From lueck at ipk-gatersleben.de  Tue Jul  1 03:40:38 2008
From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=)
Date: Tue, 1 Jul 2008 09:40:38 +0200
Subject: [BioPython] Sequence from Fasta
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<320fb6e00806290819s73f95d32x563879e9bb64b924@mail.gmail.com>
	<001901c8da91$0eedfcd0$1022a8c0@ipkgatersleben.de>
	<320fb6e00806300219j54f7f43dpe0051f54be27d402@mail.gmail.com>
Message-ID: <002701c8db4d$c1ab68a0$1022a8c0@ipkgatersleben.de>


--> Peter wrote:
> from Bio import SeqIO
> handle = open("ls_orchid.fasta")
> for seq_record in SeqIO.parse(handle, "fasta") :
>    print seq_record.id
>    print seq_record.seq.tostring()
>    print len(seq_record.seq)
> handle.close()

This works! Thanks!

--> Giovanni wrote:
>Bioperl's SeqIO has support for a 'tab sequence format' which is
>similar to this[1].
>Maybe it could be useful in the future to add support for such a
>format in biopython.

It's a very good idea because I was suprised that it dosen't work. I 
excpected it.

Regards
Stefanie


From biopython at maubp.freeserve.co.uk  Tue Jul  1 04:04:24 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Jul 2008 09:04:24 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
Message-ID: <320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>

On Mon, Jun 30, 2008 at 10:40 AM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:

>> But I'm looking for something like this:
>>
>> Name Sequence without linebreak
>>
>> Example:
>>
>> MySequence atgcgcgctcggcgcgctcgfcgcgccccccatggctcgcgcactacagcg
>> MySequence2 atgcgctctgcgcgctcgatgtagaatatgagatctctatgagatcagcatca
>
> Bioperl's SeqIO has support for a 'tab sequence format' which is
> similar to this[1].
> Maybe it could be useful in the future to add support for such a
> format in biopython.
>
> [1] http://www.bioperl.org/wiki/Tab_sequence_format
>

That does look fairly straight forward.

Do you happen to know how BioPerl reacts when the first field has spaces?
I would suggest treating the first field like the ">" line in a FASTA file and
taking the first word as the id/name and the whole field as the description.

This format could be handy for some people who use the command line.  By
converting between FASTA and the tab format (which can be done with sed
or awk), each sequence is on one line, so you use tools like grep to filter your
records.  Then convert back to fasta.  There's a nice blog page I found some
time ago where the author describes his workflow for this.

Peter

From dalloliogm at gmail.com  Tue Jul  1 05:37:53 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Tue, 1 Jul 2008 11:37:53 +0200
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
Message-ID: <5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>

On Tue, Jul 1, 2008 at 10:04 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Jun 30, 2008 at 10:40 AM, Giovanni Marco Dall'Olio
> <dalloliogm at gmail.com> wrote:
>
>>> But I'm looking for something like this:
>>>
>>> Name Sequence without linebreak
>>>
>>> Example:
>>>
>>> MySequence atgcgcgctcggcgcgctcgfcgcgccccccatggctcgcgcactacagcg
>>> MySequence2 atgcgctctgcgcgctcgatgtagaatatgagatctctatgagatcagcatca
>>
>> Bioperl's SeqIO has support for a 'tab sequence format' which is
>> similar to this[1].
>> Maybe it could be useful in the future to add support for such a
>> format in biopython.
>>
>> [1] http://www.bioperl.org/wiki/Tab_sequence_format
>>
>
> That does look fairly straight forward.
>
> Do you happen to know how BioPerl reacts when the first field has spaces?
> I would suggest treating the first field like the ">" line in a FASTA file and
> taking the first word as the id/name and the whole field as the description.
>

It ignores any field after the first space in the header.

For example:
$ cat >seq1.fasta
>seq1 field2 field3
acatcgatgcatgctagctactgtacgac

$ cat > fasta2tab.pl
my $seqin = Bio::SeqIO->newFh("-file" => "seq1.fasta", "-format" => "fasta");
my $seqout = Bio::SeqIO->newFh("-fh" => \*STDOUT, "-format" => "tab");

while (<$seqin>)
{
        print $seqout $_;
}

$ perl fasta2tab.pl
seq1    acatcgatgcatgctagctactgtacgac


Do you need some help to implement this function?


> This format could be handy for some people who use the command line.  By
> converting between FASTA and the tab format (which can be done with sed
> or awk), each sequence is on one line, so you use tools like grep to filter your
> records.  Then convert back to fasta.  There's a nice blog page I found some
> time ago where the author describes his workflow for this.
>
> Peter
>



-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it

From biopython at maubp.freeserve.co.uk  Tue Jul  1 05:45:48 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Jul 2008 10:45:48 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
Message-ID: <320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>

> It ignores any field after the first space in the header.
>
> For example:
> $ cat >seq1.fasta
>>seq1 field2 field3
> acatcgatgcatgctagctactgtacgac
>
> $ cat > fasta2tab.pl
> my $seqin = Bio::SeqIO->newFh("-file" => "seq1.fasta", "-format" => "fasta");
> my $seqout = Bio::SeqIO->newFh("-fh" => \*STDOUT, "-format" => "tab");
>
> while (<$seqin>)
> {
>        print $seqout $_;
> }
>
> $ perl fasta2tab.pl
> seq1    acatcgatgcatgctagctactgtacgac

Interesting - and now what I had expected.

Could you try getting BioPerl to read in a TSV file like this:

seq1 field2 field3(tab)acatcgatgcatgctagctactgtacgac
seq2 with a description here(tab)ctcgctgnnacatcctagctactgta

I personally would prefer this sort of output as it preserves all the
data from a FASTA input file.  On the other hand, if there are exsting
tools which wouldn't read this then it would be a bad idea.

>
> Do you need some help to implement this function?
>

Not really - but discussion of the behaviour details now is a good
idea.  And some real world example TSV files would be good to add to
Biopython as test cases.

Thanks,

Peter

From biopython at maubp.freeserve.co.uk  Tue Jul  1 07:32:26 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Jul 2008 12:32:26 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
	<320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
	<5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>
Message-ID: <320fb6e00807010432x4346a283je51c265ebf9cab61@mail.gmail.com>

>> Could you try getting BioPerl to read in a TSV file like this:
>>
>> seq1 field2 field3(tab)acatcgatgcatgctagctactgtacgac
>> seq2 with a description here(tab)ctcgctgnnacatcctagctactgta
>>
>> I personally would prefer this sort of output as it preserves all the
>> data from a FASTA input file.  On the other hand, if there are existing
>> tools which wouldn't read this then it would be a bad idea.
>
> It [BioPerl] gives an error warning for every space it encounters.
>

That isn't very nice, arguably a BioPerl limitation.  However, it does
seem best that we try and avoid writing the full description in the
tab output.  The downside is:

>identifer with a long description
acatcgatgcatgctagctactgtacgac

Would have to be saved follows to keep BioPerl happy:

identifier(tab)acatcgatgcatgctagctactgtacgac

Rather than:

identifer with a long description(tab)acatcgatgcatgctagctactgtacgac

Still - if you and Stefanie think this would be useful, I'll have a
look at implementing it.

Peter

From dalloliogm at gmail.com  Tue Jul  1 07:49:34 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Tue, 1 Jul 2008 13:49:34 +0200
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <320fb6e00807010432x4346a283je51c265ebf9cab61@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
	<320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
	<5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>
	<320fb6e00807010432x4346a283je51c265ebf9cab61@mail.gmail.com>
Message-ID: <5aa3b3570807010449k885bf53hce6a1ad58c9daad3@mail.gmail.com>

On Tue, Jul 1, 2008 at 1:32 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>>
>> It [BioPerl] gives an error warning for every space it encounters.
>>
>
> That isn't very nice, arguably a BioPerl limitation.  However, it does
> seem best that we try and avoid writing the full description in the
> tab output.  The downside is:
>
>>identifer with a long description
> acatcgatgcatgctagctactgtacgac

I am not sure, but I think it is because spaces are not allowed in the
header of standard fasta files.
Maybe a good solution would be to convert automatically all spaces to
pipes (|) in the output.


> Still - if you and Stefanie think this would be useful, I'll have a
> look at implementing it.

yes, I think it will be useful to implement.
I know of people who have written a customized fasta2tab script and
use it quite frequently, so it would be good to support such a task.
As you said before this format is commonly used in combination with
grep/gawk scripts.

>
> Peter
>



-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it

From dalloliogm at gmail.com  Tue Jul  1 06:44:49 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Tue, 1 Jul 2008 12:44:49 +0200
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
	<320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
Message-ID: <5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>

On Tue, Jul 1, 2008 at 11:45 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> It ignores any field after the first space in the header.
>>
>> For example:
>> $ cat >seq1.fasta
>>>seq1 field2 field3
>> acatcgatgcatgctagctactgtacgac
>>
>> $ cat > fasta2tab.pl
>> my $seqin = Bio::SeqIO->newFh("-file" => "seq1.fasta", "-format" => "fasta");
>> my $seqout = Bio::SeqIO->newFh("-fh" => \*STDOUT, "-format" => "tab");
>>
>> while (<$seqin>)
>> {
>>        print $seqout $_;
>> }
>>
>> $ perl fasta2tab.pl
>> seq1    acatcgatgcatgctagctactgtacgac
>
> Interesting - and now what I had expected.
>
> Could you try getting BioPerl to read in a TSV file like this:
>
> seq1 field2 field3(tab)acatcgatgcatgctagctactgtacgac
> seq2 with a description here(tab)ctcgctgnnacatcctagctactgta
>
> I personally would prefer this sort of output as it preserves all the
> data from a FASTA input file.  On the other hand, if there are exsting
> tools which wouldn't read this then it would be a bad idea.
>

It gives an error warning for every space it encounters.

Example:
"""
perl convertformat.pl seqm.tab tab fasta

-------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [seq1 field2 field3]
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [seq1 field2 field3]
---------------------------------------------------
>seq1 field2 field3
CATGGCATGCATGCATGCTAGCTAC

-------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [seq2 some description]
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [seq2 some description]
---------------------------------------------------
>seq2 some description
CATGGCATGCATGCATGCTAGCTAC
"""

Please have a look at the script code and the makefile attached.

p.s. I already sent you a similar message, but the mailing list blocked it.


-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it
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From biopython at maubp.freeserve.co.uk  Tue Jul  1 12:06:08 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Jul 2008 17:06:08 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <5aa3b3570807010449k885bf53hce6a1ad58c9daad3@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
	<320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
	<5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>
	<320fb6e00807010432x4346a283je51c265ebf9cab61@mail.gmail.com>
	<5aa3b3570807010449k885bf53hce6a1ad58c9daad3@mail.gmail.com>
Message-ID: <320fb6e00807010906v7e8e6780x92117da60cd39318@mail.gmail.com>

Giovanni wrote:
> yes, I think it will be useful to implement.
> I know of people who have written a customized fasta2tab script and
> use it quite frequently, so it would be good to support such a task.
> As you said before this format is commonly used in combination with
> grep/gawk scripts.

I've gone for the simple option about how to parse the first field, its used
as the record identifer (.id) and name only (nothing clever).  Here is my
suggested code, which you are welcome to download and try out.

Bug 2533 - Support for simple "tab" format in Bio.SeqIO
http://bugzilla.open-bio.org/show_bug.cgi?id=2533

If you want to try this yourself you'll need to download the new file
TabIO.py into the Bio/SeqIO folder and update Bio/SeqIO/__init__.py to
tell it about the new format (two new lines, see patch).

Peter

From lpritc at scri.ac.uk  Wed Jul  2 05:10:05 2008
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Wed, 02 Jul 2008 10:10:05 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <320fb6e00807010906v7e8e6780x92117da60cd39318@mail.gmail.com>
Message-ID: <C491047D.1241C%lpritc@scri.ac.uk>

Hi,

Just to chip in my two-pennorth, there's a self-defining tab-separated
format called "Axon Text File Format" that might be useful here, and which
is frequently seen in microarray work.  There's a description of its use for
.gal files here:

http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html

It's fairly flexible and straightforward as a format, and allows for
human-readable headers - which can contain column definitions, content
notes, or anything else you like - that is adaptable to a variety of output
conventions.  Of course, getting people to settle on a convention is the
tricky part, but at least any given file might be well-defined in its
headers while people argue over it ;)

It's hardly likely that going down that route in BioPython will result in an
file convention that's accepted industry-wide, but at least it might give
options for writing out FASTA file content in tab-separated form while
unambiguously retaining ID, name and definition strings along with the
sequence. 

L.

On 01/07/2008 17:06, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

> Giovanni wrote:
>> yes, I think it will be useful to implement.
>> I know of people who have written a customized fasta2tab script and
>> use it quite frequently, so it would be good to support such a task.
>> As you said before this format is commonly used in combination with
>> grep/gawk scripts.
> 
> I've gone for the simple option about how to parse the first field, its used
> as the record identifer (.id) and name only (nothing clever).  Here is my
> suggested code, which you are welcome to download and try out.
> 
> Bug 2533 - Support for simple "tab" format in Bio.SeqIO
> http://bugzilla.open-bio.org/show_bug.cgi?id=2533
> 
> If you want to try this yourself you'll need to download the new file
> TabIO.py into the Bio/SeqIO folder and update Bio/SeqIO/__init__.py to
> tell it about the new format (two new lines, see patch).
> 
> Peter
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

-- 
Dr Leighton Pritchard B.Sc.(Hons) MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405

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From biopython at maubp.freeserve.co.uk  Sat Jul  5 10:52:10 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 5 Jul 2008 15:52:10 +0100
Subject: [BioPython] Bio.IntelliGenetics (and the MASE format)
Message-ID: <320fb6e00807050752u10c8d8c9s6481238c6b959a2c@mail.gmail.com>

Dear all,

We've recently added support for parsing (reading) the IntelliGenetics
sequence file format to Bio.SeqIO, under the format name "ig"
(following the EMBOSS convention).  This file format also seems to be
known as the MASE multiple sequence alignment format.

This means that the old Bio.IntelliGenetics module is essentially
obsolete, and we could therefore deprecate it in a future Biopython
release.  Before we do that, is anyone using the Bio.IntelliGenetics
module?  Hopefully using Bio.SeqIO will a suitable substitute for you,
but please do get in touch.

More generally, do any of you currently use the IntelliGenetics or
MASE file format?  I'd love to have a few more example files to use in
our test suite.  Also, would you be interested in using Bio.SeqIO to
write out files in this format?

Thank you,

Peter

From p.j.a.cock at googlemail.com  Sat Jul  5 11:20:40 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sat, 5 Jul 2008 16:20:40 +0100
Subject: [BioPython] Biopython at BOSC 2008
Message-ID: <320fb6e00807050820y55fb240fk6feddaefe6aaf1be@mail.gmail.com>

Dear Biopython users,

Later this month Tiago Ant?o will be representing Biopython at the
Bioinformatics Open Source Conference (BOSC 2008) in Toronto, Canada.
Tiago is the most recent developer to join the Biopython project, and
has been working on the new Bio.PopGen module for population genetics.
 BOSC is an annual two-day conference organised by the Open
Bioinformatics Foundation.

http://open-bio.org/wiki/BOSC_2008

Last summer I gave the "Biopython Project Update" talk at the BOSC
2007 in Vienna, Austria.  My slides have been available online via
slideshare, but I finally got round to converting them from PowerPoint
to PDF, and they are now on the Biopython website if anyone is
interested:

http://biopython.org/wiki/Documentation#Presentations
http://open-bio.org/wiki/BOSC_2007

Although unfortunatley I won't be at BOSC 2008, perhaps some of you
will also be there - and I hope everyone there enjoys it.

Peter


From mjldehoon at yahoo.com  Sat Jul  5 20:00:17 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sat, 5 Jul 2008 17:00:17 -0700 (PDT)
Subject: [BioPython] Biopython release 1.47
Message-ID: <287726.364.qm@web62412.mail.re1.yahoo.com>

We are pleased to announce the release of Biopython 1.47.

This release includes a new Bio.AlignIO module, updates to Bio.Blast, parsers for NCBI's Entrez E-Utilities, numerous other code improvements and fixes, and an extended and updated documentation. In particular if you use Biopython to access NCBI's E-Utilities, we encourage you to download and install this release to ensure full compliance with NCBI's access rules.

Source distributions and Windows installers are available from the Biopython website at http://biopython.org. My thanks to all code contributers who made this new release possible.


--Michiel on behalf of the Biopython developers


      

From biopython at maubp.freeserve.co.uk  Wed Jul  9 09:42:35 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Jul 2008 14:42:35 +0100
Subject: [BioPython] Bio.IntelliGenetics (and the MASE format)
In-Reply-To: <320fb6e00807050752u10c8d8c9s6481238c6b959a2c@mail.gmail.com>
References: <320fb6e00807050752u10c8d8c9s6481238c6b959a2c@mail.gmail.com>
Message-ID: <320fb6e00807090642k7edc86d6r2671c251ba163edc@mail.gmail.com>

> Dear all,
>
> We've recently added support for parsing (reading) the IntelliGenetics
> sequence file format to Bio.SeqIO, under the format name "ig"
> (following the EMBOSS convention).  This file format also seems to be
> known as the MASE multiple sequence alignment format.
>
> This means that the old Bio.IntelliGenetics module is essentially
> obsolete, and we could therefore deprecate it in a future Biopython
> release.  Before we do that, is anyone using the Bio.IntelliGenetics
> module?  Hopefully using Bio.SeqIO will a suitable substitute for you,
> but please do get in touch.

The Bio.IntelliGenetics module is now deprecated in CVS.  If anyone is
using this code please get in touch.

> More generally, do any of you currently use the IntelliGenetics or
> MASE file format?  I'd love to have a few more example files to use in
> our test suite.  Also, would you be interested in using Bio.SeqIO to
> write out files in this format?

Thanks again,

Peter

From dalloliogm at gmail.com  Fri Jul 11 10:35:28 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Fri, 11 Jul 2008 16:35:28 +0200
Subject: [BioPython] proposal: Bio-Django project
Message-ID: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>

Hi,
Recently I have been using Django[1], a python web framework that
enables programmers to quickly create front-ends and web applications
for databases.

I think it is very cool. In a few minutes, I have been able to create
a database for my data, and thanks to the admin application I have a
nice and well-developed front-end to browse and manage it.
I am still looking at it, but I see there are many applications freely
available, so maybe I will be easily be able to create graphs and
diagrams of my data when I will look better at it.

My idea is: Why don't we create a repository of free/bioinfo apps for
django, like biopython is? Has any of you already used django for
bioinformatics purposes?

For example, I am writing an app to manage blood samples for the
laboratory where I am working on at the moment, and I will be glad to
share it with other people.

What do you think?


[1] http://www.djangoproject.com/

-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it

From dalloliogm at gmail.com  Fri Jul 11 11:25:56 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Fri, 11 Jul 2008 17:25:56 +0200
Subject: [BioPython] proposal: Bio-Django project
In-Reply-To: <1215787800.4877731897957@webmail.upv.es>
References: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>
	<1215787800.4877731897957@webmail.upv.es>
Message-ID: <5aa3b3570807110825r714ec06cw88ded72ea2c82d43@mail.gmail.com>

Of course I can show you the application I am writing.

I was thinking of applying to a google/summer of code. Let's propose a
few web applications that could be useful to researcher or
bioinformaticists, and ask google to fund it.

Maybe if any of the core biopython developers, who have experience in
handling a public repository for bioinformaticians, and are good
programmers, would like to partecipate as mentors, it would be a great
opportunity to learn django*, and obtain the google T shirt.


* or plone, they told me there is a similar project for plone:
http://plone.org/products/plone4bio/?searchterm=plone4bio


On Fri, Jul 11, 2008 at 4:50 PM, Blanca Postigo Jose Miguel
<jblanca at btc.upv.es> wrote:
> Hi:
> I'm not yet using Django, but I'm reading a couple of books and doing tutorials.
> I like a lot this web framework and I'm planning to use it.
> Your suggestion seems great for me.
> Also it would be great to take a look at your blood samples application, my wife
> works managing blood samples and I'm sure she would review it with pleasure.
> Best regards,
>
> Jose Blanca
>
> Mensaje citado por Giovanni Marco Dall'Olio <dalloliogm at gmail.com>:
>
>> Hi,
>> Recently I have been using Django[1], a python web framework that
>> enables programmers to quickly create front-ends and web applications
>> for databases.
>>
>> I think it is very cool. In a few minutes, I have been able to create
>> a database for my data, and thanks to the admin application I have a
>> nice and well-developed front-end to browse and manage it.
>> I am still looking at it, but I see there are many applications freely
>> available, so maybe I will be easily be able to create graphs and
>> diagrams of my data when I will look better at it.
>>
>> My idea is: Why don't we create a repository of free/bioinfo apps for
>> django, like biopython is? Has any of you already used django for
>> bioinformatics purposes?
>>
>> For example, I am writing an app to manage blood samples for the
>> laboratory where I am working on at the moment, and I will be glad to
>> share it with other people.
>>
>> What do you think?
>>
>>
>> [1] http://www.djangoproject.com/
>>
>> --
>> -----------------------------------------------------------
>>
>> My Blog on Bioinformatics (italian): http://bioinfoblog.it
>> _______________________________________________
>> BioPython mailing list  -  BioPython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
> --
>
>



-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it

From m at pavis.biodec.com  Fri Jul 11 11:45:17 2008
From: m at pavis.biodec.com (m at pavis.biodec.com)
Date: Fri, 11 Jul 2008 17:45:17 +0200
Subject: [BioPython] proposal: Bio-Django project
In-Reply-To: <5aa3b3570807110825r714ec06cw88ded72ea2c82d43@mail.gmail.com>
References: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>
	<1215787800.4877731897957@webmail.upv.es>
	<5aa3b3570807110825r714ec06cw88ded72ea2c82d43@mail.gmail.com>
Message-ID: <20080711154517.GD19973@pavis.biodec.com>

* Giovanni Marco Dall'Olio (dalloliogm at gmail.com) [080711 17:27]:
> 
> * or plone, they told me there is a similar project for plone:
> http://plone.org/products/plone4bio/?searchterm=plone4bio
>

my company hosts the plone4bio project: in our experience we have found
that using an already existing --- and quite active and complete, too
--- web content management system has been a good choice

YMMV of course, since we have been using plone since 2002, we probably
are a little skewed in our choice, but the rationale is that we have
found that sooner or later we start to add features like autenthication,
user management, workflows, and various sorts of integration and then it
is better to have a single robust system, if it is flexible enough

clarly, from time to time, you curse the fact that you have to do things
`its own way', but we can live with it

we have not added anything to the repository since a few months, but we
will soon add another predictor, give enough time to engineet it
properly ...

-- 
 .*.                            finelli
 /V\
(/ \) --------------------------------------------------------------
(   )       Linux: Friends dont let friends use Piccolosoffice
^^-^^ --------------------------------------------------------------

Boss: You forgot to assign the result of your map!

