re: [Biopython] installation as non-administrator

On Tue, May 3, 2011 at 11:56 AM,  <Paul.Czodrowski <at> merck.de> wrote:
>
> Dear folks,
>
> I'm struggling around with the biopython installation.
> As non-administrator, the manual states the following:
> http://biopython.org/DIST/docs/install/Installation.html#htoc30
>
> However, the setup.py (version 1.57) does not contain any entry "
> include_dirs=["Bio/Cluster", "your_dir/include/python"]
> ", but rather only "Bio" entries.
>
> (See attached file: setup.py)

You didn't really need to attach a whole file, you could have
linked to our repository or quoted the bit of interest.

> Or do I oversee anything?

What OS are you using? Some flavour of Linux?

What version of NumPy do you have, and how was it installed?

What command did you use to attempt the install, and what
error message did you get.

Have you tried the --prefix argument?

e.g.
(Continue reading)

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João Rodrigues | 3 May 2011 13:32
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Re: [Biopython] installation as non-administrator

Hey Paul,

I usually keep a copy of biopython in my home directory either by supplying
the keyword --home=/my/home/directory or just by making "python setup.py
build" and then adding the temp/libxxx/ directory to my PYTHONPATH.

Hope it helps,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao

On Tue, May 3, 2011 at 12:56 PM, <Paul.Czodrowski <at> merck.de> wrote:

>
> Dear folks,
>
> I'm struggling around with the biopython installation.
> As non-administrator, the manual states the following:
> http://biopython.org/DIST/docs/install/Installation.html#htoc30
>
> However, the setup.py (version 1.57) does not contain any entry "
> include_dirs=["Bio/Cluster", "your_dir/include/python"]
> ", but rather only "Bio" entries.
>
> (See attached file: setup.py)
>
> Or do I oversee anything?
>
>
> Regards,
(Continue reading)

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João Rodrigues | 3 May 2011 13:32
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Re: [Biopython] installation as non-administrator

Sorry, --prefix, not --home.
_______________________________________________
Biopython mailing list  -  Biopython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
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Martin Mokrejs | 3 May 2011 14:22
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[Biopython] How to optimize ACE file alignment (from newbler)

Hi,
  I would like to ask you how can I optimize the ACE alignment with files
produced by newbler. I see only the high-quality region is aligned while
the rest is not. I typically ask newbler to place into the ace files untrimmed
reads so the low-quality sequence is present, you can see it could have been
included in the alignment and contribute the consensus quite well.
  I found a new feature of consed-20 being able to re-align the reads 
but that seemed to be too slow for me and had to kill re-processing of one
contig.
  Is there a way to direct some program that I want to re-align just some
columns since some position? That should first align to the consensus already
defined and afterwards continue with de novo alignment as long as it is possible.
  Alternatively, how do you edit ACE alignments (I mean manually adjust gaps,
move columns back and forth, re-order rows) and do you re-calculate the
consensus?
  This is some sort of a follow-up to "Newbler ACE file to SAM?"
posted to biopython-developers list at http://web.archiveorange.com/archive/v/5dAwXxUKZDTmQdM80MqQ
;)
Martin
_______________________________________________
Biopython mailing list  -  Biopython <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biopython
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Peter Cock | 3 May 2011 15:46
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Re: [Biopython] How to optimize ACE file alignment (from newbler)

On Tue, May 3, 2011 at 1:22 PM, Martin Mokrejs
<mmokrejs <at> fold.natur.cuni.cz> wrote:
> Hi,
>  I would like to ask you how can I optimize the ACE alignment with files
> produced by newbler. I see only the high-quality region is aligned while
> the rest is not. I typically ask newbler to place into the ace files untrimmed
> reads so the low-quality sequence is present, you can see it could have been
> included in the alignment and contribute the consensus quite well.
>  I found a new feature of consed-20 being able to re-align the reads
> but that seemed to be too slow for me and had to kill re-processing of one
> contig.
>  Is there a way to direct some program that I want to re-align just some
> columns since some position? That should first align to the consensus already
> defined and afterwards continue with de novo alignment as long as it is possible.
>  Alternatively, how do you edit ACE alignments (I mean manually adjust gaps,
> move columns back and forth, re-order rows) and do you re-calculate the
> consensus?
>  This is some sort of a follow-up to "Newbler ACE file to SAM?"
> posted to biopython-developers list at http://web.archiveorange.com/archive/v/5dAwXxUKZDTmQdM80MqQ
> ;)
> Martin

Hi Martin,

Biopython only has an ACE parser, with no support for writing ACE files.
So, even if you did manipulate the parsed ACE file in Biopython, you'd
have to write your own output code (or use a simpler file format).