Hacker: Dang, I'm always forgetting my assignations...

Boss: And what's that "goto" doing there?!?

Hacker: Er, I guess my finger slipped when I was typing "getservbyport"...

Boss: Ah well, accidents will happen.  Maybe we should have picked APL.
		-- Larry Wall in <199710311732.JAA19169 at wall.org>

From bsouthey at gmail.com  Fri Jul 11 12:10:50 2008
From: bsouthey at gmail.com (Bruce Southey)
Date: Fri, 11 Jul 2008 11:10:50 -0500
Subject: [BioPython] [bip] proposal: Bio-Django project
In-Reply-To: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>
References: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>
Message-ID: <4877860A.1020305@gmail.com>

Giovanni Marco Dall'Olio wrote:
> Hi,
> Recently I have been using Django[1], a python web framework that
> enables programmers to quickly create front-ends and web applications
> for databases.
>
> I think it is very cool. In a few minutes, I have been able to create
> a database for my data, and thanks to the admin application I have a
> nice and well-developed front-end to browse and manage it.
> I am still looking at it, but I see there are many applications freely
> available, so maybe I will be easily be able to create graphs and
> diagrams of my data when I will look better at it.
>
> My idea is: Why don't we create a repository of free/bioinfo apps for
> django, like biopython is? Has any of you already used django for
> bioinformatics purposes?
>
> For example, I am writing an app to manage blood samples for the
> laboratory where I am working on at the moment, and I will be glad to
> share it with other people.
>
> What do you think?
>
>
> [1] http://www.djangoproject.com/
>
>   
Sure there are many Python-based model-viewer-control (MVC) frameworks 
(Django is just one of them) BUT what exactly do you propose to do?
In particular, how will it differ from plone4bio 
(http://www.plone4bio.org ) that was announced on BioPython by

Ivan Rossi back in February?

Do you plan something as extensive as the Biology Workbench or Next Generation Biology Workbench?
Or something like Geneious (http://www.geneious.com/)?
Or just a simple interface to BioPython or similar bioinformstics tools?

Regards
Bruce


From peter at maubp.freeserve.co.uk  Sat Jul 12 09:08:25 2008
From: peter at maubp.freeserve.co.uk (Peter)
Date: Sat, 12 Jul 2008 14:08:25 +0100
Subject: [BioPython] Bio.AlignIO and the Alignment object
Message-ID: <320fb6e00807120608s447605f6k14e67a941135c796@mail.gmail.com>

Now that Biopython 1.47 is out, I hope some of you have had a chance
to try out the new Bio.AlignIO module.

Let me just point out that this is all talking about multiple sequence
alignments where each (gapped) sequence is the same length, and the
data can be seen as a matrix or grid of letters.  I am not talking
about the related concept of an EST or contig alignment which doesn't
really fit this image (although it could if you add large leading and
trailing gap sequences).

We've had some useful feedback from Sebastian Bassi, leading me to
suspect that both the Bio.SeqIO and Bio.AlignIO input functions would
benefit from an optional alphabet argument for all those file formats
which do not declare the sequence type (enhancement bug 2443).
http://bugzilla.open-bio.org/show_bug.cgi?id=2443

Any other issues or questions about using the new Bio.AlignIO module?
I've tried to explain how to use it in the Tutorial (Chapter 5).
http://biopython.org/DIST/docs/tutorial/Tutorial.html

Any "beginners questions" on the mailing list would be useful for
pointing out how the documentation could be improved.  This would also
be useful for the wiki page which is currently a little empty - I
didn't want to just cut and past the examples from the main tutorial.
http://biopython.org/wiki/AlignIO

I'd also like to hear if there are any alignment file formats you
think Bio.AlignIO should support.

Finally, it would be great to also have some comments about the
Alignment object itself.  In particular we have some ideas on Bug 1944
for making it act more like an array of letters by supporting double
indexing like a Numeric or numpy array/matrix class.  Right now, the
next little step I want to implement is allowing access to the rows of
the alignment as SeqRecord objects using alignment[index], rather than
alignment.get_all_seqs()[index] which I find cumbersome.
http://bugzilla.open-bio.org/show_bug.cgi?id=1944

Thanks,

Peter

From peter at maubp.freeserve.co.uk  Sat Jul 12 09:16:32 2008
From: peter at maubp.freeserve.co.uk (Peter)
Date: Sat, 12 Jul 2008 14:16:32 +0100
Subject: [BioPython] Bio.AlignIO and the Alignment object
In-Reply-To: <320fb6e00807120608s447605f6k14e67a941135c796@mail.gmail.com>
References: <320fb6e00807120608s447605f6k14e67a941135c796@mail.gmail.com>
Message-ID: <320fb6e00807120616u208350c2r6313ab6667d27f62@mail.gmail.com>

> Finally, it would be great to also have some comments about the
> Alignment object itself.  In particular we have some ideas on Bug 1944
> for making it act more like an array of letters by supporting double
> indexing like a Numeric or numpy array/matrix class.
>
> Right now, the next little step I want to implement is allowing access to
> the rows of the alignment as SeqRecord objects using alignment[index],
> rather than alignment.get_all_seqs()[index] which I find cumbersome.
> http://bugzilla.open-bio.org/show_bug.cgi?id=1944

Here is a quick example using one of the test input files found in the
source code under Test/Clustalw:

>>> from Bio import AlignIO
>>> alignment = AlignIO.read(open("opuntia.aln"), "clustal")
>>> print alignment
SingleLetterAlphabet() alignment with 7 rows and 156 columns
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273285|gb|AF191659.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273284|gb|AF191658.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273287|gb|AF191661.1|AF191
TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273286|gb|AF191660.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273290|gb|AF191664.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273289|gb|AF191663.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273291|gb|AF191665.1|AF191

You can iterate over the rows as SeqRecord objects:

>>> for record in alignment :
...     print "%s length %i" % (record.id, len(record))
gi|6273285|gb|AF191659.1|AF191 length 156
gi|6273284|gb|AF191658.1|AF191 length 156
gi|6273287|gb|AF191661.1|AF191 length 156
gi|6273286|gb|AF191660.1|AF191 length 156
gi|6273290|gb|AF191664.1|AF191 length 156
gi|6273289|gb|AF191663.1|AF191 length 156
gi|6273291|gb|AF191665.1|AF191 length 156

Right now (Biopython 1.47) to get a particular row out as a SeqRecord
you must use the get_all_seqs() function:

>>> record = alignment.get_all_seqs()[3]
>>> print record.id
gi|6273286|gb|AF191660.1|AF191

I'd like to be able to do this instead:

>>> record = alignment[3]
>>> print record

This would render the get_all_seqs() function effectively obsolete,
and it could be deprecated in a later release.

Peter

From allank at sanbi.ac.za  Tue Jul 15 08:25:42 2008
From: allank at sanbi.ac.za (Allan Kamau)
Date: Tue, 15 Jul 2008 14:25:42 +0200
Subject: [BioPython] Install issues - *** Numerical Python *** is either not
 installed or out of date
Message-ID: <487C9746.2090807@sanbi.ac.za>

Hi all,
Am attempting to install biopython-1.47.
I have installed the prerequisites for  biopython including numpy 
(http://numpy.sourceforge.net/).
When I run setup.py build, i get the message below. I am sure I have 
installed numpy correctly as I can do "python -c 'import numpy; 
numpy.test()';" and not receive an error.

I think Numerical Python package had a name change some time ago from 
"Numeric" to "numpy" (meaning that import Numeric will more probably fail)

What can I do?

"*** Numerical Python *** is either not installed or out of date.

This package is optional, which means it is only used in a few
specialized modules in Biopython.  You probably don't need this if you
are unsure.  You can ignore this requirement, and install it later if
you see ImportErrors.
You can find Numerical Python at http://numpy.sourceforge.net/.

Do you want to continue this installation? (Y/n)  n
"

From biopython at maubp.freeserve.co.uk  Tue Jul 15 09:04:28 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Jul 2008 14:04:28 +0100
Subject: [BioPython] Install issues - *** Numerical Python *** is either
	not installed or out of date
In-Reply-To: <487C9746.2090807@sanbi.ac.za>
References: <487C9746.2090807@sanbi.ac.za>
Message-ID: <320fb6e00807150604t206a8586w7a7ba91f2456fa8@mail.gmail.com>

On Tue, Jul 15, 2008 at 1:25 PM, Allan Kamau <allank at sanbi.ac.za> wrote:
> Hi all,
> Am attempting to install biopython-1.47.
> I have installed the prerequisites for  biopython including numpy
> (http://numpy.sourceforge.net/).

We don't use numpy, we use the older Numeric library.  You need to
install that (you can have both installed without a problem).

Which instructions were you following?  We have tried to make this
clear on http://biopython.org/wiki/Download and in
http://biopython.org/DIST/docs/install/Installation.html (and its PDF
equivalent).

Thanks,

Peter

From allank at sanbi.ac.za  Tue Jul 15 09:37:44 2008
From: allank at sanbi.ac.za (Allan Kamau)
Date: Tue, 15 Jul 2008 15:37:44 +0200
Subject: [BioPython] Install issues - *** Numerical Python *** is either
 not installed or out of date
In-Reply-To: <320fb6e00807150604t206a8586w7a7ba91f2456fa8@mail.gmail.com>
References: <487C9746.2090807@sanbi.ac.za>
	<320fb6e00807150604t206a8586w7a7ba91f2456fa8@mail.gmail.com>
Message-ID: <487CA828.8010404@sanbi.ac.za>

Thank you Peter. I did follow your instructions and installed the 
Numeric library. All is well now.

Allan.

Peter wrote:
> On Tue, Jul 15, 2008 at 1:25 PM, Allan Kamau <allank at sanbi.ac.za> wrote:
>   
>> Hi all,
>> Am attempting to install biopython-1.47.
>> I have installed the prerequisites for  biopython including numpy
>> (http://numpy.sourceforge.net/).
>>     
>
> We don't use numpy, we use the older Numeric library.  You need to
> install that (you can have both installed without a problem).
>
> Which instructions were you following?  We have tried to make this
> clear on http://biopython.org/wiki/Download and in
> http://biopython.org/DIST/docs/install/Installation.html (and its PDF
> equivalent).
>
> Thanks,
>
> Peter
>   


From biopython at maubp.freeserve.co.uk  Tue Jul 15 17:15:15 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Jul 2008 22:15:15 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
Message-ID: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>

Now that the latest release is out, I wanted to return to a point
raised by Sebastian Bassi last month:

Do people agree that the Bio.Seq.transcibe() method should reject RNA sequences?

We already reject Seq objects with a protein alphabet.  I want to
accept Seq objects with a generic or nucleotide alphabet, and
sequences with a DNA alphabet are of course fine, but I had been on
the fence about trying to (re)transcribe RNA.

Unless anyone speaks up, I will side with Sebastian and add a check to
the  Bio.Seq.transcibe() method to reject RNA sequences, and a similar
check on the Bio.Seq.back_transcibe() method to reject DNA sequences.

Peter

From mmokrejs at ribosome.natur.cuni.cz  Tue Jul 15 18:53:14 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 00:53:14 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
Message-ID: <487D2A5A.1000305@ribosome.natur.cuni.cz>

I agree but it should require whether a plus or minus strand will be
transcribed. Otherwise, zapping 'U's with 'T's is enough. ;-) Still
somewhat artificial function.

What would be really meaningful if the object would be a genbank record
with introns and transcribe() would rip out all the introns or even
better allow me to choose which-ones to splice-out. Like to retain
exons 1, 5, 7.

;-)
Martin


Peter wrote:
> Now that the latest release is out, I wanted to return to a point
> raised by Sebastian Bassi last month:
> 
> Do people agree that the Bio.Seq.transcibe() method should reject RNA sequences?
> 
> We already reject Seq objects with a protein alphabet.  I want to
> accept Seq objects with a generic or nucleotide alphabet, and
> sequences with a DNA alphabet are of course fine, but I had been on
> the fence about trying to (re)transcribe RNA.
> 
> Unless anyone speaks up, I will side with Sebastian and add a check to
> the  Bio.Seq.transcibe() method to reject RNA sequences, and a similar
> check on the Bio.Seq.back_transcibe() method to reject DNA sequences.

From biopython at maubp.freeserve.co.uk  Tue Jul 15 19:13:43 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Jul 2008 00:13:43 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487D2A5A.1000305@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
Message-ID: <320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>

On Tue, Jul 15, 2008 at 11:53 PM, Martin MOKREJ?
<mmokrejs at ribosome.natur.cuni.cz> wrote:
> I agree but it should require whether a plus or minus strand will be
> transcribed. Otherwise, zapping 'U's with 'T's is enough. ;-) Still
> somewhat artificial function.

By convention a DNA sequence is taken as the coding strand, so a
simple U to T is enough to transcibe to RNA.  This is somewhat
artificial (and doesn't really capture double strandedness), but does
seem to be a widley used convention.

You could do my_seq.reverse_complement().transcribe() if you did want
the other strand transcribed.

> What would be really meaningful if the object would be a genbank record
> with introns and transcribe() would rip out all the introns or even
> better allow me to choose which-ones to splice-out. Like to retain
> exons 1, 5, 7.

I was thinking it would be nice to take a SeqRecord with SeqFeatures
(i.e. a parsed GenBank file) and ask Biopython to give you the
nucleotide sequence for the feature.  In the case of intron/exons
these are held using the subfeatures, so it would make sense to obey
those.  I see this as a variation on splicing/subsetting (in python
speak) a sequence.

Maybe something like my_record[my_feature] or
my_record.extract_feature(my_feature)
Or my_record.extract_feature(i) which would refer to my_record.features[i]

Peter


From mmokrejs at ribosome.natur.cuni.cz  Tue Jul 15 19:32:48 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 01:32:48 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>	
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
Message-ID: <487D33A0.5060804@ribosome.natur.cuni.cz>

Hi,

Peter wrote:
> On Tue, Jul 15, 2008 at 11:53 PM, Martin MOKREJ?
> <mmokrejs at ribosome.natur.cuni.cz> wrote:
>> I agree but it should require whether a plus or minus strand will be
>> transcribed. Otherwise, zapping 'U's with 'T's is enough. ;-) Still
>> somewhat artificial function.
> 
> By convention a DNA sequence is taken as the coding strand, so a
> simple U to T is enough to transcribe to RNA.  This is somewhat
> artificial (and doesn't really capture double strandedness), but does
> seem to be a widley used convention.

I can't say anything else except that this is extremely awkward function.
I would always rather take it as a string and replace 'U's with 'T's
myself. Then I know what is going on and do not have to read the manual
and can be sure this will never change.
> 
> You could do my_seq.reverse_complement().transcribe() if you did want
> the other strand transcribed.

Exactly, to get rid of this I would see some advantage to have
transcribe() which is more intuitive but only if it would be able to cope
with reverse strand as well.

>> What would be really meaningful if the object would be a genbank record
>> with introns and transcribe() would rip out all the introns or even
>> better allow me to choose which-ones to splice-out. Like to retain
>> exons 1, 5, 7.
> 
> I was thinking it would be nice to take a SeqRecord with SeqFeatures
> (i.e. a parsed GenBank file) and ask Biopython to give you the
> nucleotide sequence for the feature.  In the case of intron/exons
> these are held using the subfeatures, so it would make sense to obey
> those.  I see this as a variation on splicing/subsetting (in python
> speak) a sequence.

Personally I find this the only reason to justify existence of such
a function. It it can abstract me from the underlying format and give
me a true, spliced transcript. Of course I would rather prefer to raise
an exception if there would be more than one intron and I would have
not specified which intron index-positions to use.

> 
> Maybe something like my_record[my_feature] or
> my_record.extract_feature(my_feature)
> Or my_record.extract_feature(i) which would refer to my_record.features[i]

I am not much used to biopython coding style so cannot comment on this.
Again, I would never use a unknown function prone to be changed unless
I cannot code the simple transformation myself. If it cannot handle
splicing I don't need it I think. But maybe I am just a desperate user.
;-)

M.



From mmokrejs at ribosome.natur.cuni.cz  Tue Jul 15 19:57:16 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 01:57:16 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487D33A0.5060804@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>		<487D2A5A.1000305@ribosome.natur.cuni.cz>	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
	<487D33A0.5060804@ribosome.natur.cuni.cz>
Message-ID: <487D395C.7080103@ribosome.natur.cuni.cz>

Martin MOKREJ? wrote:

>>> What would be really meaningful if the object would be a genbank record
>>> with introns and transcribe() would rip out all the introns or even
>>> better allow me to choose which-ones to splice-out. Like to retain
>>> exons 1, 5, 7.
>>
>> I was thinking it would be nice to take a SeqRecord with SeqFeatures
>> (i.e. a parsed GenBank file) and ask Biopython to give you the
>> nucleotide sequence for the feature.  In the case of intron/exons
>> these are held using the subfeatures, so it would make sense to obey
>> those.  I see this as a variation on splicing/subsetting (in python
>> speak) a sequence.
> 
> Personally I find this the only reason to justify existence of such
> a function. It it can abstract me from the underlying format and give
--------------^^ If

> me a true, spliced transcript. Of course I would rather prefer to raise
> an exception if there would be more than one intron and I would have
> not specified which intron index-positions to use.
----------------------^^^^^^ exon

Sorry for the typos.



From biopython at maubp.freeserve.co.uk  Wed Jul 16 06:38:36 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Jul 2008 11:38:36 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
Message-ID: <320fb6e00807160338ub5dc2dayf0c3b51ad768af69@mail.gmail.com>

I wrote:
> Unless anyone speaks up, I will side with Sebastian and add a check to
> the  Bio.Seq.transcibe() method to reject RNA sequences, and a similar
> check on the Bio.Seq.back_transcibe() method to reject DNA sequences.

This change is now in CVS, Bio/Seq.py revision 1.13

Peter

From p.j.a.cock at googlemail.com  Wed Jul 16 07:08:44 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 16 Jul 2008 12:08:44 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487D33A0.5060804@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
	<487D33A0.5060804@ribosome.natur.cuni.cz>
Message-ID: <320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>

I wrote:
>> You could do my_seq.reverse_complement().transcribe() if you did want
>> the other strand transcribed.

Actually right now the Seq object doesn't have a transcribe method
(but I think maybe it should, see Bug 2381).  In the meantime, you
would have to use either of these:

from Bio.Seq import transcribe, reverse_complement
print transcribe(reverse_complement(my_seq))
print transcribe(my_seq.reverse_complement())

Martin wrote:
> Exactly, to get rid of this I would see some advantage to have
> transcribe() which is more intuitive but only if it would be able to cope
> with reverse strand as well.

You would really prefer a single function call to do a combined
"transcribe reverse-complement" or "transcribe the other strand" over
doing the reverse complement and transcription in two steps?

e.g.
print transcribe(my_seq, use_reverse_complement=True)

or,
print transcribe(my_seq, strand=-1)

or, maybe:
print transcribe_rc(my_seq)

Peter

From mmokrejs at ribosome.natur.cuni.cz  Wed Jul 16 09:20:48 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 15:20:48 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>	
	<487D2A5A.1000305@ribosome.natur.cuni.cz>	
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>	
	<487D33A0.5060804@ribosome.natur.cuni.cz>
	<320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>
Message-ID: <487DF5B0.1050000@ribosome.natur.cuni.cz>

Peter Cock wrote:
> I wrote:
>>> You could do my_seq.reverse_complement().transcribe() if you did want
>>> the other strand transcribed.
> 
> Actually right now the Seq object doesn't have a transcribe method
> (but I think maybe it should, see Bug 2381).  In the meantime, you
> would have to use either of these:
> 
> from Bio.Seq import transcribe, reverse_complement
> print transcribe(reverse_complement(my_seq))
> print transcribe(my_seq.reverse_complement())
> 
> Martin wrote:
>> Exactly, to get rid of this I would see some advantage to have
>> transcribe() which is more intuitive but only if it would be able to cope
>> with reverse strand as well.
> 
> You would really prefer a single function call to do a combined
> "transcribe reverse-complement" or "transcribe the other strand" over
> doing the reverse complement and transcription in two steps?

Yes, a single function handling arguments would be nice.

> 
> e.g.
> print transcribe(my_seq, use_reverse_complement=True)
> 
> or,
> print transcribe(my_seq, strand=-1)
> 
> or, maybe:
> print transcribe_rc(my_seq)

This one handling optional argument strand with default value -1,
but accepting [-1, 1, +1, 'watson', 'crick']. Ideally extended
in the future to splice-out the single intron by default or raise
an exception unless told to remove introns a,c,d,e or maybe instructed
to keep specific exons ... I am not sure what one would need more
often. I haven't checked but guess that GenBank files have more
often annotated introns and the exon region are more deeply buried
in the file structure so probably the first would impose less work
onto the parser.

Martin

From biopython at maubp.freeserve.co.uk  Wed Jul 16 10:37:43 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Jul 2008 15:37:43 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487DF5B0.1050000@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
	<487D33A0.5060804@ribosome.natur.cuni.cz>
	<320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>
	<487DF5B0.1050000@ribosome.natur.cuni.cz>
Message-ID: <320fb6e00807160737v5b6a18d6n78986412c8abaad@mail.gmail.com>

I asked Martin:
>> You would really prefer a single function call to do a combined
>> "transcribe reverse-complement" or "transcribe the other strand" over
>> doing the reverse complement and transcription in two steps?

Martin wrote:
> Yes, a single function handling arguments would be nice.
> ...
> This one handling optional argument strand with default value -1,
> but accepting [-1, 1, +1, 'watson', 'crick'].

No.  The default would have to be the coding strand (aka strand +1, or
the Crick strand).  I know that biologically translation works on the
template strand (aka strand -1, or the Watson strand), but that is not
the convention in computational biology (at least in Biopython).

In case we are talking at cross-purposes, consider this double
stranded bit of DNA,

5' ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG 3'
3' TACCCTTTCCATCCCGTTCGAAGGTCAATC 5'

and associated mRNA,
5' AUGGGAAAGGUAGGGCAAGCUUCCAGUUAG 3'

This DNA made up of two strands, which by convention are always read
from the 5' end to the 3' end.  i.e.

DNA coding strand (aka Crick strand, strand +1):
5' ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG 3'

DNA template strand (aka Watson strand, strand -1):
5' CTAACTGGAAGCTTGCCCTACCTTTCCCAT 3'

If this region were to be transcribed into mRNA and translated it would give:

protein,
MGKVGQASS (and stop)

In Bioinformatics in general, people tend to work with the coding
strand rather than the template strand.  In Biopython using strings
you could represent all this as follows:

from Bio.Seq import reverse_complement, translate, transcribe, back_transcribe

coding_strand_dna = "ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG"
template_strand_dna = reverse_complement(coding_strand_dna)
assert template_strand_dna == "CTAACTGGAAGCTTGCCCTACCTTTCCCAT"
assert coding_strand_dna == reverse_complement(template_strand_dna)

#Note transcribe() goes from the CODING strand to the mRNA
messenger_rna = transcribe(coding_strand_dna)
assert coding_strand_dna == back_transcribe(messenger_rna)

protein = translate(messenger_rna)
#Note you can also use translate() directly on the CODING strand:
assert protein == translate(coding_strand_dna)
assert protein == translate(reverse_complement(template_strand_dna))
assert protein == "MGKVGQASS*"

If that makes things clearer, maybe I should put something like this
in the Biopython tutorial... and/or the Bio.Seq docstring
documentation?  What do you think?

Peter

From mmokrejs at ribosome.natur.cuni.cz  Wed Jul 16 17:50:37 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 23:50:37 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807160737v5b6a18d6n78986412c8abaad@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>	
	<487D2A5A.1000305@ribosome.natur.cuni.cz>	
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>	
	<487D33A0.5060804@ribosome.natur.cuni.cz>	
	<320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>	
	<487DF5B0.1050000@ribosome.natur.cuni.cz>
	<320fb6e00807160737v5b6a18d6n78986412c8abaad@mail.gmail.com>
Message-ID: <487E6D2D.70104@ribosome.natur.cuni.cz>

Hi Peter,
  thank you for nice explanation. Definitely pasting the text&code from
your answer into BioPython Wiki or Tutorial would be sufficient and
should be there.

  Regarding the issue with transcribing coding strand ... probably
you have convinced me. ;-) I agree that one usually has annotated
sequence in GenBank format with annotated introns and wants to
concatenate some exons and get it translated. From this perspective
it does not make sense to un-necessarily reverse-complement the
sequence.
Martin


Peter wrote:
> I asked Martin:
>>> You would really prefer a single function call to do a combined
>>> "transcribe reverse-complement" or "transcribe the other strand" over
>>> doing the reverse complement and transcription in two steps?
> 
> Martin wrote:
>> Yes, a single function handling arguments would be nice.
>> ...
>> This one handling optional argument strand with default value -1,
>> but accepting [-1, 1, +1, 'watson', 'crick'].
> 
> No.  The default would have to be the coding strand (aka strand +1, or
> the Crick strand).  I know that biologically translation works on the
> template strand (aka strand -1, or the Watson strand), but that is not
> the convention in computational biology (at least in Biopython).
> 
> In case we are talking at cross-purposes, consider this double
> stranded bit of DNA,
> 
> 5' ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG 3'
> 3' TACCCTTTCCATCCCGTTCGAAGGTCAATC 5'
> 
> and associated mRNA,
> 5' AUGGGAAAGGUAGGGCAAGCUUCCAGUUAG 3'
> 
> This DNA made up of two strands, which by convention are always read
> from the 5' end to the 3' end.  i.e.
> 
> DNA coding strand (aka Crick strand, strand +1):
> 5' ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG 3'
> 
> DNA template strand (aka Watson strand, strand -1):
> 5' CTAACTGGAAGCTTGCCCTACCTTTCCCAT 3'
> 
> If this region were to be transcribed into mRNA and translated it would give:
> 
> protein,
> MGKVGQASS (and stop)
> 
> In Bioinformatics in general, people tend to work with the coding
> strand rather than the template strand.  In Biopython using strings
> you could represent all this as follows:
> 
> from Bio.Seq import reverse_complement, translate, transcribe, back_transcribe
> 
> coding_strand_dna = "ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG"
> template_strand_dna = reverse_complement(coding_strand_dna)
> assert template_strand_dna == "CTAACTGGAAGCTTGCCCTACCTTTCCCAT"
> assert coding_strand_dna == reverse_complement(template_strand_dna)
> 
> #Note transcribe() goes from the CODING strand to the mRNA
> messenger_rna = transcribe(coding_strand_dna)
> assert coding_strand_dna == back_transcribe(messenger_rna)
> 
> protein = translate(messenger_rna)
> #Note you can also use translate() directly on the CODING strand:
> assert protein == translate(coding_strand_dna)
> assert protein == translate(reverse_complement(template_strand_dna))
> assert protein == "MGKVGQASS*"
> 
> If that makes things clearer, maybe I should put something like this
> in the Biopython tutorial... and/or the Bio.Seq docstring
> documentation?  What do you think?
> 
> Peter
> 
> 

-- 
Dr. Martin Mokrejs
Dept. of Genetics and Microbiology
Faculty of Science, Charles University
Vinicna 5, 128 43 Prague, Czech Republic
tel: +420-2-2195 1716
http://www.iresite.org
http://www.iresite.org/~mmokrejs

From biopython at maubp.freeserve.co.uk  Thu Jul 17 09:56:05 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Jul 2008 14:56:05 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487E6D2D.70104@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
	<487D33A0.5060804@ribosome.natur.cuni.cz>
	<320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>
	<487DF5B0.1050000@ribosome.natur.cuni.cz>
	<320fb6e00807160737v5b6a18d6n78986412c8abaad@mail.gmail.com>
	<487E6D2D.70104@ribosome.natur.cuni.cz>
Message-ID: <320fb6e00807170656m2040d17fsdc3cd0b8ca519315@mail.gmail.com>

Martin MOKREJ? wrote:
> Hi Peter,
>  thank you for nice explanation. Definitely pasting the text&code from
> your answer into BioPython Wiki or Tutorial would be sufficient and
> should be there.

I've added something similar to the tutorial in CVS, but using Seq
objects instead of strings.

Peter


From dalloliogm at gmail.com  Fri Jul 18 09:20:48 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Fri, 18 Jul 2008 15:20:48 +0200
Subject: [BioPython] biopython 1.47 installation fails - and modified how to
	install instructions on wiki
Message-ID: <5aa3b3570807180620o224f4d53q812d15297a49d92e@mail.gmail.com>

Hi,
I have two things to say.

First, I have added instructions on how to install biopython with
easy_install to the biopython wiki:
- http://biopython.org/wiki/Download#Easy_Install

for those of you who don't know what easy_install is, it's a nice way to
install python packages on the fly, something similar to perl -MCPAN.
Can you please check whether the easy_install installation works fine for
you too?


Second, I was trying to install biopython 1.47 using the tar/zip archives on
http://biopython.org/DIST/biopython-1.47.tar.gz

There it seems to be a problem with the installation; after running sudo
python setup.py install, I receive the following error:

Would you like to build Bio.KDTree ? (y/N)
running build
running build_py
running build_ext
building 'Bio.clistfns' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC -I/usr/include/python2.5 -c Bio/clistfnsmodule.c
-o build/temp.linux-i686-2.5/Bio/clistfnsmodule.o
Bio/clistfnsmodule.c:10:20: error: Python.h: No such file or directory
Bio/clistfnsmodule.c:25: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
Bio/clistfnsmodule.c:80: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
Bio/clistfnsmodule.c:146: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'clistfnsMethods'
Bio/clistfnsmodule.c: In function 'initclistfns':
Bio/clistfnsmodule.c:160: warning: implicit declaration of function
'Py_InitModule3'
Bio/clistfnsmodule.c:160: error: 'clistfnsMethods' undeclared (first use in
this function)
Bio/clistfnsmodule.c:160: error: (Each undeclared identifier is reported
only once
Bio/clistfnsmodule.c:160: error: for each function it appears in.)
error: command 'gcc' failed with exit status 1


It seems a file Python.h is missing or mispelled.
Con you confirm that?

Cheers


-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it

From biopython at maubp.freeserve.co.uk  Fri Jul 18 09:36:25 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Jul 2008 14:36:25 +0100
Subject: [BioPython] biopython 1.47 installation fails - and modified
	how to install instructions on wiki
In-Reply-To: <5aa3b3570807180620o224f4d53q812d15297a49d92e@mail.gmail.com>
References: <5aa3b3570807180620o224f4d53q812d15297a49d92e@mail.gmail.com>
Message-ID: <320fb6e00807180636y4d1b819dgd4ad68aa81178b39@mail.gmail.com>

Giovanni Marco Dall'Olio wrote:
> Second, I was trying to install biopython 1.47 using the tar/zip archives on
> http://biopython.org/DIST/biopython-1.47.tar.gz
>
> There it seems to be a problem with the installation; after running sudo
> python setup.py install, I receive the following error:
>
> Would you like to build Bio.KDTree ? (y/N)
> running build
> running build_py
> running build_ext
> building 'Bio.clistfns' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> -Wstrict-prototypes -fPIC -I/usr/include/python2.5 -c Bio/clistfnsmodule.c
> -o build/temp.linux-i686-2.5/Bio/clistfnsmodule.o
> Bio/clistfnsmodule.c:10:20: error: Python.h: No such file or directory
> ...
>
> It seems a file Python.h is missing or mispelled.
> Can you confirm that?

You are probably missing the python header files - you didn't say what
OS you are using but from the path names its some form of Unix I
think.  Under Debian Linux you can use apt-get to install the build
dependencies of the Biopython package, and then install the latest
Biopython from source (specifically I think you are missing the
equivalent of the Debian python-dev package).

Peter

From dalloliogm at gmail.com  Fri Jul 18 09:48:52 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Fri, 18 Jul 2008 15:48:52 +0200
Subject: [BioPython] biopython 1.47 installation fails - and modified
	how to install instructions on wiki
In-Reply-To: <320fb6e00807180636y4d1b819dgd4ad68aa81178b39@mail.gmail.com>
References: <5aa3b3570807180620o224f4d53q812d15297a49d92e@mail.gmail.com>
	<320fb6e00807180636y4d1b819dgd4ad68aa81178b39@mail.gmail.com>
Message-ID: <5aa3b3570807180648q292bb750u60197af8daffb493@mail.gmail.com>

On Fri, Jul 18, 2008 at 3:36 PM, Peter <biopython at maubp.freeserve.co.uk>
wrote:

> Giovanni Marco Dall'Olio wrote:
> > gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> > -Wstrict-prototypes -fPIC -I/usr/include/python2.5 -c
> Bio/clistfnsmodule.c
> > -o build/temp.linux-i686-2.5/Bio/clistfnsmodule.o
> > Bio/clistfnsmodule.c:10:20: error: Python.h: No such file or directory
> > ...
>
> You are probably missing the python header files - you didn't say what
> OS you are using but from the path names its some form of Unix I
> think.  Under Debian Linux you can use apt-get to install the build
> dependencies of the Biopython package, and then install the latest
> Biopython from source (specifically I think you are missing the
> equivalent of the Debian python-dev package).
>

it's true!
I was missing the python-dev package.
Now the compilation goes well.

Thanks!


>
> Peter
>



-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it

From biopython at maubp.freeserve.co.uk  Mon Jul 21 11:42:56 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 21 Jul 2008 16:42:56 +0100
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
Message-ID: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>

Dear all,

I've recently filed Bug 2547 about changing the behaviour of
Bio.Seq.translate() when given ambiguous codons like NNN or TAN which
could be either an amino acid OR a stop codon.

http://bugzilla.open-bio.org/show_bug.cgi?id=2547

In my opinion it would be nice if there was an established convention
for how to represent an ambiguous character meaning {X or stop}, for
the TAN example even {Y or stop}.  However, as far as I am aware,
people just use X to mean any amino acid OR a stop codon.  This is the
behaviour in both the EMBOSS transeq tool and in BioPerl.

I am proposing to change Bio.Seq.translate() be able to translate
codons like NNN and TAN as X (rather than throwing a translation error
as happens now).

Comments please?

[Any implementation suggestions on the development mailing list please.]

Peter

From bsouthey at gmail.com  Mon Jul 21 15:23:34 2008
From: bsouthey at gmail.com (Bruce Southey)
Date: Mon, 21 Jul 2008 14:23:34 -0500
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>
Message-ID: <4884E236.1090605@gmail.com>

Peter wrote:
> Dear all,
>
> I've recently filed Bug 2547 about changing the behaviour of
> Bio.Seq.translate() when given ambiguous codons like NNN or TAN which
> could be either an amino acid OR a stop codon.
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2547
>
> In my opinion it would be nice if there was an established convention
> for how to represent an ambiguous character meaning {X or stop}, for
> the TAN example even {Y or stop}.  However, as far as I am aware,
> people just use X to mean any amino acid OR a stop codon.  This is the
> behaviour in both the EMBOSS transeq tool and in BioPerl.
>
> I am proposing to change Bio.Seq.translate() be able to translate
> codons like NNN and TAN as X (rather than throwing a translation error
> as happens now).
>
> Comments please?
>
> [Any implementation suggestions on the development mailing list please.]
>
> Peter
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>   
The relevant document here is the IUPAC 'Nomenclature for Incompletely 
Specified Bases in Nucleic Acid Sequences'  
(http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html).

Table 4 provides some examples such as showing the correspondence 
between the triplet  'NNN' and the amino acid 'Unknown' with one letter 
code 'X'.  Consequently, here must also be a correspondence between 
triplet 'TAN' (or any other related triplet for that matter) and the 
amino acid 'X' because the triple 'NNN' must also include the stop 
codons which have no corresponding amino acid (okay ignoring 
selenocysteine etc.).

Bruce


From biopython at maubp.freeserve.co.uk  Mon Jul 21 17:04:34 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 21 Jul 2008 22:04:34 +0100
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <4884E236.1090605@gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>
	<4884E236.1090605@gmail.com>
Message-ID: <320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>

> The relevant document here is the IUPAC 'Nomenclature for Incompletely
> Specified Bases in Nucleic Acid Sequences'
>  (http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html).
>
> Table 4 provides some examples such as showing the correspondence between
> the triplet  'NNN' and the amino acid 'Unknown' with one letter code 'X'.
> Consequently, here must also be a correspondence between triplet 'TAN' (or
> any other related triplet for that matter) and the amino acid 'X' because
> the triple 'NNN' must also include the stop codons which have no
> corresponding amino acid (okay ignoring selenocysteine etc.).
>
> Bruce

I'd seen that table, but hadn't interpreted it in quite the same way
as you seem to have.  Table 4 shows a mapping from amino acids to
ambiguous codons - but it is not a bijection (it is NOT a reversible
mapping).  Or to put it another way, Table 4 just shows the narrowest
possible ambiguous codon which covers all possible codons for that
amino acid (or stop).  This does NOT mean that ambiguous codon will
allways translate to the given amino acid.

Here are two explicit examples to try and explain myself (using a
little set notation).  In the standard genetic code, stop codons are
{TAA, TGA, TAG} = {TAR, TGA} = {TAA, TRA}.  If you have to use a
single codon, the best you can do is TRR = {TAA, TAG, TGA, TGG} =
{stop codons}U{TGG}.  Table 4 maps "*" to "TRR".  While TRR does cover
all the possible stop codons, it also includes a codon for Trp (W).  I
would NOT want TRR translated as a stop!  It codes for a stop or a W.

Similarly, for Leucine (L) the possible codons are {TTA, TTG, CTT,
CTC, CTA, CTG} = {TTR, CTN}.  If you have to use a single codon then
YTN covers this - but it also covers CTA and CTG which code for Phe
(F).  I would NOT want YTN translated as L - it codes for L or F, so
would have to be translated as X.

So on the basis of Table 4, there is no reason to infer that IUPAC
explicitly suggest NNN should be translated as X.

Peter

From biopython at maubp.freeserve.co.uk  Tue Jul 22 04:51:26 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 22 Jul 2008 09:51:26 +0100
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>
	<4884E236.1090605@gmail.com>
	<320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>
Message-ID: <320fb6e00807220151r20a49511ue61fed8f244bc65@mail.gmail.com>

On Mon, Jul 21, 2008 at 10:04 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> The relevant document here is the IUPAC 'Nomenclature for Incompletely
>> Specified Bases in Nucleic Acid Sequences'
>>  (http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html).
>>
>> Table 4 ...
>
> I'd seen that table, but hadn't interpreted it in quite the same way
> as you seem to have.  ...
> So on the basis of Table 4, there is no reason to infer that IUPAC
> explicitly suggest NNN should be translated as X.

Re-reading that, I can be pedantic sometime, can't I?

Putting our differences of opinion about exactly what the IUPAC Table
4 is intended to convey, do you agree that Biopython's
Bio.Seq.translate() function should turn NNN and TAN into X?

Thanks

Peter

From bsouthey at gmail.com  Tue Jul 22 09:20:37 2008
From: bsouthey at gmail.com (Bruce Southey)
Date: Tue, 22 Jul 2008 08:20:37 -0500
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <320fb6e00807220151r20a49511ue61fed8f244bc65@mail.gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>	
	<4884E236.1090605@gmail.com>	
	<320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>
	<320fb6e00807220151r20a49511ue61fed8f244bc65@mail.gmail.com>
Message-ID: <4885DEA5.8070706@gmail.com>

Peter wrote:
> On Mon, Jul 21, 2008 at 10:04 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>   
>>> The relevant document here is the IUPAC 'Nomenclature for Incompletely
>>> Specified Bases in Nucleic Acid Sequences'
>>>  (http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html).
>>>
>>> Table 4 ...
>>>       
>> I'd seen that table, but hadn't interpreted it in quite the same way
>> as you seem to have.  ...
>> So on the basis of Table 4, there is no reason to infer that IUPAC
>> explicitly suggest NNN should be translated as X.
>>     
>
> Re-reading that, I can be pedantic sometime, can't I?
>   
Sure, why not? Some one must be pedantic otherwise all these corner 
cases get missed and lead to bigger problems.

> Putting our differences of opinion about exactly what the IUPAC Table
> 4 is intended to convey, do you agree that Biopython's
> Bio.Seq.translate() function should turn NNN and TAN into X?
>
> Thanks
>
> Peter
>
>   
Yes because if you accept that 'NNN should be translated as X' then, by 
the same reasoning, you must also accept 'TAN into X' as well as similar 
cases.

For Biopython, there could a be flag or similar that causes translate() 
to either return an error for any ambiguous codons or just continues on 
using 'X'.

Bruce

From mmokrejs at ribosome.natur.cuni.cz  Tue Jul 22 10:04:29 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Tue, 22 Jul 2008 16:04:29 +0200
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <4885DEA5.8070706@gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>		<4884E236.1090605@gmail.com>		<320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>	<320fb6e00807220151r20a49511ue61fed8f244bc65@mail.gmail.com>
	<4885DEA5.8070706@gmail.com>
Message-ID: <4885E8ED.3010205@ribosome.natur.cuni.cz>

Bruce Southey wrote:
>>   
> Yes because if you accept that 'NNN should be translated as X' then, by 
> the same reasoning, you must also accept 'TAN into X' as well as similar 
> cases.
> 
> For Biopython, there could a be flag or similar that causes translate() 
> to either return an error for any ambiguous codons or just continues on 
> using 'X'.

Yes, I agree as well. When translating ESTs I don't to get my code bailing
out due to sequencing errors. But I agree that usually people would like to
get an error instead.

Martin

From biopython at maubp.freeserve.co.uk  Tue Jul 22 11:38:36 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 22 Jul 2008 16:38:36 +0100
Subject: [BioPython] Deprecating the HTML parser in Bio.Blast.NCBIWWW
In-Reply-To: <320fb6e00807120645u26321d71q30f72ed5808f700@mail.gmail.com>
References: <320fb6e00807120645u26321d71q30f72ed5808f700@mail.gmail.com>
Message-ID: <320fb6e00807220838x3aae8246w8a6e3108bf6feec8@mail.gmail.com>

For any Biopython and Blast users,

For some time now we've been discouraging the use of the HTML
and plain text Blast parsers in favour of the XML format.

I think it would be a good idea to now officially deprecate the
HTML parser in Bio.Blast.NCBIWWW with warning messages
when it is used.  I don't even know if it still works with the recent
big revision to the BLAST webpages, but I suspect not.

However, the plain text parser in Bio.Blast.NCBIStandalone still
has its uses - even if it doesn't support the current BLAST output
100%. In particular, right now the PSI-BLAST output in XML format
lacks some of the information found in the plain text output (new
vs reused entries) so it would be premature to deprecate our plain
text (PSI) BLAST parser.

Is anyone still using Biopython to parse the HTML output from BLAST?
If so, please speak up.

Peter

From winter at biotec.tu-dresden.de  Wed Jul 23 05:55:23 2008
From: winter at biotec.tu-dresden.de (Christof Winter)
Date: Wed, 23 Jul 2008 11:55:23 +0200
Subject: [BioPython] Deprecating the HTML parser in Bio.Blast.NCBIWWW
In-Reply-To: <320fb6e00807220838x3aae8246w8a6e3108bf6feec8@mail.gmail.com>
References: <320fb6e00807120645u26321d71q30f72ed5808f700@mail.gmail.com>
	<320fb6e00807220838x3aae8246w8a6e3108bf6feec8@mail.gmail.com>
Message-ID: <4887000B.1070409@biotec.tu-dresden.de>

Peter wrote, On 22.07.2008 17:38:
> For any Biopython and Blast users,
> 
> For some time now we've been discouraging the use of the HTML
> and plain text Blast parsers in favour of the XML format.
> 
> I think it would be a good idea to now officially deprecate the
> HTML parser in Bio.Blast.NCBIWWW with warning messages
> when it is used.

Full ack.

Christof


From jcigar at ulb.ac.be  Wed Jul 23 10:51:21 2008
From: jcigar at ulb.ac.be (Julien Cigar)
Date: Wed, 23 Jul 2008 16:51:21 +0200
Subject: [BioPython] blast
Message-ID: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>

Hello list,

I'm working on a project (on African rats) which has a "blast"
functionnality. In our (PostgreSQL) database sequences are linked to a
specimen. The sequence table contains the sequence itself (which is just
a text field) and additional things like the accession number (if
exists), etc.

The idea behind this is that a user can enter a part of DNA and see what
kind of specimen (taxonomy) it could be.

So I created a FASTA file with all the sequences, and then I used
formatdb to be able to BLAST on it.

It works quite well, you can see it in action on
http://projects.biodiversity.be/africanrodentia/search/dna 
In the output I use the score attribute to show how close the entered
sequence is (is it OK ?). The problem is that the users would prefer a
kind of percentage. This is a copy of a mail I received :

"Yet I have a question regarding the BLAST function: It works well but
the output is unclear. Could one not indicate the % similarity  of the
ranked sequences versus the pasted sequence instead of te rather
enigmatic scores that we see now?  Such an output would make the
interpretation clearer,  particularly in cases where we do not have the
sequence of the investigated species. In such a case the species with
the most similar sequence will be given as a potential species name, in
itself not a problem as long as one knows how different they are (e.g.
in rodents wthin species variability approx less <3%, between species
differences typically >4%). This provides a direct indication whether
the output is likely to be yield a correct species name."

I wondered how this "score" is calculated, and if there's already a
function to convert it to a percentage ? Otherwise, is it OK to take the
hsp.sbjct field as 100% and then compare it to hsp.query ?