Regarding assembly editors, have you looked at Gap4 or Gap5?
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Paul.Czodrowski | 3 May 2011 16:38
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[Biopython] Antwort: Re: installation as non-administrator

Dear Peter,

> >
> > Dear folks,
> >
> > I'm struggling around with the biopython installation.
> > As non-administrator, the manual states the following:
> > http://biopython.org/DIST/docs/install/Installation.html#htoc30
> >
> > However, the setup.py (version 1.57) does not contain any entry "
> > include_dirs=["Bio/Cluster", "your_dir/include/python"]
> > ", but rather only "Bio" entries.
> >
> > (See attached file: setup.py)
>
> You didn't really need to attach a whole file, you could have
> linked to our repository or quoted the bit of interest.
I'm sorry for this!

>
> > Or do I oversee anything?
>
> What OS are you using? Some flavour of Linux?
OpenSuse 11.3

>
> What version of NumPy do you have, and how was it installed?
NumPy version 1.3.0, installed locally by the built-in python routines.

>
(Continue reading)

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Paul.Czodrowski | 3 May 2011 16:47
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[Biopython] Antwort: Re: installation as non-administrator

Dear Peter,

maybe as additonal question/issue:
numpy is not located in
"/usr/lib/python2.6/site-packages/numpy/core/include "
but in another, rather global, python-lib-directory.

As stated in my previous email,
python setup.py build gives
"gcc -pthread -fno-strict-aliasing -DNDEBUG -fomit-frame-pointer
-fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
-funwind-tables -fasynchronous-unwind-tables -g -fPIC
-I/usr/lib/python2.6/site-packages/numpy/core/include
-I/usr/include/python2.6 -c Bio/Cluster/clustermodule.c -o
build/temp.linux-i686-2.6/Bio/Cluster/clustermodule.o
Bio/Cluster/clustermodule.c:2:31: fatal error: numpy/arrayobject.h: No such
file or directory"

and I would like to adapt the
"-I/usr/lib/python2.6/site-packages/numpy/core/includ" accordingly to the
directory where it is actually located.

Cheers & thanks,
Paul

> >
> > Dear folks,
> >
> > I'm struggling around with the biopython installation.
> > As non-administrator, the manual states the following:
(Continue reading)

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Peter Cock | 3 May 2011 17:10
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Re: [Biopython] Antwort: Re: installation as non-administrator

On Tue, May 3, 2011 at 3:38 PM,  <Paul.Czodrowski <at> merck.de> wrote:
> Dear Peter,
>
>
>> >
>> > Dear folks,
>> >
>> > I'm struggling around with the biopython installation.
>> > As non-administrator, the manual states the following:
>> > http://biopython.org/DIST/docs/install/Installation.html#htoc30
>> >
>> > However, the setup.py (version 1.57) does not contain any entry "
>> > include_dirs=["Bio/Cluster", "your_dir/include/python"]
>> > ", but rather only "Bio" entries.
>> >
>> > (See attached file: setup.py)
>>
>> You didn't really need to attach a whole file, you could have
>> linked to our repository or quoted the bit of interest.
>
> I'm sorry for this!

Don't worry too much, its a fairly small file otherwise I wouldn't
have let it though the moderation queue.

>> > Or do I oversee anything?
>>
>> What OS are you using? Some flavour of Linux?
>
> OpenSuse 11.3
(Continue reading)

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Martin Mokrejs | 4 May 2011 01:20
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Re: [Biopython] How to optimize ACE file alignment (from newbler)

Hi Peter,
  no I haven't played with gap5 yet, so far only with consed and tablet.
Thanks for noting biopython has no write support for ACE.
Martin

Peter Cock wrote:
> On Tue, May 3, 2011 at 1:22 PM, Martin Mokrejs
> <mmokrejs <at> fold.natur.cuni.cz> wrote:
>> Hi,
>>  I would like to ask you how can I optimize the ACE alignment with files
>> produced by newbler. I see only the high-quality region is aligned while
>> the rest is not. I typically ask newbler to place into the ace files untrimmed
>> reads so the low-quality sequence is present, you can see it could have been
>> included in the alignment and contribute the consensus quite well.
>>  I found a new feature of consed-20 being able to re-align the reads
>> but that seemed to be too slow for me and had to kill re-processing of one
>> contig.
>>  Is there a way to direct some program that I want to re-align just some
>> columns since some position? That should first align to the consensus already
>> defined and afterwards continue with de novo alignment as long as it is possible.
>>  Alternatively, how do you edit ACE alignments (I mean manually adjust gaps,
>> move columns back and forth, re-order rows) and do you re-calculate the
>> consensus?
>>  This is some sort of a follow-up to "Newbler ACE file to SAM?"
>> posted to biopython-developers list at http://web.archiveorange.com/archive/v/5dAwXxUKZDTmQdM80MqQ
>> ;)
>> Martin
> 
> Hi Martin,
>
(Continue reading)

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