For example if I have :

CCTATTCCTAGCTATACACTACACATCGGACACAACAAC
|||||||||||| ||||||||||||||||||||||||||
CCTATTCCTAGCCATACACTACACATCGGACACAACAAC

The score is shown as "35", is it OK if I do something like :

percentage = (100.0 / len(hsp.sbjct)) * hsp.match.count('|')

so with my example it will be: (100 / 39) * 38

Many thanks,
Julien

-- 
Julien Cigar
Belgian Biodiversity Platform
http://www.biodiversity.be
Universit? Libre de Bruxelles (ULB)
Campus de la Plaine CP 257
B?timent NO, Bureau 4 N4 115C (Niveau 4)
Boulevard du Triomphe, entr?e ULB 2
B-1050 Bruxelles
Mail: jcigar at ulb.ac.be
@biobel: http://biobel.biodiversity.be/person/show/471
Tel : 02 650 57 52


From lueck at ipk-gatersleben.de  Wed Jul 23 09:17:26 2008
From: lueck at ipk-gatersleben.de (=?UTF-8?Q?Stefanie_L=C3=BCck?=)
Date: Wed, 23 Jul 2008 15:17:26 +0200
Subject: [BioPython] blast
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
Message-ID: <00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>

Hi!

I calculated like this for my program (you blast against your own primer 
stock database and get % match per primers to your query sequence):

percent = float(100) * float(hsp.score) / float(alignment.length)

Regards
Stefanie 

From p.j.a.cock at googlemail.com  Wed Jul 23 09:53:50 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 14:53:50 +0100
Subject: [BioPython] blast
In-Reply-To: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
Message-ID: <320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>

On Wed, Jul 23, 2008 at 3:51 PM, Julien Cigar <jcigar at ulb.ac.be> wrote:
> Hello list,
>
> I'm working on a project (on African rats) which has a "blast"
> functionnality. In our (PostgreSQL) database sequences are linked to a
> specimen. The sequence table contains the sequence itself (which is just
> a text field) and additional things like the accession number (if
> exists), etc.
>
> The idea behind this is that a user can enter a part of DNA and see what
> kind of specimen (taxonomy) it could be.
>
> So I created a FASTA file with all the sequences, and then I used
> formatdb to be able to BLAST on it.
>
> It works quite well, you can see it in action on
> http://projects.biodiversity.be/africanrodentia/search/dna
> In the output I use the score attribute to show how close the entered
> sequence is (is it OK ?). The problem is that the users would prefer a
> kind of percentage. This is a copy of a mail I received :

It is pretty, but doesn't look like the BLAST output many biologists
will be used to, so I think I understand why the want some more
information to judge the similarity.

> "Yet I have a question regarding the BLAST function: It works well but
> the output is unclear. Could one not indicate the % similarity  of the
> ranked sequences versus the pasted sequence instead of te rather
> enigmatic scores that we see now?  Such an output would make the
> interpretation clearer,  particularly in cases where we do not have the
> sequence of the investigated species. In such a case the species with
> the most similar sequence will be given as a potential species name, in
> itself not a problem as long as one knows how different they are (e.g.
> in rodents wthin species variability approx less <3%, between species
> differences typically >4%). This provides a direct indication whether
> the output is likely to be yield a correct species name."

I think they are asking for the percentage identify.  Another
possiblity is the bit-score which should be in the BLAST output as a
floating point number (hsp.score).

> I wondered how this "score" is calculated, and if there's already a
> function to convert it to a percentage ? Otherwise, is it OK to take the
> hsp.sbjct field as 100% and then compare it to hsp.query ?
>
> For example if I have :
>
> CCTATTCCTAGCTATACACTACACATCGGACACAACAAC
> |||||||||||| ||||||||||||||||||||||||||
> CCTATTCCTAGCCATACACTACACATCGGACACAACAAC
>
> The score is shown as "35", is it OK if I do something like :
>
> percentage = (100.0 / len(hsp.sbjct)) * hsp.match.count('|')
>
> so with my example it will be: (100 / 39) * 38

To get the percentage identify over the alignment, yes.  Watch out for
integer division, but because you multiplied by 100.0 it should be
fine.

I would also go directly from the relevant integer fields (which
should be the same).  Something like this (assuming you are using the
XML parser):

assert hsp.identities == hsp.match.count('|') #Only works on nucleotide blasts!
assert hsp.align_length == len(hsp.sbjct)
assert hsp.align_length == len(hsp.match)
assert hsp.align_length == len(hsp.query)
percentage_identity = (100.0 * hsp.identities) / hsp.align_length

Have you considered actually showing the blast alignment too?

Peter

From p.j.a.cock at googlemail.com  Wed Jul 23 10:05:14 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 15:05:14 +0100
Subject: [BioPython] blast
In-Reply-To: <00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
Message-ID: <320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>

I wrote:
> I think they are asking for the percentage identify.  Another
> possiblity is the bit-score which should be in the BLAST output as a
> floating point number (hsp.score).

I should have said raw score (hsp.score) or bit score (hsp.bits), both
of which might be of interest to your users.

Steganie wrote:
> Hi!
>
> I calculated like this for my program (you blast against your own primer
> stock database and get % match per primers to your query sequence):
>
> percent = float(100) * float(hsp.score) / float(alignment.length)
>

Using hsp.score gives the raw score, which you are then scaling by the
length and 100.  I'm not sure offhand what you've calculated, but if
you want the percentage identity, I think its just the number of
identically match letters divided by the alignment length:

percentage_identity = (100.0 * hsp.identities) / hsp.align_length

In the plain text output BLAST gives this number explicitly, e.g.
Identities = 112/146 (76%), Positives = 127/146 (86%), Gaps = 2/146 (1%)

There is also hsp.bits which gives the bit score.

Peter

From p.j.a.cock at googlemail.com  Wed Jul 23 10:18:08 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 15:18:08 +0100
Subject: [BioPython] blast
In-Reply-To: <1216830021.2612.65.camel@frodon.be-bif.ulb.ac.be>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>
	<1216830021.2612.65.camel@frodon.be-bif.ulb.ac.be>
Message-ID: <320fb6e00807230718v4edbe5f1x707ece2608e05582@mail.gmail.com>

> Thanks, I got another formula which seems to work well too (and which
> seems cleaner than counting the number of '|') :
>
> float(100) * float(hsp.score) / float(alignment.length)

I don't think that gives you the same thing as the percentage identify
(see my other email).

>> Have you considered actually showing the blast alignment too?
>>
> Yes, it's in the output, I just replaced the '|' with a red background
> and the ' ' with a green background, so they see directly where it
> doesn't match

Since the graphical representation of the match/mismatch string is
done using the colours red and green, it is useless for anyone who is
colour blind.

Also the user can't cut and paste the alignment into an email or other
document (electronic lab book?), which seems like an obvious thing to
want to do.

Personally, I would try and keep the output looking more similar to
traditional blast, as then its easier to understand (assuming you
already know BLAST!).

Peter

From jcigar at ulb.ac.be  Wed Jul 23 12:20:21 2008
From: jcigar at ulb.ac.be (Julien Cigar)
Date: Wed, 23 Jul 2008 18:20:21 +0200
Subject: [BioPython] blast
In-Reply-To: <320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>
Message-ID: <1216830021.2612.65.camel@frodon.be-bif.ulb.ac.be>

On Wed, 2008-07-23 at 14:53 +0100, Peter Cock wrote:
> On Wed, Jul 23, 2008 at 3:51 PM, Julien Cigar <jcigar at ulb.ac.be> wrote:
> > Hello list,
> >
> > I'm working on a project (on African rats) which has a "blast"
> > functionnality. In our (PostgreSQL) database sequences are linked to a
> > specimen. The sequence table contains the sequence itself (which is just
> > a text field) and additional things like the accession number (if
> > exists), etc.
> >
> > The idea behind this is that a user can enter a part of DNA and see what
> > kind of specimen (taxonomy) it could be.
> >
> > So I created a FASTA file with all the sequences, and then I used
> > formatdb to be able to BLAST on it.
> >
> > It works quite well, you can see it in action on
> > http://projects.biodiversity.be/africanrodentia/search/dna
> > In the output I use the score attribute to show how close the entered
> > sequence is (is it OK ?). The problem is that the users would prefer a
> > kind of percentage. This is a copy of a mail I received :
> 
> It is pretty, but doesn't look like the BLAST output many biologists
> will be used to, so I think I understand why the want some more
> information to judge the similarity.
> 

Yes, I'm not a biologist, I'm learning on the job .. so that explains
it :) (but it's interresting to learn)

> > "Yet I have a question regarding the BLAST function: It works well but
> > the output is unclear. Could one not indicate the % similarity  of the
> > ranked sequences versus the pasted sequence instead of te rather
> > enigmatic scores that we see now?  Such an output would make the
> > interpretation clearer,  particularly in cases where we do not have the
> > sequence of the investigated species. In such a case the species with
> > the most similar sequence will be given as a potential species name, in
> > itself not a problem as long as one knows how different they are (e.g.
> > in rodents wthin species variability approx less <3%, between species
> > differences typically >4%). This provides a direct indication whether
> > the output is likely to be yield a correct species name."
> 
> I think they are asking for the percentage identify.  Another
> possiblity is the bit-score which should be in the BLAST output as a
> floating point number (hsp.score).
> 

Yes, it's should be that, I forgot to take the alignement length into
account. I already showed the bit-score, but apparently it's not too
usefull for them.

> > I wondered how this "score" is calculated, and if there's already a
> > function to convert it to a percentage ? Otherwise, is it OK to take the
> > hsp.sbjct field as 100% and then compare it to hsp.query ?
> >
> > For example if I have :
> >
> > CCTATTCCTAGCTATACACTACACATCGGACACAACAAC
> > |||||||||||| ||||||||||||||||||||||||||
> > CCTATTCCTAGCCATACACTACACATCGGACACAACAAC
> >
> > The score is shown as "35", is it OK if I do something like :
> >
> > percentage = (100.0 / len(hsp.sbjct)) * hsp.match.count('|')
> >
> > so with my example it will be: (100 / 39) * 38
> 
> To get the percentage identify over the alignment, yes.  Watch out for
> integer division, but because you multiplied by 100.0 it should be
> fine.
> 
> I would also go directly from the relevant integer fields (which
> should be the same).  Something like this (assuming you are using the
> XML parser):
> 
> assert hsp.identities == hsp.match.count('|') #Only works on nucleotide blasts!
> assert hsp.align_length == len(hsp.sbjct)
> assert hsp.align_length == len(hsp.match)
> assert hsp.align_length == len(hsp.query)
> percentage_identity = (100.0 * hsp.identities) / hsp.align_length
> 

Thanks, I got another formula which seems to work well too (and which
seems cleaner than counting the number of '|') :

float(100) * float(hsp.score) / float(alignment.length)

> Have you considered actually showing the blast alignment too?
> 

Yes, it's in the output, I just replaced the '|' with a red background
and the ' ' with a green background, so they see directly where it
doesn't match

> Peter

Thanks,
Julien

-- 
Julien Cigar
Belgian Biodiversity Platform
http://www.biodiversity.be
Universit? Libre de Bruxelles (ULB)
Campus de la Plaine CP 257
B?timent NO, Bureau 4 N4 115C (Niveau 4)
Boulevard du Triomphe, entr?e ULB 2
B-1050 Bruxelles
Mail: jcigar at ulb.ac.be
@biobel: http://biobel.biodiversity.be/person/show/471
Tel : 02 650 57 52


From lueck at ipk-gatersleben.de  Wed Jul 23 10:30:10 2008
From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=)
Date: Wed, 23 Jul 2008 16:30:10 +0200
Subject: [BioPython] blast
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
Message-ID: <010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>

 >Peter wrote:
> Using hsp.score gives the raw score, which you are then scaling by the
> length and 100.  I'm not sure offhand what you've calculated, but if
> you want the percentage identity, I think its just the number of
> identically match letters divided by the alignment length:
> 
> percentage_identity = (100.0 * hsp.identities) / hsp.align_length


I tried and it dosen't work in my case. It's gives me wrong percentage. 

 

I need to know at which % my primer match to the query part:

 

query          --------taggcctcgcgcgcc-------

               ||||||||||||||||||||||||||||||

primer         tagcgctataggcctcgcgcgccatatagc

 

Here 50 %. 


From jcigar at ulb.ac.be  Wed Jul 23 12:46:34 2008
From: jcigar at ulb.ac.be (Julien Cigar)
Date: Wed, 23 Jul 2008 18:46:34 +0200
Subject: [BioPython] blast
In-Reply-To: <320fb6e00807230718v4edbe5f1x707ece2608e05582@mail.gmail.com>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>
	<1216830021.2612.65.camel@frodon.be-bif.ulb.ac.be>
	<320fb6e00807230718v4edbe5f1x707ece2608e05582@mail.gmail.com>
Message-ID: <1216831594.2612.85.camel@frodon.be-bif.ulb.ac.be>

On Wed, 2008-07-23 at 15:18 +0100, Peter Cock wrote:
> > Thanks, I got another formula which seems to work well too (and which
> > seems cleaner than counting the number of '|') :
> >
> > float(100) * float(hsp.score) / float(alignment.length)
> 
> I don't think that gives you the same thing as the percentage identify
> (see my other email).
> 

Indeed..! (sorry I sended my last mail before reading yours).

> >> Have you considered actually showing the blast alignment too?
> >>
> > Yes, it's in the output, I just replaced the '|' with a red background
> > and the ' ' with a green background, so they see directly where it
> > doesn't match
> 
> Since the graphical representation of the match/mismatch string is
> done using the colours red and green, it is useless for anyone who is
> colour blind.
> 

You're right .. I haven't thought about this

> Also the user can't cut and paste the alignment into an email or other
> document (electronic lab book?), which seems like an obvious thing to
> want to do.
> 
> Personally, I would try and keep the output looking more similar to
> traditional blast, as then its easier to understand (assuming you
> already know BLAST!).
> 

ok, I'll ask them what they prefer.

> Peter

Thanks,
Julien

-- 
Julien Cigar
Belgian Biodiversity Platform
http://www.biodiversity.be
Universit? Libre de Bruxelles (ULB)
Campus de la Plaine CP 257
B?timent NO, Bureau 4 N4 115C (Niveau 4)
Boulevard du Triomphe, entr?e ULB 2
B-1050 Bruxelles
Mail: jcigar at ulb.ac.be
@biobel: http://biobel.biodiversity.be/person/show/471
Tel : 02 650 57 52


From p.j.a.cock at googlemail.com  Wed Jul 23 10:49:39 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 15:49:39 +0100
Subject: [BioPython] blast
In-Reply-To: <010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
Message-ID: <320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>

On Wed, Jul 23, 2008 at 3:30 PM, Stefanie L?ck <lueck at ipk-gatersleben.de> wrote:
>>Peter wrote:
>>
>> Using hsp.score gives the raw score, which you are then scaling by the
>> length and 100.  I'm not sure offhand what you've calculated, but if
>> you want the percentage identity, I think its just the number of
>> identically match letters divided by the alignment length:
>>
>> percentage_identity = (100.0 * hsp.identities) / hsp.align_length
>
> I tried and it dosen't work in my case. It's gives me wrong percentage.
>
> I need to know at which % my primer match to the query part:
>
>
> query          --------taggcctcgcgcgcc-------
>              ||||||||||||||||||||||||||||||
> primer         tagcgctataggcctcgcgcgccatatagc
>
> Here 50 %.

Your query match region has an un-gapped length of 15, and gapped length of 30
Your subject match region has a length of 30
Your query and subject have 15 identical matches
The alignment length is 30, therefore 100*15/30 = 50%

Using my suggested formula correctly gives the percentage identies
relative to the alignment length:
percentage_identity = (100.0 * hsp.identities) / hsp.align_length

It seems what you want to calculate is 100*15/15 = 100%  i.e. The
percentage identites relative to the ungapped query length?  This
would probably work but isn't very elegant:

percentage_identity_ref_matched_query = (100.0 * hsp.identities) /
(hsp.align_length - hsp.query.count("-"))

Or even relative to the full original query?  If record is the blast
record object that the hsp cam from,

percentage_identity_ref_full_query = (100.0 * hsp.identities) /
record.query_letters)

(For a short query sequence like a probe, these may be the same)

Peter


From p.j.a.cock at googlemail.com  Wed Jul 23 10:54:42 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 15:54:42 +0100
Subject: [BioPython] blast
In-Reply-To: <320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
Message-ID: <320fb6e00807230754k52bebba4v453933ef0a215351@mail.gmail.com>

>> I need to know at which % my primer match to the query part:
>>
>>
>> query          --------taggcctcgcgcgcc-------
>>              ||||||||||||||||||||||||||||||
>> primer         tagcgctataggcctcgcgcgccatatagc
>>
>> Here 50 %.

How did you get this example?  NCBI Blast doesn't include the leading
and trailing gaps (in plain text, XML or HTML), e.g.

 Features in this part of subject sequence:
   transcription elongation factor protein, GreA/GreB family

 Score = 30.2 bits (15),  Expect =    39
 Identities = 15/15 (100%), Gaps = 0/15 (0%)
 Strand=Plus/Plus

Query  1        TAGGCCTCGCGCGCC  15
                |||||||||||||||
Sbjct  2614347  TAGGCCTCGCGCGCC  2614361


Peter

From lueck at ipk-gatersleben.de  Wed Jul 23 11:20:04 2008
From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=)
Date: Wed, 23 Jul 2008 17:20:04 +0200
Subject: [BioPython] blast
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
	<320fb6e00807230754k52bebba4v453933ef0a215351@mail.gmail.com>
Message-ID: <013e01c8ecd7$95731490$1022a8c0@ipkgatersleben.de>

Sorry, I forgot to say that I do the alignment myself. It's was just for 
demonstration.

Yes. I have a 30 bp primer. 15 bp from the primer bind to my query sequence. 
The percentage would be 50 %.
percent = match * 100 / full length primer

>
percentage_identity = (100.0 * hsp.identities) / hsp.align_length
percentage_identity_ref_matched_query = (100.0 * hsp.identities) / 
(hsp.align_length - hsp.query.count("-"))
>

Sorry, both give me wrong percentage if I try on my database.

Look here, compare alignment and percentage:

http://picasaweb.google.de/luecks/Python02/photo#5226228430697476754

e.g Hit 13 should give 60 %

What you recommend to use instead of hsp.score?

Nice quitting time
Stefanie



From p.j.a.cock at googlemail.com  Wed Jul 23 11:36:40 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 16:36:40 +0100
Subject: [BioPython] blast
In-Reply-To: <013e01c8ecd7$95731490$1022a8c0@ipkgatersleben.de>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
	<320fb6e00807230754k52bebba4v453933ef0a215351@mail.gmail.com>
	<013e01c8ecd7$95731490$1022a8c0@ipkgatersleben.de>
Message-ID: <320fb6e00807230836j1196ad41s303927af1c1645c3@mail.gmail.com>

> Sorry, both give me wrong percentage if I try on my database.
>
> Look here, compare alignment and percentage:
>
> http://picasaweb.google.de/luecks/Python02/photo#5226228430697476754
>
> e.g Hit 13 should give 60 %
>
> What you recommend to use instead of hsp.score?

I am assuming you want to parse some BLAST output in order to populate
this database.  How about something based on this:

from Bio.Blast import NCBIXML
for record in NCBIXML.parse(open("test.xml")) :
    print "Query %i length %i" % (record.query_id, record.query_letters)
    for alignment in record.alignments :
        for hsp in alignment.hsps :
            percentage_identities_versus_full_query = (100.0 *
hsp.identities) / record.query_letters
            print " vs %s gives %0.1f%% identities" \
              % (alignment.hit_id, percentage_identities_versus_full_query)

This uses the fact the the original query length is recorded in the
record object as the "query_letters" property (this name was a
historical choice based on the plain text blast output).

For the example you gave, then then I would expect hsp.identities ==
12 (and hsp.alignment_length == 12) while record.query_letters == 60
which will give you the desired output of 60%.

Peter

From biopython at maubp.freeserve.co.uk  Wed Jul 23 18:12:34 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Jul 2008 23:12:34 +0100
Subject: [BioPython] Deprecating Bio.Saf (PredictProtein Simple Alignment
	Format)
Message-ID: <320fb6e00807231512s507d2652jc0f26764a62b01d5@mail.gmail.com>

Is anyone using Bio.Saf or PredictProtein's "Simple Alignment Format" (SAF)?

Bio.Saf is one of the older parsers in Biopython.  It parses the
PredictProtein "Simple Alignment Format" (SAF), a fairly free-format
multiple sequence alignment file format described here:
http://www.predictprotein.org/Dexa/optin_saf.html

Potentially we could support this file format within Bio.AlignIO (if
there was any demand).  However, as far as I can tell, this file
format is ONLY used for PredictProtein, and they will accept several
other more mainstream alignment file formats as alternatives.

Bio.Saf uses Martel for parsing, which is not entirely compatible with
mxTextTools 3.0.  If we did want to integrate SAF support into
Bio.AlignIO it might be best to reimplement the parser in plain
python.

If no one is using it, I would like to deprecate Bio.Saf in the next
release of Biopython.

Peter

From biopython at maubp.freeserve.co.uk  Wed Jul 23 18:29:37 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Jul 2008 23:29:37 +0100
Subject: [BioPython] Deprecating the HTML parser in Bio.Blast.NCBIWWW
In-Reply-To: <4887000B.1070409@biotec.tu-dresden.de>
References: <320fb6e00807120645u26321d71q30f72ed5808f700@mail.gmail.com>
	<320fb6e00807220838x3aae8246w8a6e3108bf6feec8@mail.gmail.com>
	<4887000B.1070409@biotec.tu-dresden.de>
Message-ID: <320fb6e00807231529w5a6d4ee0n9d595234764eea02@mail.gmail.com>

Christof Winter wrote:
> Peter wrote:
>>
>> For any Biopython and Blast users,
>>
>> For some time now we've been discouraging the use of the HTML
>> and plain text Blast parsers in favour of the XML format.
>>
>> I think it would be a good idea to now officially deprecate the
>> HTML parser in Bio.Blast.NCBIWWW with warning messages
>> when it is used.
>
> Full ack.
>
> Christof

This is now deprecated in CVS, and I'll update the tutorial shortly.
For the next couple of releases of Biopython the parser will still be
there, but will now issue a warning message. if you try and use it.
If there is anyone out there still using the HTML BLAST parser, it
isn't too late to undo this change.

Peter

From alexl at users.sourceforge.net  Thu Jul 24 04:23:21 2008
From: alexl at users.sourceforge.net (Alex Lancaster)
Date: Thu, 24 Jul 2008 01:23:21 -0700
Subject: [BioPython] Fedora biopython packages updated for 1.47
Message-ID: <xvmyk7y9l2.fsf@allele2.eebweb.arizona.edu>

Hi there,

For all Fedora users, new packages for biopython 1.47 are now
available the "updates-testing" repository for F-8 and F-9

To test them out simply run (as root):

yum --enablerepo=updates-testing install python-biopython

You can provide feedback on packages here:

For F-9:

https://admin.fedoraproject.org/updates/F9/FEDORA-2008-6235

For F-8:

https://admin.fedoraproject.org/updates/F8/FEDORA-2008-6243

(You can leave feedback anonymously, or using your Fedora account name
if you happen to be a Fedora contributor)

The more positive feedback from testing, the faster the packages can
go into the stable "updates" repo (or conversely if there are any
problems, they can be fixed before being pushed).

Thanks!
Alex

From matzke at berkeley.edu  Fri Jul 25 01:27:55 2008
From: matzke at berkeley.edu (Nick Matzke)
Date: Thu, 24 Jul 2008 22:27:55 -0700
Subject: [BioPython] problem installing mxTextTools
Message-ID: <4889645B.9080400@berkeley.edu>

Hi all,

I am trying to install biopython and am carefully following the 
directions at:

http://biopython.org/DIST/docs/install/Installation.html

...as instructed, here are the steps I took:


1. I start by successfully installing Python2.4.4 on my Mac OSX 10.4.  I 
set the environment variable so that Python2.4.4 is the default version 
of Python at the terminal.

2. Then, as instructed I try to install mxTextTools.  Downloaded:
egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt

...from here:
http://www.egenix.com/products/python/mxBase/


3. However, none of these (the official instructions, or several 
alternatives proposed in various online fora) work for installing 
mxTextTools.  Here are the results:

3a. instructions here:
http://biopython.org/DIST/docs/install/Installation.html#htoc9

======================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
root# python -V
Python 2.4.4

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
root# python setup.py build
running build
running mx_autoconf
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
-L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
macros to define: [('HAVE_STRPTIME', '1')]
macros to undefine: []
running build_ext

building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
building 'mx.DateTime.mxDateTime.mxDateTime' extension
creating build/temp.macosx-10.3-fat-2.4_ucs2
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
-DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
mx/DateTime/mxDateTime/mxDateTime.c -o 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o
i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
i686-apple-darwin8-gcc-4.0.1: no input files
powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
powerpc-apple-darwin8-gcc-4.0.1: no input files
lipo: can't figure out the architecture type of: /var/tmp//cch9pAof.out
error: command 'gcc' failed with exit status 1

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
root#
======================


3b. Instructions here:
http://www.egenix.com/products/python/mxBase/

sudo python setup.py install

==================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ python -V
Python 2.4.4

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py install
running install
running build
running mx_autoconf
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
-L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
macros to define: [('HAVE_STRPTIME', '1')]
macros to undefine: []
running build_ext

building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
building 'mx.DateTime.mxDateTime.mxDateTime' extension
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
-DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
mx/DateTime/mxDateTime/mxDateTime.c -o 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o
i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
i686-apple-darwin8-gcc-4.0.1: no input files
powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
powerpc-apple-darwin8-gcc-4.0.1: no input files
lipo: can't figure out the architecture type of: /var/tmp//ccGUEnk3.out
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

==================




3c. Instructions here:
http://www.egenix.com/mailman-archives/egenix-users/2007-October/114291.html

sudo python setup.py build --skip install
================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ python -V
Python 2.4.4
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py build --skip install
running build
skipping the build process and reusing the existing build files and data
error: build/build-macosx-10.3-fat-py2.4_ucs2.pck: No such file or directory
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ ls
COPYRIGHT               PKG-INFO                build 
installer.bmp           mxSetup.pyc             wininst.bat
LICENSE                 README                  egenix_mx_base.py 
mx                      setup.cfg
MANIFEST                bdist_zope.bat          egenix_mx_base.pyc 
mxSetup.py              setup.py
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ ls ./build
build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
temp.darwin-8.11.1-i386-2.3_ucs2
lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 
temp.macosx-10.3-fat-2.4_ucs2
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$
================


4. Give up and email the biopython list.  Help!!  Please!!


5. Ask existential questions about why, oh why, all useful software 
comes with dependencies that you have to compile yourself and which 
never, ever compile correctly when the instructions are followed even on 
utterly standard systems like Mac OSX 10.4.


Thanks very very much,
Nick







-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab website: http://ib.berkeley.edu/people/lab_detail.php?lab=54
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: 
http://fisher.berkeley.edu/~edna/lab_test/members/matzke.html
Lab phone: 510-643-6299
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Office hours for Bio1B: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================

From matzke at berkeley.edu  Fri Jul 25 01:46:20 2008
From: matzke at berkeley.edu (Nick Matzke)
Date: Thu, 24 Jul 2008 22:46:20 -0700
Subject: [BioPython] problem installing mxTextTools
In-Reply-To: <4889645B.9080400@berkeley.edu>
References: <4889645B.9080400@berkeley.edu>
Message-ID: <488968AC.4000303@berkeley.edu>

Hi all,

An update -- I found a solution by copying the .pck file the download 
actually gave me to the filename that the install was apparently looking 
for.  This was not exactly obvious (!!!!) but apparently it worked:

<snipping output of solution which made the email too long for the 
auto-moderator>

==============================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ cd build

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ ls
build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
temp.darwin-8.11.1-i386-2.3_ucs2
lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 temp.macosx-10.3-fat-2.4_ucs2

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ cp build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
build-macosx-10.3-fat-py2.4_ucs2.pck

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ cd ..

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py build --skip installPassword:
running build
skipping the build process and reusing the existing build files and data
restoring build data from a previous build run
running install
running install_lib
running build_ext
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating

[...]

writing byte-compilation script '/tmp/tmpIfqFr6.py'
/Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/Python 
-O /tmp/tmpIfqFr6.py
removing /tmp/tmpIfqFr6.py
running install_data


wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ more README
=============================================================================
eGenix mx Base Distribution for Python
-----------------------------------------------------------------------------

Source Installation
-------------------

In order to build and install the distribution, run

     python setup.py install

Then change to some other directory and try to import the packages:

$ cd ~
$ python
Python 2.4.3 (#1, May  9 2007, 00:48:21)
[GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> from mx.DateTime import now
 >>> print now()
2007-05-30 11:00:03.24
 >>>

Note that trying this from the installation directory will cause
Python to pick up the source tree packages which do not contain the
compiled binaries.  This will likely fail with strange error messages.


Prebuilt Installation
---------------------

If you have downloaded a prebuilt distribution archive, the
installation is slightly different. You have to run

     python setup.py build --skip install

Then follow the same instructions as for the source installation.


Copyrights & Licenses
---------------------

The software in this distribution is copyrighted and protected by
international, EU and German copyright law. Please see the COPYRIGHT
file for details.

The software is licensed to you under the eGenix.com Public License as
stated in the LICENSE file of the distribution directory.  Some
subpackages may contain third-party software which is licensed under
different conditions. Please see the documentation and/or LICENSE
files of the subpackages for details.

If in doubt, please check the web-site at http://www.egenix.com or
contact sales at egenix.com for more information on copyright, licensing
conditions and authorized use.


-----------------------------------------------------------------------------
eGenix.com GmbH
Pastor-Loeh-Str. 48
D-40764 Langenfeld
Germany
info at egenix.com

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ cd ..

wright:/bioinformatics/pythonstuff nick$ ls
egenix python_notes.rtf
egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt

wright:/bioinformatics/pythonstuff nick$ python
Python 2.4.4 (#1, Oct 18 2006, 10:34:39)
[GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

 >>> from mx.DateTime import now
 >>>

 >>> print now()
2008-07-24 22:39:17.66
 >>>
==============================

Several hours of my life gone, but yay!

Cheers,
Nick

From matzke at berkeley.edu  Fri Jul 25 03:37:15 2008
From: matzke at berkeley.edu (Nick Matzke)
Date: Fri, 25 Jul 2008 00:37:15 -0700
Subject: [BioPython] problem installing mxTextTools
In-Reply-To: <488968AC.4000303@berkeley.edu>
References: <4889645B.9080400@berkeley.edu> <488968AC.4000303@berkeley.edu>
Message-ID: <488982AB.8000209@berkeley.edu>

Or, even better, version 2 of mxTextTools should be downloaded and used, 
it installs easily, and is supposed to work better anyway, however you 
can only find this from this page:

http://biopython.org/wiki/Download#Optional_Software
http://www.egenix.com/www2002/python/eGenix-mx-Extensions-v2.x.html/

...but not the "complete instructions" page:
http://biopython.org/DIST/docs/install/Installation.html#htoc9

(Sorry if this stuff is annoying but probably someone else naive will 
have these same problems in the future.)

Cheers,
Nick




Nick Matzke wrote:
> Hi all,
> 
> An update -- I found a solution by copying the .pck file the download 
> actually gave me to the filename that the install was apparently looking 
> for.  This was not exactly obvious (!!!!) but apparently it worked:
> 
> <snipping output of solution which made the email too long for the 
> auto-moderator>
> 
> ==============================
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ cd build
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
> nick$ ls
> build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
> temp.darwin-8.11.1-i386-2.3_ucs2
> lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 temp.macosx-10.3-fat-2.4_ucs2
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
> nick$ cp build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
> build-macosx-10.3-fat-py2.4_ucs2.pck
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
> nick$ cd ..
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ sudo python setup.py build --skip installPassword:
> running build
> skipping the build process and reusing the existing build files and data
> restoring build data from a previous build run
> running install
> running install_lib
> running build_ext
> creating 
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx 
> 
> copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/__init__.py 
> -> 
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx 
> 
> creating
> 
> [...]
> 
> writing byte-compilation script '/tmp/tmpIfqFr6.py'
> /Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/Python 
> -O /tmp/tmpIfqFr6.py
> removing /tmp/tmpIfqFr6.py
> running install_data
> 
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ more README
> ============================================================================= 
> 
> eGenix mx Base Distribution for Python
> ----------------------------------------------------------------------------- 
> 
> 
> Source Installation
> -------------------
> 
> In order to build and install the distribution, run
> 
>     python setup.py install
> 
> Then change to some other directory and try to import the packages:
> 
> $ cd ~
> $ python
> Python 2.4.3 (#1, May  9 2007, 00:48:21)
> [GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> from mx.DateTime import now
>  >>> print now()
> 2007-05-30 11:00:03.24
>  >>>
> 
> Note that trying this from the installation directory will cause
> Python to pick up the source tree packages which do not contain the
> compiled binaries.  This will likely fail with strange error messages.
> 
> 
> Prebuilt Installation
> ---------------------
> 
> If you have downloaded a prebuilt distribution archive, the
> installation is slightly different. You have to run
> 
>     python setup.py build --skip install
> 
> Then follow the same instructions as for the source installation.
> 
> 
> Copyrights & Licenses
> ---------------------
> 
> The software in this distribution is copyrighted and protected by
> international, EU and German copyright law. Please see the COPYRIGHT
> file for details.
> 
> The software is licensed to you under the eGenix.com Public License as
> stated in the LICENSE file of the distribution directory.  Some
> subpackages may contain third-party software which is licensed under
> different conditions. Please see the documentation and/or LICENSE
> files of the subpackages for details.
> 
> If in doubt, please check the web-site at http://www.egenix.com or
> contact sales at egenix.com for more information on copyright, licensing
> conditions and authorized use.
> 
> 
> ----------------------------------------------------------------------------- 
> 
> eGenix.com GmbH
> Pastor-Loeh-Str. 48
> D-40764 Langenfeld
> Germany
> info at egenix.com
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ cd ..
> 
> wright:/bioinformatics/pythonstuff nick$ ls
> egenix python_notes.rtf
> egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> 
> wright:/bioinformatics/pythonstuff nick$ python
> Python 2.4.4 (#1, Oct 18 2006, 10:34:39)
> [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> 
>  >>> from mx.DateTime import now
>  >>>
> 
>  >>> print now()
> 2008-07-24 22:39:17.66
>  >>>
> ==============================
> 
> Several hours of my life gone, but yay!
> 
> Cheers,
> Nick
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab website: http://ib.berkeley.edu/people/lab_detail.php?lab=54
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: 
http://fisher.berkeley.edu/~edna/lab_test/members/matzke.html
Lab phone: 510-643-6299
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Office hours for Bio1B: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================

From biopython at maubp.freeserve.co.uk  Fri Jul 25 05:11:29 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 25 Jul 2008 10:11:29 +0100
Subject: [BioPython] problem installing mxTextTools
In-Reply-To: <488982AB.8000209@berkeley.edu>
References: <4889645B.9080400@berkeley.edu> <488968AC.4000303@berkeley.edu>
	<488982AB.8000209@berkeley.edu>
Message-ID: <320fb6e00807250211x4a9cdd31jfdaf4762204e522e@mail.gmail.com>

On Fri, Jul 25, 2008 at 8:37 AM, Nick Matzke <matzke at berkeley.edu> wrote:
> Or, even better, version 2 of mxTextTools should be downloaded and used, it
> installs easily, and is supposed to work better anyway, however you can only
> find this from this page:
>
> http://biopython.org/wiki/Download#Optional_Software
> http://www.egenix.com/www2002/python/eGenix-mx-Extensions-v2.x.html/
>
> ...but not the "complete instructions" page:
> http://biopython.org/DIST/docs/install/Installation.html#htoc9
>
> (Sorry if this stuff is annoying but probably someone else naive will have
> these same problems in the future.)

As you have discovered the wiki is more up to date, but we should
update that document too.

On the wiki we do explicitly recommend mxTextTools 2.0 rather than 3.0
(there were some unicode related API changes), but in any case
mxTextTools is now optional as it is only needed for a few less used
parsers.  As the install script says, you can delay installing
mxTextTools until when using Biopython you see an import error
relating to it.

At least you've succeeded in the installation now :)

Peter

From dalke at dalkescientific.com  Mon Jul 28 17:58:22 2008
From: dalke at dalkescientific.com (Andrew Dalke)
Date: Mon, 28 Jul 2008 23:58:22 +0200
Subject: [BioPython] training in Python for cheminformatics
Message-ID: <B20E21E1-166C-4631-95B7-6843E6878261@dalkescientific.com>

Hi all,

   This isn't quite bioinformatics, but maybe if you squint
hard enough you might see the purines and pyrimidines in DNA. :)

   I'm going to teach a two-day intensive course in Python
programming, focusing on cheminformatics/small molecules.
The target audience is computational chemists who want to
be more effective at doing science by learning more about
how to program.  Most of my examples will be directly
based on problems that come up in a normal research
environment.

   The course is scheduled for 6-7 October in Leipzig, Germany.

   More details are at:
      http://dalkescientific.com/training/

				Andrew
				dalke at dalkescientific.com



From shulin.zhuang at gmail.com  Tue Jul 29 20:34:23 2008
From: shulin.zhuang at gmail.com (Shulin Zhuang)
Date: Tue, 29 Jul 2008 17:34:23 -0700
Subject: [BioPython] how to using python to multiply call a program for
	caculation
Message-ID: <4f1a9e210807291734t6d7c7e9fq6d34df63e3e172d6@mail.gmail.com>

Dear All,

Here just disturb you a question.

I make a simple script to execute one program, the script content:

import string, re, sys, os, time, math
calc = '/usr/local/bin/resc 1bmp.pdb 8 A > 8.txt '
os.system(calc)

I can sucessfully execute this script and get the result file"8.txt.


In the calc column,  8 is a residue number,  resc is a program. The aim is
to use resc to calculate residue 8 and get the output 8.txt.


 I want to calculate the whole residues from 1, 2, 3, ..... to 100, if I use
above simple script, I should execute 100 times. Therefore, I want to write
a script to let the python do all the calculations at one time.

Then I write the script as following:

import string, re, sys, os, time, math
i = 1
while i <=100:
       calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + abc
       i = i +1
os.system(calc)


However, when I execute the script and get an error:"The first argument
should bu numerical"

Would you like to tell me how to write a good script to tackle this problem.
great thanks

Best regards

From shulin.zhuang at gmail.com  Tue Jul 29 21:35:51 2008
From: shulin.zhuang at gmail.com (Shulin Zhuang)
Date: Tue, 29 Jul 2008 18:35:51 -0700
Subject: [BioPython] how to using python to multiply call a program for
	caculation
In-Reply-To: <4f1a9e210807291734t6d7c7e9fq6d34df63e3e172d6@mail.gmail.com>
References: <4f1a9e210807291734t6d7c7e9fq6d34df63e3e172d6@mail.gmail.com>
Message-ID: <4f1a9e210807291835l929aeebs4035d312bc0809a7@mail.gmail.com>

Dear All,

Sorry to disturb you again.
If I edit the sentence to:
import string, re, sys, os, time, math
i = 1
while i <=100:
         calc = "/usr/local/bin/resc 1bmp.pdb %d  A >%d.txt"%(i,i)
         os.system(calc)

in above A is the chain name of 1bmp.pdb.


Now I can execute it and get the result.

Thanks for your notice.  It is because that I am just a beginner and not
familiar with the string and value.
Best regards
Shulin





On Tue, Jul 29, 2008 at 5:34 PM, Shulin Zhuang <shulin.zhuang at gmail.com>wrote:

> Dear All,
>
> Here just disturb you a question.
>
> I make a simple script to execute one program, the script content:
>
> import string, re, sys, os, time, math
> calc = '/usr/local/bin/resc 1bmp.pdb 8 A > 8.txt '
> os.system(calc)
>
> I can sucessfully execute this script and get the result file"8.txt.
>
>
> In the calc column,  8 is a residue number,  resc is a program. The aim is
> to use resc to calculate residue 8 and get the output 8.txt.
>
>
>  I want to calculate the whole residues from 1, 2, 3, ..... to 100, if I
> use above simple script, I should execute 100 times. Therefore, I want to
> write a script to let the python do all the calculations at one time.
>
> Then I write the script as following:
>
> import string, re, sys, os, time, math
> i = 1
> while i <=100:
>        calc = '/home/shulin/program/rescP/resc 1bmp.pdb  ' + abc
>        i = i +1
> os.system(calc)
>
>
> However, when I execute the script and get an error:"The first argument
> should bu numerical"
>
> Would you like to tell me how to write a good script to tackle this
> problem. great thanks
>
> Best regards
>
>
>

From lpritc at scri.ac.uk  Wed Jul 30 04:00:50 2008
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Wed, 30 Jul 2008 09:00:50 +0100
Subject: [BioPython] how to using python to multiply call a program for
 caculation
In-Reply-To: <4f1a9e210807291734t6d7c7e9fq6d34df63e3e172d6@mail.gmail.com>
Message-ID: <C4B5DE42.13CC7%lpritc@scri.ac.uk>

Hi Shulin,

I can't see in your code with the while condition where you are specifying
the residue on the command-line string: the variable 'abc' appears to be
undefined in your code:

calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + abc

So the above should throw an error.

>From your code, the variable containing the residue number you want to use
in the command line appears to be 'i', and there are a number of ways you
can get your variable 'i' into the command-line string from there,
including:

calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + str(i)
calc = '/home/shulin/program/rescP/resc 1PGA.pdb %d' % i
calc = ' '.join(['/home/shulin/program/rescP/resc 1PGA.pdb', str(i)])


I've not tested the following code, but it may be the sort of thing you're
looking for:

# For this code you only need to import os
import os
# Define the command-line string components once
cmdexe = "/home/shulkin/program/rescP/resc"    # executable location
cmdstructure = "1PGA.pdb"                      # structure for analysis
# Then loop over the residue numbers, building a new command line
# and calling each time
for residue in range(1, 101):
    cmdstr = "%s %s %d > %d.txt" % (cmdexe, cmdstructure, residue, residue)
    #print cmdstr                 # does the command-line look right?
    os.system(cmdstr)             # make the system call
    
Sections of the Python documentation you might find useful here are:

string formatting
http://docs.python.org/lib/typesseq-strings.html

subprocess (which is favoured over os.system):
http://docs.python.org/lib/module-subprocess.html

And you may also be interested in the Python Tutor mailing list:
http://mail.python.org/mailman/listinfo/tutor

I hope this is useful,

L.

On 30/07/2008 01:34, "Shulin Zhuang" <shulin.zhuang at gmail.com> wrote:

> Dear All,
> 
> Here just disturb you a question.
> 
> I make a simple script to execute one program, the script content:
> 
> import string, re, sys, os, time, math
> calc = '/usr/local/bin/resc 1bmp.pdb 8 A > 8.txt '
> os.system(calc)
> 
> I can sucessfully execute this script and get the result file"8.txt.
> 
> 
> In the calc column,  8 is a residue number,  resc is a program. The aim is
> to use resc to calculate residue 8 and get the output 8.txt.
> 
> 
>  I want to calculate the whole residues from 1, 2, 3, ..... to 100, if I use
> above simple script, I should execute 100 times. Therefore, I want to write
> a script to let the python do all the calculations at one time.
> 
> Then I write the script as following:
> 
> import string, re, sys, os, time, math
> i = 1
> while i <=100:
>        calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + abc
>        i = i +1
> os.system(calc)
> 
> 
> However, when I execute the script and get an error:"The first argument
> should bu numerical"
> 
> Would you like to tell me how to write a good script to tackle this problem.
> great thanks
> 
> Best regards
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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From cmckay at u.washington.edu  Thu Jul 31 21:45:15 2008
From: cmckay at u.washington.edu (Cedar McKay)
Date: Thu, 31 Jul 2008 18:45:15 -0700
Subject: [BioPython] SeqRecord to Genbank: use SeqIO?
Message-ID: <0B3D0CC5-820B-4D98-8EB6-6ED6F7D2B6C8@u.washington.edu>

Hello, I have SeqRecord objects that I'd like to convert to a string  
that is in Genbank format. That way I can do whatever with it,  
including write it to a file. The only way I can see to do anything  
similar is using SeqIO and doing something like:

SeqIO.write(my_records, out_file_handle, "genbank")
which I found here:
http://biopython.org/DIST/docs/tutorial/Tutorial.html#chapter:Bio.SeqIO

The problem is, it doesn't support something like:
SeqIO.write(seq_record, out_file_handle, "genbank")
Because it requires an iterable object I guess? And it has to write to  
a file handle for some reason, and won't just give me the string to do  
whatever I want with.

I've done a lot of searching and mailing lists, and googling, and  
surely I must be missing something? What is the simplest way to get a  
string representing a genbank file, starting with a SeqRecord?

I'm sort of shocked that there isn't some sort of  
SeqRecord.to_genbank() method.

Hope someone can point me in the right direction!

best,
Cedar



From jcigar at ulb.ac.be  Wed Jul 23 14:02:48 2008
From: jcigar at ulb.ac.be (Julien Cigar)
Date: Wed, 23 Jul 2008 18:02:48 -0000
Subject: [BioPython] blast
In-Reply-To: <320fb6e00807230836j1196ad41s303927af1c1645c3@mail.gmail.com>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
	<320fb6e00807230754k52bebba4v453933ef0a215351@mail.gmail.com>
	<013e01c8ecd7$95731490$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230836j1196ad41s303927af1c1645c3@mail.gmail.com>
Message-ID: <1216830497.1019.2.camel@rivendell.lan>

Just FYI and another point of view (?), I asked one of the user about
which method is the best and he said that "one should not depend on the
length of the sequence to know how different/similar the use fragment
is", so it's really percentage identity which is needed

Julien

On Wed, 2008-07-23 at 16:36 +0100, Peter Cock wrote:
> > Sorry, both give me wrong percentage if I try on my database.
> >
> > Look here, compare alignment and percentage:
> >
> > http://picasaweb.google.de/luecks/Python02/photo#5226228430697476754
> >
> > e.g Hit 13 should give 60 %
> >
> > What you recommend to use instead of hsp.score?
> 
> I am assuming you want to parse some BLAST output in order to populate
> this database.  How about something based on this:
> 
> from Bio.Blast import NCBIXML
> for record in NCBIXML.parse(open("test.xml")) :
>     print "Query %i length %i" % (record.query_id, record.query_letters)
>     for alignment in record.alignments :
>         for hsp in alignment.hsps :
>             percentage_identities_versus_full_query = (100.0 *
> hsp.identities) / record.query_letters
>             print " vs %s gives %0.1f%% identities" \
>               % (alignment.hit_id, percentage_identities_versus_full_query)
> 
> This uses the fact the the original query length is recorded in the
> record object as the "query_letters" property (this name was a
> historical choice based on the plain text blast output).
> 
> For the example you gave, then then I would expect hsp.identities ==
> 12 (and hsp.alignment_length == 12) while record.query_letters == 60
> which will give you the desired output of 60%.
> 
> Peter
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython


From matzke at berkeley.edu  Fri Jul 25 01:44:01 2008
From: matzke at berkeley.edu (Nick Matzke)
Date: Fri, 25 Jul 2008 05:44:01 -0000
Subject: [BioPython] problem installing mxTextTools
In-Reply-To: <4889645B.9080400@berkeley.edu>
References: <4889645B.9080400@berkeley.edu>
Message-ID: <48896815.10104@berkeley.edu>

Hi all,

An update -- I found a solution by copying the .pck file the download 
actually gave me to the filename that the install was apparently looking 
for.  This was not exactly obvious (!!!!) but apparently it worked:


==============================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ cd build

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ ls
build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
temp.darwin-8.11.1-i386-2.3_ucs2
lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 
temp.macosx-10.3-fat-2.4_ucs2

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ cp build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
build-macosx-10.3-fat-py2.4_ucs2.pck

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ cd ..

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py build --skip installPassword:
running build
skipping the build process and reusing the existing build files and data
restoring build data from a previous build run
running install
running install_lib
running build_ext
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/BeeBase.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/BeeDict.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/BeeIndex.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/BeeStorage.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/Cache.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/Doc/mxBeeBase.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/ExitFunctions.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/FileLock.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/btr.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/mxBeeBase.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/mxBeeBase.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/testjohn.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/README -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/showBeeDict.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/ARPA.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/COPYRIGHT 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/DateTime.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Doc/mxDateTime.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Doc
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/alarm.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/AtomicClock.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/CommandLine.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/lifespan.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/numdate.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/Y2000.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Feasts.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/ISO.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/LazyModule.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Locale.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/mxDateTime.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/mxDateTime.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/mxDateTime_Python.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testcmp.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testcoerce.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testcomdates.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testnow.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testpydatetime.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testrichard.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testroundoff.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/teststrftime.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testsubclassing.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testticks.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/NIST.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/ODMG.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Parser.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/README -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/timegm.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Timezone.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/eGenix-mx-Extensions.html 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxBeeBase.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxDateTime.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxProxy.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxQueue.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxStack.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxTextTools.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxTools.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxUID.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxURL.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Log.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/Cache.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/CommandLine.py 
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/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/ConfigFile.py 
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/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/Cookie.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/CSV.py 
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/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/ExitFunctions.py 
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/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/FileLock.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/LazyModule.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/LICENSE 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/Namespace.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/OrderedMapping.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/PackageTools.py 
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/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/NewBuiltins.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/Doc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/Doc/mxProxy.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/Doc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/LICENSE -> 
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creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/mxProxy/__init__.py 
-> 
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/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
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-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
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-> 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/mxProxy/weakreftest.py 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/Proxy.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/Doc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/Doc/mxQueue.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/Doc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
creating 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/mxQueue/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/mxQueue/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/mxQueue/mxQueue.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/mxQueue/mxQueue.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/mxQueue/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/queuebench.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/UserQueue.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/Doc/mxStack.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/mxStack/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/mxStack/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack
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-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/mxStack/mxStack.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/mxStack/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/stackbench.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/UserStack.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Constants/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Constants/Sets.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Constants/TagTables.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/COPYRIGHT 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Doc/mxTextTools.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Doc
creating 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/altRTF.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/HTML.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/Loop.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/mysplit.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/pytag.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/Python.py 
-> 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/RegExp.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/RTF.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/Tim.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/Words.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
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-> 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
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-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
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-> 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/testHTML.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/testkj.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
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-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/testSegFault.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/README -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/TextTools.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/Doc/mxTools.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Doc
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/Examples/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/Examples/Acquisition.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/bench1.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/bench2.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/hack.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/mxTools.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/mxTools.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/test_safecall.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/NewBuiltins.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/Tools.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/Doc/mxUID.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/Doc
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/LICENSE 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/mxh.h -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/mxUID.h -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/mxUID.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/test.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/UID.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/Doc/mxURL.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/LazyModule.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/LICENSE 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/Listing.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/mxh.h -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/mxURL.h -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/mxURL.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/test.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/URL.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/BeeBase.py 
to BeeBase.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/BeeDict.py 
to BeeDict.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/BeeIndex.py 
to BeeIndex.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/BeeStorage.py 
to BeeStorage.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/Cache.py 
to Cache.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/ExitFunctions.py 
to ExitFunctions.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/FileLock.py 
to FileLock.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase/testjohn.py 
to testjohn.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/showBeeDict.py 
to showBeeDict.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/ARPA.py 
to ARPA.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/DateTime.py 
to DateTime.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/alarm.py 
to alarm.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/AtomicClock.py 
to AtomicClock.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/CommandLine.py 
to CommandLine.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/lifespan.py 
to lifespan.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/numdate.py 
to numdate.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/Y2000.py 
to Y2000.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Feasts.py 
to Feasts.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/ISO.py 
to ISO.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/LazyModule.py 
to LazyModule.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Locale.py 
to Locale.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/mxDateTime_Python.py 
to mxDateTime_Python.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testcmp.py 
to testcmp.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testcoerce.py 
to testcoerce.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testcomdates.py 
to testcomdates.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testnow.py 
to testnow.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testpydatetime.py 
to testpydatetime.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testrichard.py 
to testrichard.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testroundoff.py 
to testroundoff.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/teststrftime.py 
to teststrftime.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testsubclassing.py 
to testsubclassing.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testticks.py 
to testticks.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/NIST.py 
to NIST.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/ODMG.py 
to ODMG.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Parser.py 
to Parser.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/timegm.py 
to timegm.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Timezone.py 
to Timezone.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Log.py 
to Log.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/Cache.py 
to Cache.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/CommandLine.py 
to CommandLine.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/ConfigFile.py 
to ConfigFile.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/Cookie.py 
to Cookie.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/CSV.py 
to CSV.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/ExitFunctions.py 
to ExitFunctions.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/FileLock.py 
to FileLock.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/LazyModule.py 
to LazyModule.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/Namespace.py 
to Namespace.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/OrderedMapping.py 
to OrderedMapping.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/PackageTools.py 
to PackageTools.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/NewBuiltins.py 
to NewBuiltins.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy/testvlad.py 
to testvlad.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy/weakreftest.py 
to weakreftest.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/Proxy.py 
to Proxy.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/queuebench.py 
to queuebench.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/UserQueue.py 
to UserQueue.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/stackbench.py 
to stackbench.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/UserStack.py 
to UserStack.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants/Sets.py 
to Sets.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants/TagTables.py 
to TagTables.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/altRTF.py 
to altRTF.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/HTML.py 
to HTML.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/Loop.py 
to Loop.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/mysplit.py 
to mysplit.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/pytag.py 
to pytag.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/Python.py 
to Python.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/RegExp.py 
to RegExp.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/RTF.py 
to RTF.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/Tim.py 
to Tim.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/Words.py 
to Words.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/testHTML.py 
to testHTML.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/testkj.py 
to testkj.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/testPickleSegFault.py 
to testPickleSegFault.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/testSegFault.py 
to testSegFault.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/TextTools.py 
to TextTools.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Examples/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Examples/Acquisition.py 
to Acquisition.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/bench1.py 
to bench1.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/bench2.py 
to bench2.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/hack.py 
to hack.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/test_safecall.py 
to test_safecall.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/NewBuiltins.py 
to NewBuiltins.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Tools.py 
to Tools.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/UID.py 
to UID.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/LazyModule.py 
to LazyModule.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/Listing.py 
to Listing.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/URL.py 
to URL.pyc
writing byte-compilation script '/tmp/tmpIfqFr6.py'
/Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/Python 
-O /tmp/tmpIfqFr6.py
removing /tmp/tmpIfqFr6.py
running install_data


wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ more README
=============================================================================
eGenix mx Base Distribution for Python
-----------------------------------------------------------------------------

Source Installation
-------------------

In order to build and install the distribution, run

     python setup.py install

Then change to some other directory and try to import the packages:

$ cd ~
$ python
Python 2.4.3 (#1, May  9 2007, 00:48:21)
[GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> from mx.DateTime import now
 >>> print now()
2007-05-30 11:00:03.24
 >>>

Note that trying this from the installation directory will cause
Python to pick up the source tree packages which do not contain the
compiled binaries.  This will likely fail with strange error messages.


Prebuilt Installation
---------------------

If you have downloaded a prebuilt distribution archive, the
installation is slightly different. You have to run

     python setup.py build --skip install

Then follow the same instructions as for the source installation.


Copyrights & Licenses
---------------------

The software in this distribution is copyrighted and protected by
international, EU and German copyright law. Please see the COPYRIGHT
file for details.

The software is licensed to you under the eGenix.com Public License as
stated in the LICENSE file of the distribution directory.  Some
subpackages may contain third-party software which is licensed under
different conditions. Please see the documentation and/or LICENSE
files of the subpackages for details.

If in doubt, please check the web-site at http://www.egenix.com or
contact sales at egenix.com for more information on copyright, licensing
conditions and authorized use.


-----------------------------------------------------------------------------
eGenix.com GmbH
Pastor-Loeh-Str. 48
D-40764 Langenfeld
Germany
info at egenix.com

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ cd ..

wright:/bioinformatics/pythonstuff nick$ ls
egenix 
python_notes.rtf
egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt

wright:/bioinformatics/pythonstuff nick$ python
Python 2.4.4 (#1, Oct 18 2006, 10:34:39)
[GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

 >>> from mx.DateTime import now
 >>>

 >>> print now()
2008-07-24 22:39:17.66
 >>>
==============================

Several hours of my life gone, but yay!

Cheers,
Nick




Nick Matzke wrote:
> Hi all,
> 
> I am trying to install biopython and am carefully following the 
> directions at:
> 
> http://biopython.org/DIST/docs/install/Installation.html
> 
> ...as instructed, here are the steps I took:
> 
> 
> 1. I start by successfully installing Python2.4.4 on my Mac OSX 10.4.  I 
> set the environment variable so that Python2.4.4 is the default version 
> of Python at the terminal.
> 
> 2. Then, as instructed I try to install mxTextTools.  Downloaded:
> egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> 
> ...from here:
> http://www.egenix.com/products/python/mxBase/
> 
> 
> 3. However, none of these (the official instructions, or several 
> alternatives proposed in various online fora) work for installing 
> mxTextTools.  Here are the results:
> 
> 3a. instructions here:
> http://biopython.org/DIST/docs/install/Installation.html#htoc9
> 
> ======================
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> root# python -V
> Python 2.4.4
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> root# python setup.py build
> running build
> running mx_autoconf
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> _configtest.c -o _configtest.o
> gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
> -L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
> success!
> removing: _configtest.c _configtest.o _configtest
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> _configtest.c -o _configtest.o
> success!
> removing: _configtest.c _configtest.o
> macros to define: [('HAVE_STRPTIME', '1')]
> macros to undefine: []
> running build_ext
> 
> building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
> building 'mx.DateTime.mxDateTime.mxDateTime' extension
> creating build/temp.macosx-10.3-fat-2.4_ucs2
> creating 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime
> creating 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx
> creating 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime 
> 
> creating 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime 
> 
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
> -DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> mx/DateTime/mxDateTime/mxDateTime.c -o 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o 
> 
> i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
> such file or directory
> i686-apple-darwin8-gcc-4.0.1: no input files
> powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
> such file or directory
> powerpc-apple-darwin8-gcc-4.0.1: no input files
> lipo: can't figure out the architecture type of: /var/tmp//cch9pAof.out
> error: command 'gcc' failed with exit status 1
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> root#
> ======================
> 
> 
> 3b. Instructions here:
> http://www.egenix.com/products/python/mxBase/
> 
> sudo python setup.py install
> 
> ==================
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ python -V
> Python 2.4.4
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ sudo python setup.py install
> running install
> running build
> running mx_autoconf
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> _configtest.c -o _configtest.o
> gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
> -L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
> success!
> removing: _configtest.c _configtest.o _configtest
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> _configtest.c -o _configtest.o
> success!
> removing: _configtest.c _configtest.o
> macros to define: [('HAVE_STRPTIME', '1')]
> macros to undefine: []
> running build_ext
> 
> building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
> building 'mx.DateTime.mxDateTime.mxDateTime' extension
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
> -DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> mx/DateTime/mxDateTime/mxDateTime.c -o 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o 
> 
> i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
> such file or directory
> i686-apple-darwin8-gcc-4.0.1: no input files
> powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
> such file or directory
> powerpc-apple-darwin8-gcc-4.0.1: no input files
> lipo: can't figure out the architecture type of: /var/tmp//ccGUEnk3.out
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> 
> ==================
> 
> 
> 
> 
> 3c. Instructions here:
> http://www.egenix.com/mailman-archives/egenix-users/2007-October/114291.html 
> 
> 
> sudo python setup.py build --skip install
> ================
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ python -V
> Python 2.4.4
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ sudo python setup.py build --skip install
> running build
> skipping the build process and reusing the existing build files and data
> error: build/build-macosx-10.3-fat-py2.4_ucs2.pck: No such file or 
> directory
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ ls
> COPYRIGHT               PKG-INFO                build 
> installer.bmp           mxSetup.pyc             wininst.bat
> LICENSE                 README                  egenix_mx_base.py 
> mx                      setup.cfg
> MANIFEST                bdist_zope.bat          egenix_mx_base.pyc 
> mxSetup.py              setup.py
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ ls ./build
> build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
> temp.darwin-8.11.1-i386-2.3_ucs2
> lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 temp.macosx-10.3-fat-2.4_ucs2
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> ================
> 
> 
> 4. Give up and email the biopython list.  Help!!  Please!!
> 
> 
> 5. Ask existential questions about why, oh why, all useful software 
> comes with dependencies that you have to compile yourself and which 
> never, ever compile correctly when the instructions are followed even on 
> utterly standard systems like Mac OSX 10.4.
> 
> 
> Thanks very very much,
> Nick
> 
> 
> 
> 
> 
> 
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab website: http://ib.berkeley.edu/people/lab_detail.php?lab=54
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: 
http://fisher.berkeley.edu/~edna/lab_test/members/matzke.html
Lab phone: 510-643-6299
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Office hours for Bio1B: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================

From lueck at ipk-gatersleben.de  Tue Jul  1 07:40:38 2008
From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=)
Date: Tue, 1 Jul 2008 09:40:38 +0200
Subject: [BioPython] Sequence from Fasta
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<320fb6e00806290819s73f95d32x563879e9bb64b924@mail.gmail.com>
	<001901c8da91$0eedfcd0$1022a8c0@ipkgatersleben.de>
	<320fb6e00806300219j54f7f43dpe0051f54be27d402@mail.gmail.com>
Message-ID: <002701c8db4d$c1ab68a0$1022a8c0@ipkgatersleben.de>


--> Peter wrote:
> from Bio import SeqIO
> handle = open("ls_orchid.fasta")
> for seq_record in SeqIO.parse(handle, "fasta") :
>    print seq_record.id
>    print seq_record.seq.tostring()
>    print len(seq_record.seq)
> handle.close()

This works! Thanks!

--> Giovanni wrote:
>Bioperl's SeqIO has support for a 'tab sequence format' which is
>similar to this[1].
>Maybe it could be useful in the future to add support for such a
>format in biopython.

It's a very good idea because I was suprised that it dosen't work. I 
excpected it.

Regards
Stefanie



From biopython at maubp.freeserve.co.uk  Tue Jul  1 08:04:24 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Jul 2008 09:04:24 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
Message-ID: <320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>

On Mon, Jun 30, 2008 at 10:40 AM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:

>> But I'm looking for something like this:
>>
>> Name Sequence without linebreak
>>
>> Example:
>>
>> MySequence atgcgcgctcggcgcgctcgfcgcgccccccatggctcgcgcactacagcg
>> MySequence2 atgcgctctgcgcgctcgatgtagaatatgagatctctatgagatcagcatca
>
> Bioperl's SeqIO has support for a 'tab sequence format' which is
> similar to this[1].
> Maybe it could be useful in the future to add support for such a
> format in biopython.
>
> [1] http://www.bioperl.org/wiki/Tab_sequence_format
>

That does look fairly straight forward.

Do you happen to know how BioPerl reacts when the first field has spaces?
I would suggest treating the first field like the ">" line in a FASTA file and
taking the first word as the id/name and the whole field as the description.

This format could be handy for some people who use the command line.  By
converting between FASTA and the tab format (which can be done with sed
or awk), each sequence is on one line, so you use tools like grep to filter your
records.  Then convert back to fasta.  There's a nice blog page I found some
time ago where the author describes his workflow for this.

Peter


From dalloliogm at gmail.com  Tue Jul  1 09:37:53 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Tue, 1 Jul 2008 11:37:53 +0200
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
Message-ID: <5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>

On Tue, Jul 1, 2008 at 10:04 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Jun 30, 2008 at 10:40 AM, Giovanni Marco Dall'Olio
> <dalloliogm at gmail.com> wrote:
>
>>> But I'm looking for something like this:
>>>
>>> Name Sequence without linebreak
>>>
>>> Example:
>>>
>>> MySequence atgcgcgctcggcgcgctcgfcgcgccccccatggctcgcgcactacagcg
>>> MySequence2 atgcgctctgcgcgctcgatgtagaatatgagatctctatgagatcagcatca
>>
>> Bioperl's SeqIO has support for a 'tab sequence format' which is
>> similar to this[1].
>> Maybe it could be useful in the future to add support for such a
>> format in biopython.
>>
>> [1] http://www.bioperl.org/wiki/Tab_sequence_format
>>
>
> That does look fairly straight forward.
>
> Do you happen to know how BioPerl reacts when the first field has spaces?
> I would suggest treating the first field like the ">" line in a FASTA file and
> taking the first word as the id/name and the whole field as the description.
>

It ignores any field after the first space in the header.

For example:
$ cat >seq1.fasta
>seq1 field2 field3
acatcgatgcatgctagctactgtacgac

$ cat > fasta2tab.pl
my $seqin = Bio::SeqIO->newFh("-file" => "seq1.fasta", "-format" => "fasta");
my $seqout = Bio::SeqIO->newFh("-fh" => \*STDOUT, "-format" => "tab");

while (<$seqin>)
{
        print $seqout $_;
}

$ perl fasta2tab.pl
seq1    acatcgatgcatgctagctactgtacgac


Do you need some help to implement this function?


> This format could be handy for some people who use the command line.  By
> converting between FASTA and the tab format (which can be done with sed
> or awk), each sequence is on one line, so you use tools like grep to filter your
> records.  Then convert back to fasta.  There's a nice blog page I found some
> time ago where the author describes his workflow for this.
>
> Peter
>



-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it


From biopython at maubp.freeserve.co.uk  Tue Jul  1 09:45:48 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Jul 2008 10:45:48 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
Message-ID: <320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>

> It ignores any field after the first space in the header.
>
> For example:
> $ cat >seq1.fasta
>>seq1 field2 field3
> acatcgatgcatgctagctactgtacgac
>
> $ cat > fasta2tab.pl
> my $seqin = Bio::SeqIO->newFh("-file" => "seq1.fasta", "-format" => "fasta");
> my $seqout = Bio::SeqIO->newFh("-fh" => \*STDOUT, "-format" => "tab");
>
> while (<$seqin>)
> {
>        print $seqout $_;
> }
>
> $ perl fasta2tab.pl
> seq1    acatcgatgcatgctagctactgtacgac

Interesting - and now what I had expected.

Could you try getting BioPerl to read in a TSV file like this:

seq1 field2 field3(tab)acatcgatgcatgctagctactgtacgac
seq2 with a description here(tab)ctcgctgnnacatcctagctactgta

I personally would prefer this sort of output as it preserves all the
data from a FASTA input file.  On the other hand, if there are exsting
tools which wouldn't read this then it would be a bad idea.

>
> Do you need some help to implement this function?
>

Not really - but discussion of the behaviour details now is a good
idea.  And some real world example TSV files would be good to add to
Biopython as test cases.

Thanks,

Peter


From biopython at maubp.freeserve.co.uk  Tue Jul  1 11:32:26 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Jul 2008 12:32:26 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
	<320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
	<5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>
Message-ID: <320fb6e00807010432x4346a283je51c265ebf9cab61@mail.gmail.com>

>> Could you try getting BioPerl to read in a TSV file like this:
>>
>> seq1 field2 field3(tab)acatcgatgcatgctagctactgtacgac
>> seq2 with a description here(tab)ctcgctgnnacatcctagctactgta
>>
>> I personally would prefer this sort of output as it preserves all the
>> data from a FASTA input file.  On the other hand, if there are existing
>> tools which wouldn't read this then it would be a bad idea.
>
> It [BioPerl] gives an error warning for every space it encounters.
>

That isn't very nice, arguably a BioPerl limitation.  However, it does
seem best that we try and avoid writing the full description in the
tab output.  The downside is:

>identifer with a long description
acatcgatgcatgctagctactgtacgac

Would have to be saved follows to keep BioPerl happy:

identifier(tab)acatcgatgcatgctagctactgtacgac

Rather than:

identifer with a long description(tab)acatcgatgcatgctagctactgtacgac

Still - if you and Stefanie think this would be useful, I'll have a
look at implementing it.

Peter


From dalloliogm at gmail.com  Tue Jul  1 11:49:34 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Tue, 1 Jul 2008 13:49:34 +0200
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <320fb6e00807010432x4346a283je51c265ebf9cab61@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
	<320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
	<5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>
	<320fb6e00807010432x4346a283je51c265ebf9cab61@mail.gmail.com>
Message-ID: <5aa3b3570807010449k885bf53hce6a1ad58c9daad3@mail.gmail.com>

On Tue, Jul 1, 2008 at 1:32 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>>
>> It [BioPerl] gives an error warning for every space it encounters.
>>
>
> That isn't very nice, arguably a BioPerl limitation.  However, it does
> seem best that we try and avoid writing the full description in the
> tab output.  The downside is:
>
>>identifer with a long description
> acatcgatgcatgctagctactgtacgac

I am not sure, but I think it is because spaces are not allowed in the
header of standard fasta files.
Maybe a good solution would be to convert automatically all spaces to
pipes (|) in the output.


> Still - if you and Stefanie think this would be useful, I'll have a
> look at implementing it.

yes, I think it will be useful to implement.
I know of people who have written a customized fasta2tab script and
use it quite frequently, so it would be good to support such a task.
As you said before this format is commonly used in combination with
grep/gawk scripts.

>
> Peter
>



-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it


From dalloliogm at gmail.com  Tue Jul  1 10:44:49 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Tue, 1 Jul 2008 12:44:49 +0200
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
	<320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
Message-ID: <5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>

On Tue, Jul 1, 2008 at 11:45 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> It ignores any field after the first space in the header.
>>
>> For example:
>> $ cat >seq1.fasta
>>>seq1 field2 field3
>> acatcgatgcatgctagctactgtacgac
>>
>> $ cat > fasta2tab.pl
>> my $seqin = Bio::SeqIO->newFh("-file" => "seq1.fasta", "-format" => "fasta");
>> my $seqout = Bio::SeqIO->newFh("-fh" => \*STDOUT, "-format" => "tab");
>>
>> while (<$seqin>)
>> {
>>        print $seqout $_;
>> }
>>
>> $ perl fasta2tab.pl
>> seq1    acatcgatgcatgctagctactgtacgac
>
> Interesting - and now what I had expected.
>
> Could you try getting BioPerl to read in a TSV file like this:
>
> seq1 field2 field3(tab)acatcgatgcatgctagctactgtacgac
> seq2 with a description here(tab)ctcgctgnnacatcctagctactgta
>
> I personally would prefer this sort of output as it preserves all the
> data from a FASTA input file.  On the other hand, if there are exsting
> tools which wouldn't read this then it would be a bad idea.
>

It gives an error warning for every space it encounters.

Example:
"""
perl convertformat.pl seqm.tab tab fasta

-------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [seq1 field2 field3]
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [seq1 field2 field3]
---------------------------------------------------
>seq1 field2 field3
CATGGCATGCATGCATGCTAGCTAC

-------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [seq2 some description]
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [seq2 some description]
---------------------------------------------------
>seq2 some description
CATGGCATGCATGCATGCTAGCTAC
"""

Please have a look at the script code and the makefile attached.

p.s. I already sent you a similar message, but the mailing list blocked it.


-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it
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From biopython at maubp.freeserve.co.uk  Tue Jul  1 16:06:08 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 1 Jul 2008 17:06:08 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <5aa3b3570807010449k885bf53hce6a1ad58c9daad3@mail.gmail.com>
References: <001e01c8d9f6$66134420$1022a8c0@ipkgatersleben.de>
	<5aa3b3570806300240g25a5c311y1d5e1872a9fa97d5@mail.gmail.com>
	<320fb6e00807010104n4bb26266s8916eb6184c62024@mail.gmail.com>
	<5aa3b3570807010237k61e23260uc02c43487c6efa84@mail.gmail.com>
	<320fb6e00807010245n2650e1c1mdde4bd61e3b1fcdd@mail.gmail.com>
	<5aa3b3570807010344k5470a190i6284f0cc8e33f92b@mail.gmail.com>
	<320fb6e00807010432x4346a283je51c265ebf9cab61@mail.gmail.com>
	<5aa3b3570807010449k885bf53hce6a1ad58c9daad3@mail.gmail.com>
Message-ID: <320fb6e00807010906v7e8e6780x92117da60cd39318@mail.gmail.com>

Giovanni wrote:
> yes, I think it will be useful to implement.
> I know of people who have written a customized fasta2tab script and
> use it quite frequently, so it would be good to support such a task.
> As you said before this format is commonly used in combination with
> grep/gawk scripts.

I've gone for the simple option about how to parse the first field, its used
as the record identifer (.id) and name only (nothing clever).  Here is my
suggested code, which you are welcome to download and try out.

Bug 2533 - Support for simple "tab" format in Bio.SeqIO
http://bugzilla.open-bio.org/show_bug.cgi?id=2533

If you want to try this yourself you'll need to download the new file
TabIO.py into the Bio/SeqIO folder and update Bio/SeqIO/__init__.py to
tell it about the new format (two new lines, see patch).

Peter


From lpritc at scri.ac.uk  Wed Jul  2 09:10:05 2008
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Wed, 02 Jul 2008 10:10:05 +0100
Subject: [BioPython] Sequence from Fasta
In-Reply-To: <320fb6e00807010906v7e8e6780x92117da60cd39318@mail.gmail.com>
Message-ID: <C491047D.1241C%lpritc@scri.ac.uk>

Hi,

Just to chip in my two-pennorth, there's a self-defining tab-separated
format called "Axon Text File Format" that might be useful here, and which
is frequently seen in microarray work.  There's a description of its use for
.gal files here:

http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html

It's fairly flexible and straightforward as a format, and allows for
human-readable headers - which can contain column definitions, content
notes, or anything else you like - that is adaptable to a variety of output
conventions.  Of course, getting people to settle on a convention is the
tricky part, but at least any given file might be well-defined in its
headers while people argue over it ;)

It's hardly likely that going down that route in BioPython will result in an
file convention that's accepted industry-wide, but at least it might give
options for writing out FASTA file content in tab-separated form while
unambiguously retaining ID, name and definition strings along with the
sequence. 

L.

On 01/07/2008 17:06, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

> Giovanni wrote:
>> yes, I think it will be useful to implement.
>> I know of people who have written a customized fasta2tab script and
>> use it quite frequently, so it would be good to support such a task.
>> As you said before this format is commonly used in combination with
>> grep/gawk scripts.
> 
> I've gone for the simple option about how to parse the first field, its used
> as the record identifer (.id) and name only (nothing clever).  Here is my
> suggested code, which you are welcome to download and try out.
> 
> Bug 2533 - Support for simple "tab" format in Bio.SeqIO
> http://bugzilla.open-bio.org/show_bug.cgi?id=2533
> 
> If you want to try this yourself you'll need to download the new file
> TabIO.py into the Bio/SeqIO folder and update Bio/SeqIO/__init__.py to
> tell it about the new format (two new lines, see patch).
> 
> Peter
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

-- 
Dr Leighton Pritchard B.Sc.(Hons) MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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From biopython at maubp.freeserve.co.uk  Sat Jul  5 14:52:10 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Sat, 5 Jul 2008 15:52:10 +0100
Subject: [BioPython] Bio.IntelliGenetics (and the MASE format)
Message-ID: <320fb6e00807050752u10c8d8c9s6481238c6b959a2c@mail.gmail.com>

Dear all,

We've recently added support for parsing (reading) the IntelliGenetics
sequence file format to Bio.SeqIO, under the format name "ig"
(following the EMBOSS convention).  This file format also seems to be
known as the MASE multiple sequence alignment format.

This means that the old Bio.IntelliGenetics module is essentially
obsolete, and we could therefore deprecate it in a future Biopython
release.  Before we do that, is anyone using the Bio.IntelliGenetics
module?  Hopefully using Bio.SeqIO will a suitable substitute for you,
but please do get in touch.

More generally, do any of you currently use the IntelliGenetics or
MASE file format?  I'd love to have a few more example files to use in
our test suite.  Also, would you be interested in using Bio.SeqIO to
write out files in this format?

Thank you,

Peter


From p.j.a.cock at googlemail.com  Sat Jul  5 15:20:40 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Sat, 5 Jul 2008 16:20:40 +0100
Subject: [BioPython] Biopython at BOSC 2008
Message-ID: <320fb6e00807050820y55fb240fk6feddaefe6aaf1be@mail.gmail.com>

Dear Biopython users,

Later this month Tiago Ant?o will be representing Biopython at the
Bioinformatics Open Source Conference (BOSC 2008) in Toronto, Canada.
Tiago is the most recent developer to join the Biopython project, and
has been working on the new Bio.PopGen module for population genetics.
 BOSC is an annual two-day conference organised by the Open
Bioinformatics Foundation.

http://open-bio.org/wiki/BOSC_2008

Last summer I gave the "Biopython Project Update" talk at the BOSC
2007 in Vienna, Austria.  My slides have been available online via
slideshare, but I finally got round to converting them from PowerPoint
to PDF, and they are now on the Biopython website if anyone is
interested:

http://biopython.org/wiki/Documentation#Presentations
http://open-bio.org/wiki/BOSC_2007

Although unfortunatley I won't be at BOSC 2008, perhaps some of you
will also be there - and I hope everyone there enjoys it.

Peter



From mjldehoon at yahoo.com  Sun Jul  6 00:00:17 2008
From: mjldehoon at yahoo.com (Michiel de Hoon)
Date: Sat, 5 Jul 2008 17:00:17 -0700 (PDT)
Subject: [BioPython] Biopython release 1.47
Message-ID: <287726.364.qm@web62412.mail.re1.yahoo.com>

We are pleased to announce the release of Biopython 1.47.

This release includes a new Bio.AlignIO module, updates to Bio.Blast, parsers for NCBI's Entrez E-Utilities, numerous other code improvements and fixes, and an extended and updated documentation. In particular if you use Biopython to access NCBI's E-Utilities, we encourage you to download and install this release to ensure full compliance with NCBI's access rules.

Source distributions and Windows installers are available from the Biopython website at http://biopython.org. My thanks to all code contributers who made this new release possible.


--Michiel on behalf of the Biopython developers


      


From biopython at maubp.freeserve.co.uk  Wed Jul  9 13:42:35 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 9 Jul 2008 14:42:35 +0100
Subject: [BioPython] Bio.IntelliGenetics (and the MASE format)
In-Reply-To: <320fb6e00807050752u10c8d8c9s6481238c6b959a2c@mail.gmail.com>
References: <320fb6e00807050752u10c8d8c9s6481238c6b959a2c@mail.gmail.com>
Message-ID: <320fb6e00807090642k7edc86d6r2671c251ba163edc@mail.gmail.com>

> Dear all,
>
> We've recently added support for parsing (reading) the IntelliGenetics
> sequence file format to Bio.SeqIO, under the format name "ig"
> (following the EMBOSS convention).  This file format also seems to be
> known as the MASE multiple sequence alignment format.
>
> This means that the old Bio.IntelliGenetics module is essentially
> obsolete, and we could therefore deprecate it in a future Biopython
> release.  Before we do that, is anyone using the Bio.IntelliGenetics
> module?  Hopefully using Bio.SeqIO will a suitable substitute for you,
> but please do get in touch.

The Bio.IntelliGenetics module is now deprecated in CVS.  If anyone is
using this code please get in touch.

> More generally, do any of you currently use the IntelliGenetics or
> MASE file format?  I'd love to have a few more example files to use in
> our test suite.  Also, would you be interested in using Bio.SeqIO to
> write out files in this format?

Thanks again,

Peter


From dalloliogm at gmail.com  Fri Jul 11 14:35:28 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Fri, 11 Jul 2008 16:35:28 +0200
Subject: [BioPython] proposal: Bio-Django project
Message-ID: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>

Hi,
Recently I have been using Django[1], a python web framework that
enables programmers to quickly create front-ends and web applications
for databases.

I think it is very cool. In a few minutes, I have been able to create
a database for my data, and thanks to the admin application I have a
nice and well-developed front-end to browse and manage it.
I am still looking at it, but I see there are many applications freely
available, so maybe I will be easily be able to create graphs and
diagrams of my data when I will look better at it.

My idea is: Why don't we create a repository of free/bioinfo apps for
django, like biopython is? Has any of you already used django for
bioinformatics purposes?

For example, I am writing an app to manage blood samples for the
laboratory where I am working on at the moment, and I will be glad to
share it with other people.

What do you think?


[1] http://www.djangoproject.com/

-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it


From dalloliogm at gmail.com  Fri Jul 11 15:25:56 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Fri, 11 Jul 2008 17:25:56 +0200
Subject: [BioPython] proposal: Bio-Django project
In-Reply-To: <1215787800.4877731897957@webmail.upv.es>
References: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>
	<1215787800.4877731897957@webmail.upv.es>
Message-ID: <5aa3b3570807110825r714ec06cw88ded72ea2c82d43@mail.gmail.com>

Of course I can show you the application I am writing.

I was thinking of applying to a google/summer of code. Let's propose a
few web applications that could be useful to researcher or
bioinformaticists, and ask google to fund it.

Maybe if any of the core biopython developers, who have experience in
handling a public repository for bioinformaticians, and are good
programmers, would like to partecipate as mentors, it would be a great
opportunity to learn django*, and obtain the google T shirt.


* or plone, they told me there is a similar project for plone:
http://plone.org/products/plone4bio/?searchterm=plone4bio


On Fri, Jul 11, 2008 at 4:50 PM, Blanca Postigo Jose Miguel
<jblanca at btc.upv.es> wrote:
> Hi:
> I'm not yet using Django, but I'm reading a couple of books and doing tutorials.
> I like a lot this web framework and I'm planning to use it.
> Your suggestion seems great for me.
> Also it would be great to take a look at your blood samples application, my wife
> works managing blood samples and I'm sure she would review it with pleasure.
> Best regards,
>
> Jose Blanca
>
> Mensaje citado por Giovanni Marco Dall'Olio <dalloliogm at gmail.com>:
>
>> Hi,
>> Recently I have been using Django[1], a python web framework that
>> enables programmers to quickly create front-ends and web applications
>> for databases.
>>
>> I think it is very cool. In a few minutes, I have been able to create
>> a database for my data, and thanks to the admin application I have a
>> nice and well-developed front-end to browse and manage it.
>> I am still looking at it, but I see there are many applications freely
>> available, so maybe I will be easily be able to create graphs and
>> diagrams of my data when I will look better at it.
>>
>> My idea is: Why don't we create a repository of free/bioinfo apps for
>> django, like biopython is? Has any of you already used django for
>> bioinformatics purposes?
>>
>> For example, I am writing an app to manage blood samples for the
>> laboratory where I am working on at the moment, and I will be glad to
>> share it with other people.
>>
>> What do you think?
>>
>>
>> [1] http://www.djangoproject.com/
>>
>> --
>> -----------------------------------------------------------
>>
>> My Blog on Bioinformatics (italian): http://bioinfoblog.it
>> _______________________________________________
>> BioPython mailing list  -  BioPython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
>
>
> --
>
>



-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it


From m at pavis.biodec.com  Fri Jul 11 15:45:17 2008
From: m at pavis.biodec.com (m at pavis.biodec.com)
Date: Fri, 11 Jul 2008 17:45:17 +0200
Subject: [BioPython] proposal: Bio-Django project
In-Reply-To: <5aa3b3570807110825r714ec06cw88ded72ea2c82d43@mail.gmail.com>
References: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>
	<1215787800.4877731897957@webmail.upv.es>
	<5aa3b3570807110825r714ec06cw88ded72ea2c82d43@mail.gmail.com>
Message-ID: <20080711154517.GD19973@pavis.biodec.com>

* Giovanni Marco Dall'Olio (dalloliogm at gmail.com) [080711 17:27]:
> 
> * or plone, they told me there is a similar project for plone:
> http://plone.org/products/plone4bio/?searchterm=plone4bio
>

my company hosts the plone4bio project: in our experience we have found
that using an already existing --- and quite active and complete, too
--- web content management system has been a good choice

YMMV of course, since we have been using plone since 2002, we probably
are a little skewed in our choice, but the rationale is that we have
found that sooner or later we start to add features like autenthication,
user management, workflows, and various sorts of integration and then it
is better to have a single robust system, if it is flexible enough

clarly, from time to time, you curse the fact that you have to do things
`its own way', but we can live with it

we have not added anything to the repository since a few months, but we
will soon add another predictor, give enough time to engineet it
properly ...

-- 
 .*.                            finelli
 /V\
(/ \) --------------------------------------------------------------
(   )       Linux: Friends dont let friends use Piccolosoffice
^^-^^ --------------------------------------------------------------

Boss: You forgot to assign the result of your map!

Hacker: Dang, I'm always forgetting my assignations...

Boss: And what's that "goto" doing there?!?

Hacker: Er, I guess my finger slipped when I was typing "getservbyport"...

Boss: Ah well, accidents will happen.  Maybe we should have picked APL.
		-- Larry Wall in <199710311732.JAA19169 at wall.org>


From bsouthey at gmail.com  Fri Jul 11 16:10:50 2008
From: bsouthey at gmail.com (Bruce Southey)
Date: Fri, 11 Jul 2008 11:10:50 -0500
Subject: [BioPython] [bip] proposal: Bio-Django project
In-Reply-To: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>
References: <5aa3b3570807110735g5f8ce560y12aa0e302db1703e@mail.gmail.com>
Message-ID: <4877860A.1020305@gmail.com>

Giovanni Marco Dall'Olio wrote:
> Hi,
> Recently I have been using Django[1], a python web framework that
> enables programmers to quickly create front-ends and web applications
> for databases.
>
> I think it is very cool. In a few minutes, I have been able to create
> a database for my data, and thanks to the admin application I have a
> nice and well-developed front-end to browse and manage it.
> I am still looking at it, but I see there are many applications freely
> available, so maybe I will be easily be able to create graphs and
> diagrams of my data when I will look better at it.
>
> My idea is: Why don't we create a repository of free/bioinfo apps for
> django, like biopython is? Has any of you already used django for
> bioinformatics purposes?
>
> For example, I am writing an app to manage blood samples for the
> laboratory where I am working on at the moment, and I will be glad to
> share it with other people.
>
> What do you think?
>
>
> [1] http://www.djangoproject.com/
>
>   
Sure there are many Python-based model-viewer-control (MVC) frameworks 
(Django is just one of them) BUT what exactly do you propose to do?
In particular, how will it differ from plone4bio 
(http://www.plone4bio.org ) that was announced on BioPython by

Ivan Rossi back in February?

Do you plan something as extensive as the Biology Workbench or Next Generation Biology Workbench?
Or something like Geneious (http://www.geneious.com/)?
Or just a simple interface to BioPython or similar bioinformstics tools?

Regards
Bruce



From peter at maubp.freeserve.co.uk  Sat Jul 12 13:08:25 2008
From: peter at maubp.freeserve.co.uk (Peter)
Date: Sat, 12 Jul 2008 14:08:25 +0100
Subject: [BioPython] Bio.AlignIO and the Alignment object
Message-ID: <320fb6e00807120608s447605f6k14e67a941135c796@mail.gmail.com>

Now that Biopython 1.47 is out, I hope some of you have had a chance
to try out the new Bio.AlignIO module.

Let me just point out that this is all talking about multiple sequence
alignments where each (gapped) sequence is the same length, and the
data can be seen as a matrix or grid of letters.  I am not talking
about the related concept of an EST or contig alignment which doesn't
really fit this image (although it could if you add large leading and
trailing gap sequences).

We've had some useful feedback from Sebastian Bassi, leading me to
suspect that both the Bio.SeqIO and Bio.AlignIO input functions would
benefit from an optional alphabet argument for all those file formats
which do not declare the sequence type (enhancement bug 2443).
http://bugzilla.open-bio.org/show_bug.cgi?id=2443

Any other issues or questions about using the new Bio.AlignIO module?
I've tried to explain how to use it in the Tutorial (Chapter 5).
http://biopython.org/DIST/docs/tutorial/Tutorial.html

Any "beginners questions" on the mailing list would be useful for
pointing out how the documentation could be improved.  This would also
be useful for the wiki page which is currently a little empty - I
didn't want to just cut and past the examples from the main tutorial.
http://biopython.org/wiki/AlignIO

I'd also like to hear if there are any alignment file formats you
think Bio.AlignIO should support.

Finally, it would be great to also have some comments about the
Alignment object itself.  In particular we have some ideas on Bug 1944
for making it act more like an array of letters by supporting double
indexing like a Numeric or numpy array/matrix class.  Right now, the
next little step I want to implement is allowing access to the rows of
the alignment as SeqRecord objects using alignment[index], rather than
alignment.get_all_seqs()[index] which I find cumbersome.
http://bugzilla.open-bio.org/show_bug.cgi?id=1944

Thanks,

Peter


From peter at maubp.freeserve.co.uk  Sat Jul 12 13:16:32 2008
From: peter at maubp.freeserve.co.uk (Peter)
Date: Sat, 12 Jul 2008 14:16:32 +0100
Subject: [BioPython] Bio.AlignIO and the Alignment object
In-Reply-To: <320fb6e00807120608s447605f6k14e67a941135c796@mail.gmail.com>
References: <320fb6e00807120608s447605f6k14e67a941135c796@mail.gmail.com>
Message-ID: <320fb6e00807120616u208350c2r6313ab6667d27f62@mail.gmail.com>

> Finally, it would be great to also have some comments about the
> Alignment object itself.  In particular we have some ideas on Bug 1944
> for making it act more like an array of letters by supporting double
> indexing like a Numeric or numpy array/matrix class.
>
> Right now, the next little step I want to implement is allowing access to
> the rows of the alignment as SeqRecord objects using alignment[index],
> rather than alignment.get_all_seqs()[index] which I find cumbersome.
> http://bugzilla.open-bio.org/show_bug.cgi?id=1944

Here is a quick example using one of the test input files found in the
source code under Test/Clustalw:

>>> from Bio import AlignIO
>>> alignment = AlignIO.read(open("opuntia.aln"), "clustal")
>>> print alignment
SingleLetterAlphabet() alignment with 7 rows and 156 columns
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273285|gb|AF191659.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273284|gb|AF191658.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273287|gb|AF191661.1|AF191
TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273286|gb|AF191660.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273290|gb|AF191664.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273289|gb|AF191663.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA
gi|6273291|gb|AF191665.1|AF191

You can iterate over the rows as SeqRecord objects:

>>> for record in alignment :
...     print "%s length %i" % (record.id, len(record))
gi|6273285|gb|AF191659.1|AF191 length 156
gi|6273284|gb|AF191658.1|AF191 length 156
gi|6273287|gb|AF191661.1|AF191 length 156
gi|6273286|gb|AF191660.1|AF191 length 156
gi|6273290|gb|AF191664.1|AF191 length 156
gi|6273289|gb|AF191663.1|AF191 length 156
gi|6273291|gb|AF191665.1|AF191 length 156

Right now (Biopython 1.47) to get a particular row out as a SeqRecord
you must use the get_all_seqs() function:

>>> record = alignment.get_all_seqs()[3]
>>> print record.id
gi|6273286|gb|AF191660.1|AF191

I'd like to be able to do this instead:

>>> record = alignment[3]
>>> print record

This would render the get_all_seqs() function effectively obsolete,
and it could be deprecated in a later release.

Peter


From allank at sanbi.ac.za  Tue Jul 15 12:25:42 2008
From: allank at sanbi.ac.za (Allan Kamau)
Date: Tue, 15 Jul 2008 14:25:42 +0200
Subject: [BioPython] Install issues - *** Numerical Python *** is either not
 installed or out of date
Message-ID: <487C9746.2090807@sanbi.ac.za>

Hi all,
Am attempting to install biopython-1.47.
I have installed the prerequisites for  biopython including numpy 
(http://numpy.sourceforge.net/).
When I run setup.py build, i get the message below. I am sure I have 
installed numpy correctly as I can do "python -c 'import numpy; 
numpy.test()';" and not receive an error.

I think Numerical Python package had a name change some time ago from 
"Numeric" to "numpy" (meaning that import Numeric will more probably fail)

What can I do?

"*** Numerical Python *** is either not installed or out of date.

This package is optional, which means it is only used in a few
specialized modules in Biopython.  You probably don't need this if you
are unsure.  You can ignore this requirement, and install it later if
you see ImportErrors.
You can find Numerical Python at http://numpy.sourceforge.net/.

Do you want to continue this installation? (Y/n)  n
"


From biopython at maubp.freeserve.co.uk  Tue Jul 15 13:04:28 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Jul 2008 14:04:28 +0100
Subject: [BioPython] Install issues - *** Numerical Python *** is either
	not installed or out of date
In-Reply-To: <487C9746.2090807@sanbi.ac.za>
References: <487C9746.2090807@sanbi.ac.za>
Message-ID: <320fb6e00807150604t206a8586w7a7ba91f2456fa8@mail.gmail.com>

On Tue, Jul 15, 2008 at 1:25 PM, Allan Kamau <allank at sanbi.ac.za> wrote:
> Hi all,
> Am attempting to install biopython-1.47.
> I have installed the prerequisites for  biopython including numpy
> (http://numpy.sourceforge.net/).

We don't use numpy, we use the older Numeric library.  You need to
install that (you can have both installed without a problem).

Which instructions were you following?  We have tried to make this
clear on http://biopython.org/wiki/Download and in
http://biopython.org/DIST/docs/install/Installation.html (and its PDF
equivalent).

Thanks,

Peter


From allank at sanbi.ac.za  Tue Jul 15 13:37:44 2008
From: allank at sanbi.ac.za (Allan Kamau)
Date: Tue, 15 Jul 2008 15:37:44 +0200
Subject: [BioPython] Install issues - *** Numerical Python *** is either
 not installed or out of date
In-Reply-To: <320fb6e00807150604t206a8586w7a7ba91f2456fa8@mail.gmail.com>
References: <487C9746.2090807@sanbi.ac.za>
	<320fb6e00807150604t206a8586w7a7ba91f2456fa8@mail.gmail.com>
Message-ID: <487CA828.8010404@sanbi.ac.za>

Thank you Peter. I did follow your instructions and installed the 
Numeric library. All is well now.

Allan.

Peter wrote:
> On Tue, Jul 15, 2008 at 1:25 PM, Allan Kamau <allank at sanbi.ac.za> wrote:
>   
>> Hi all,
>> Am attempting to install biopython-1.47.
>> I have installed the prerequisites for  biopython including numpy
>> (http://numpy.sourceforge.net/).
>>     
>
> We don't use numpy, we use the older Numeric library.  You need to
> install that (you can have both installed without a problem).
>
> Which instructions were you following?  We have tried to make this
> clear on http://biopython.org/wiki/Download and in
> http://biopython.org/DIST/docs/install/Installation.html (and its PDF
> equivalent).
>
> Thanks,
>
> Peter
>   



From biopython at maubp.freeserve.co.uk  Tue Jul 15 21:15:15 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 15 Jul 2008 22:15:15 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
Message-ID: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>

Now that the latest release is out, I wanted to return to a point
raised by Sebastian Bassi last month:

Do people agree that the Bio.Seq.transcibe() method should reject RNA sequences?

We already reject Seq objects with a protein alphabet.  I want to
accept Seq objects with a generic or nucleotide alphabet, and
sequences with a DNA alphabet are of course fine, but I had been on
the fence about trying to (re)transcribe RNA.

Unless anyone speaks up, I will side with Sebastian and add a check to
the  Bio.Seq.transcibe() method to reject RNA sequences, and a similar
check on the Bio.Seq.back_transcibe() method to reject DNA sequences.

Peter


From mmokrejs at ribosome.natur.cuni.cz  Tue Jul 15 22:53:14 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 00:53:14 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
Message-ID: <487D2A5A.1000305@ribosome.natur.cuni.cz>

I agree but it should require whether a plus or minus strand will be
transcribed. Otherwise, zapping 'U's with 'T's is enough. ;-) Still
somewhat artificial function.

What would be really meaningful if the object would be a genbank record
with introns and transcribe() would rip out all the introns or even
better allow me to choose which-ones to splice-out. Like to retain
exons 1, 5, 7.

;-)
Martin


Peter wrote:
> Now that the latest release is out, I wanted to return to a point
> raised by Sebastian Bassi last month:
> 
> Do people agree that the Bio.Seq.transcibe() method should reject RNA sequences?
> 
> We already reject Seq objects with a protein alphabet.  I want to
> accept Seq objects with a generic or nucleotide alphabet, and
> sequences with a DNA alphabet are of course fine, but I had been on
> the fence about trying to (re)transcribe RNA.
> 
> Unless anyone speaks up, I will side with Sebastian and add a check to
> the  Bio.Seq.transcibe() method to reject RNA sequences, and a similar
> check on the Bio.Seq.back_transcibe() method to reject DNA sequences.


From biopython at maubp.freeserve.co.uk  Tue Jul 15 23:13:43 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Jul 2008 00:13:43 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487D2A5A.1000305@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
Message-ID: <320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>

On Tue, Jul 15, 2008 at 11:53 PM, Martin MOKREJ?
<mmokrejs at ribosome.natur.cuni.cz> wrote:
> I agree but it should require whether a plus or minus strand will be
> transcribed. Otherwise, zapping 'U's with 'T's is enough. ;-) Still
> somewhat artificial function.

By convention a DNA sequence is taken as the coding strand, so a
simple U to T is enough to transcibe to RNA.  This is somewhat
artificial (and doesn't really capture double strandedness), but does
seem to be a widley used convention.

You could do my_seq.reverse_complement().transcribe() if you did want
the other strand transcribed.

> What would be really meaningful if the object would be a genbank record
> with introns and transcribe() would rip out all the introns or even
> better allow me to choose which-ones to splice-out. Like to retain
> exons 1, 5, 7.

I was thinking it would be nice to take a SeqRecord with SeqFeatures
(i.e. a parsed GenBank file) and ask Biopython to give you the
nucleotide sequence for the feature.  In the case of intron/exons
these are held using the subfeatures, so it would make sense to obey
those.  I see this as a variation on splicing/subsetting (in python
speak) a sequence.

Maybe something like my_record[my_feature] or
my_record.extract_feature(my_feature)
Or my_record.extract_feature(i) which would refer to my_record.features[i]

Peter



From mmokrejs at ribosome.natur.cuni.cz  Tue Jul 15 23:32:48 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 01:32:48 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>	
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
Message-ID: <487D33A0.5060804@ribosome.natur.cuni.cz>

Hi,

Peter wrote:
> On Tue, Jul 15, 2008 at 11:53 PM, Martin MOKREJ?
> <mmokrejs at ribosome.natur.cuni.cz> wrote:
>> I agree but it should require whether a plus or minus strand will be
>> transcribed. Otherwise, zapping 'U's with 'T's is enough. ;-) Still
>> somewhat artificial function.
> 
> By convention a DNA sequence is taken as the coding strand, so a
> simple U to T is enough to transcribe to RNA.  This is somewhat
> artificial (and doesn't really capture double strandedness), but does
> seem to be a widley used convention.

I can't say anything else except that this is extremely awkward function.
I would always rather take it as a string and replace 'U's with 'T's
myself. Then I know what is going on and do not have to read the manual
and can be sure this will never change.
> 
> You could do my_seq.reverse_complement().transcribe() if you did want
> the other strand transcribed.

Exactly, to get rid of this I would see some advantage to have
transcribe() which is more intuitive but only if it would be able to cope
with reverse strand as well.

>> What would be really meaningful if the object would be a genbank record
>> with introns and transcribe() would rip out all the introns or even
>> better allow me to choose which-ones to splice-out. Like to retain
>> exons 1, 5, 7.
> 
> I was thinking it would be nice to take a SeqRecord with SeqFeatures
> (i.e. a parsed GenBank file) and ask Biopython to give you the
> nucleotide sequence for the feature.  In the case of intron/exons
> these are held using the subfeatures, so it would make sense to obey
> those.  I see this as a variation on splicing/subsetting (in python
> speak) a sequence.

Personally I find this the only reason to justify existence of such
a function. It it can abstract me from the underlying format and give
me a true, spliced transcript. Of course I would rather prefer to raise
an exception if there would be more than one intron and I would have
not specified which intron index-positions to use.

> 
> Maybe something like my_record[my_feature] or
> my_record.extract_feature(my_feature)
> Or my_record.extract_feature(i) which would refer to my_record.features[i]

I am not much used to biopython coding style so cannot comment on this.
Again, I would never use a unknown function prone to be changed unless
I cannot code the simple transformation myself. If it cannot handle
splicing I don't need it I think. But maybe I am just a desperate user.
;-)

M.




From mmokrejs at ribosome.natur.cuni.cz  Tue Jul 15 23:57:16 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 01:57:16 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487D33A0.5060804@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>		<487D2A5A.1000305@ribosome.natur.cuni.cz>	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
	<487D33A0.5060804@ribosome.natur.cuni.cz>
Message-ID: <487D395C.7080103@ribosome.natur.cuni.cz>

Martin MOKREJ? wrote:

>>> What would be really meaningful if the object would be a genbank record
>>> with introns and transcribe() would rip out all the introns or even
>>> better allow me to choose which-ones to splice-out. Like to retain
>>> exons 1, 5, 7.
>>
>> I was thinking it would be nice to take a SeqRecord with SeqFeatures
>> (i.e. a parsed GenBank file) and ask Biopython to give you the
>> nucleotide sequence for the feature.  In the case of intron/exons
>> these are held using the subfeatures, so it would make sense to obey
>> those.  I see this as a variation on splicing/subsetting (in python
>> speak) a sequence.
> 
> Personally I find this the only reason to justify existence of such
> a function. It it can abstract me from the underlying format and give
--------------^^ If

> me a true, spliced transcript. Of course I would rather prefer to raise
> an exception if there would be more than one intron and I would have
> not specified which intron index-positions to use.
----------------------^^^^^^ exon

Sorry for the typos.




From biopython at maubp.freeserve.co.uk  Wed Jul 16 10:38:36 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Jul 2008 11:38:36 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
Message-ID: <320fb6e00807160338ub5dc2dayf0c3b51ad768af69@mail.gmail.com>

I wrote:
> Unless anyone speaks up, I will side with Sebastian and add a check to
> the  Bio.Seq.transcibe() method to reject RNA sequences, and a similar
> check on the Bio.Seq.back_transcibe() method to reject DNA sequences.

This change is now in CVS, Bio/Seq.py revision 1.13

Peter


From p.j.a.cock at googlemail.com  Wed Jul 16 11:08:44 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 16 Jul 2008 12:08:44 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487D33A0.5060804@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
	<487D33A0.5060804@ribosome.natur.cuni.cz>
Message-ID: <320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>

I wrote:
>> You could do my_seq.reverse_complement().transcribe() if you did want
>> the other strand transcribed.

Actually right now the Seq object doesn't have a transcribe method
(but I think maybe it should, see Bug 2381).  In the meantime, you
would have to use either of these:

from Bio.Seq import transcribe, reverse_complement
print transcribe(reverse_complement(my_seq))
print transcribe(my_seq.reverse_complement())

Martin wrote:
> Exactly, to get rid of this I would see some advantage to have
> transcribe() which is more intuitive but only if it would be able to cope
> with reverse strand as well.

You would really prefer a single function call to do a combined
"transcribe reverse-complement" or "transcribe the other strand" over
doing the reverse complement and transcription in two steps?

e.g.
print transcribe(my_seq, use_reverse_complement=True)

or,
print transcribe(my_seq, strand=-1)

or, maybe:
print transcribe_rc(my_seq)

Peter


From mmokrejs at ribosome.natur.cuni.cz  Wed Jul 16 13:20:48 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 15:20:48 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>	
	<487D2A5A.1000305@ribosome.natur.cuni.cz>	
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>	
	<487D33A0.5060804@ribosome.natur.cuni.cz>
	<320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>
Message-ID: <487DF5B0.1050000@ribosome.natur.cuni.cz>

Peter Cock wrote:
> I wrote:
>>> You could do my_seq.reverse_complement().transcribe() if you did want
>>> the other strand transcribed.
> 
> Actually right now the Seq object doesn't have a transcribe method
> (but I think maybe it should, see Bug 2381).  In the meantime, you
> would have to use either of these:
> 
> from Bio.Seq import transcribe, reverse_complement
> print transcribe(reverse_complement(my_seq))
> print transcribe(my_seq.reverse_complement())
> 
> Martin wrote:
>> Exactly, to get rid of this I would see some advantage to have
>> transcribe() which is more intuitive but only if it would be able to cope
>> with reverse strand as well.
> 
> You would really prefer a single function call to do a combined
> "transcribe reverse-complement" or "transcribe the other strand" over
> doing the reverse complement and transcription in two steps?

Yes, a single function handling arguments would be nice.

> 
> e.g.
> print transcribe(my_seq, use_reverse_complement=True)
> 
> or,
> print transcribe(my_seq, strand=-1)
> 
> or, maybe:
> print transcribe_rc(my_seq)

This one handling optional argument strand with default value -1,
but accepting [-1, 1, +1, 'watson', 'crick']. Ideally extended
in the future to splice-out the single intron by default or raise
an exception unless told to remove introns a,c,d,e or maybe instructed
to keep specific exons ... I am not sure what one would need more
often. I haven't checked but guess that GenBank files have more
often annotated introns and the exon region are more deeply buried
in the file structure so probably the first would impose less work
onto the parser.

Martin


From biopython at maubp.freeserve.co.uk  Wed Jul 16 14:37:43 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 16 Jul 2008 15:37:43 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487DF5B0.1050000@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
	<487D33A0.5060804@ribosome.natur.cuni.cz>
	<320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>
	<487DF5B0.1050000@ribosome.natur.cuni.cz>
Message-ID: <320fb6e00807160737v5b6a18d6n78986412c8abaad@mail.gmail.com>

I asked Martin:
>> You would really prefer a single function call to do a combined
>> "transcribe reverse-complement" or "transcribe the other strand" over
>> doing the reverse complement and transcription in two steps?

Martin wrote:
> Yes, a single function handling arguments would be nice.
> ...
> This one handling optional argument strand with default value -1,
> but accepting [-1, 1, +1, 'watson', 'crick'].

No.  The default would have to be the coding strand (aka strand +1, or
the Crick strand).  I know that biologically translation works on the
template strand (aka strand -1, or the Watson strand), but that is not
the convention in computational biology (at least in Biopython).

In case we are talking at cross-purposes, consider this double
stranded bit of DNA,

5' ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG 3'
3' TACCCTTTCCATCCCGTTCGAAGGTCAATC 5'

and associated mRNA,
5' AUGGGAAAGGUAGGGCAAGCUUCCAGUUAG 3'

This DNA made up of two strands, which by convention are always read
from the 5' end to the 3' end.  i.e.

DNA coding strand (aka Crick strand, strand +1):
5' ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG 3'

DNA template strand (aka Watson strand, strand -1):
5' CTAACTGGAAGCTTGCCCTACCTTTCCCAT 3'

If this region were to be transcribed into mRNA and translated it would give:

protein,
MGKVGQASS (and stop)

In Bioinformatics in general, people tend to work with the coding
strand rather than the template strand.  In Biopython using strings
you could represent all this as follows:

from Bio.Seq import reverse_complement, translate, transcribe, back_transcribe

coding_strand_dna = "ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG"
template_strand_dna = reverse_complement(coding_strand_dna)
assert template_strand_dna == "CTAACTGGAAGCTTGCCCTACCTTTCCCAT"
assert coding_strand_dna == reverse_complement(template_strand_dna)

#Note transcribe() goes from the CODING strand to the mRNA
messenger_rna = transcribe(coding_strand_dna)
assert coding_strand_dna == back_transcribe(messenger_rna)

protein = translate(messenger_rna)
#Note you can also use translate() directly on the CODING strand:
assert protein == translate(coding_strand_dna)
assert protein == translate(reverse_complement(template_strand_dna))
assert protein == "MGKVGQASS*"

If that makes things clearer, maybe I should put something like this
in the Biopython tutorial... and/or the Bio.Seq docstring
documentation?  What do you think?

Peter


From mmokrejs at ribosome.natur.cuni.cz  Wed Jul 16 21:50:37 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Wed, 16 Jul 2008 23:50:37 +0200
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <320fb6e00807160737v5b6a18d6n78986412c8abaad@mail.gmail.com>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>	
	<487D2A5A.1000305@ribosome.natur.cuni.cz>	
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>	
	<487D33A0.5060804@ribosome.natur.cuni.cz>	
	<320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>	
	<487DF5B0.1050000@ribosome.natur.cuni.cz>
	<320fb6e00807160737v5b6a18d6n78986412c8abaad@mail.gmail.com>
Message-ID: <487E6D2D.70104@ribosome.natur.cuni.cz>

Hi Peter,
  thank you for nice explanation. Definitely pasting the text&code from
your answer into BioPython Wiki or Tutorial would be sufficient and
should be there.

  Regarding the issue with transcribing coding strand ... probably
you have convinced me. ;-) I agree that one usually has annotated
sequence in GenBank format with annotated introns and wants to
concatenate some exons and get it translated. From this perspective
it does not make sense to un-necessarily reverse-complement the
sequence.
Martin


Peter wrote:
> I asked Martin:
>>> You would really prefer a single function call to do a combined
>>> "transcribe reverse-complement" or "transcribe the other strand" over
>>> doing the reverse complement and transcription in two steps?
> 
> Martin wrote:
>> Yes, a single function handling arguments would be nice.
>> ...
>> This one handling optional argument strand with default value -1,
>> but accepting [-1, 1, +1, 'watson', 'crick'].
> 
> No.  The default would have to be the coding strand (aka strand +1, or
> the Crick strand).  I know that biologically translation works on the
> template strand (aka strand -1, or the Watson strand), but that is not
> the convention in computational biology (at least in Biopython).
> 
> In case we are talking at cross-purposes, consider this double
> stranded bit of DNA,
> 
> 5' ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG 3'
> 3' TACCCTTTCCATCCCGTTCGAAGGTCAATC 5'
> 
> and associated mRNA,
> 5' AUGGGAAAGGUAGGGCAAGCUUCCAGUUAG 3'
> 
> This DNA made up of two strands, which by convention are always read
> from the 5' end to the 3' end.  i.e.
> 
> DNA coding strand (aka Crick strand, strand +1):
> 5' ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG 3'
> 
> DNA template strand (aka Watson strand, strand -1):
> 5' CTAACTGGAAGCTTGCCCTACCTTTCCCAT 3'
> 
> If this region were to be transcribed into mRNA and translated it would give:
> 
> protein,
> MGKVGQASS (and stop)
> 
> In Bioinformatics in general, people tend to work with the coding
> strand rather than the template strand.  In Biopython using strings
> you could represent all this as follows:
> 
> from Bio.Seq import reverse_complement, translate, transcribe, back_transcribe
> 
> coding_strand_dna = "ATGGGAAAGGTAGGGCAAGCTTCCAGTTAG"
> template_strand_dna = reverse_complement(coding_strand_dna)
> assert template_strand_dna == "CTAACTGGAAGCTTGCCCTACCTTTCCCAT"
> assert coding_strand_dna == reverse_complement(template_strand_dna)
> 
> #Note transcribe() goes from the CODING strand to the mRNA
> messenger_rna = transcribe(coding_strand_dna)
> assert coding_strand_dna == back_transcribe(messenger_rna)
> 
> protein = translate(messenger_rna)
> #Note you can also use translate() directly on the CODING strand:
> assert protein == translate(coding_strand_dna)
> assert protein == translate(reverse_complement(template_strand_dna))
> assert protein == "MGKVGQASS*"
> 
> If that makes things clearer, maybe I should put something like this
> in the Biopython tutorial... and/or the Bio.Seq docstring
> documentation?  What do you think?
> 
> Peter
> 
> 

-- 
Dr. Martin Mokrejs
Dept. of Genetics and Microbiology
Faculty of Science, Charles University
Vinicna 5, 128 43 Prague, Czech Republic
tel: +420-2-2195 1716
http://www.iresite.org
http://www.iresite.org/~mmokrejs


From biopython at maubp.freeserve.co.uk  Thu Jul 17 13:56:05 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 17 Jul 2008 14:56:05 +0100
Subject: [BioPython] Trying to transcribe RNA = error?
In-Reply-To: <487E6D2D.70104@ribosome.natur.cuni.cz>
References: <320fb6e00807151415r6110c4dfs4ef2b74e9b64495a@mail.gmail.com>
	<487D2A5A.1000305@ribosome.natur.cuni.cz>
	<320fb6e00807151613u35024f30p731a5bd22a8987fe@mail.gmail.com>
	<487D33A0.5060804@ribosome.natur.cuni.cz>
	<320fb6e00807160408h5754b780jd72a5c39dabe5e11@mail.gmail.com>
	<487DF5B0.1050000@ribosome.natur.cuni.cz>
	<320fb6e00807160737v5b6a18d6n78986412c8abaad@mail.gmail.com>
	<487E6D2D.70104@ribosome.natur.cuni.cz>
Message-ID: <320fb6e00807170656m2040d17fsdc3cd0b8ca519315@mail.gmail.com>

Martin MOKREJ? wrote:
> Hi Peter,
>  thank you for nice explanation. Definitely pasting the text&code from
> your answer into BioPython Wiki or Tutorial would be sufficient and
> should be there.

I've added something similar to the tutorial in CVS, but using Seq
objects instead of strings.

Peter



From dalloliogm at gmail.com  Fri Jul 18 13:20:48 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Fri, 18 Jul 2008 15:20:48 +0200
Subject: [BioPython] biopython 1.47 installation fails - and modified how to
	install instructions on wiki
Message-ID: <5aa3b3570807180620o224f4d53q812d15297a49d92e@mail.gmail.com>

Hi,
I have two things to say.

First, I have added instructions on how to install biopython with
easy_install to the biopython wiki:
- http://biopython.org/wiki/Download#Easy_Install

for those of you who don't know what easy_install is, it's a nice way to
install python packages on the fly, something similar to perl -MCPAN.
Can you please check whether the easy_install installation works fine for
you too?


Second, I was trying to install biopython 1.47 using the tar/zip archives on
http://biopython.org/DIST/biopython-1.47.tar.gz

There it seems to be a problem with the installation; after running sudo
python setup.py install, I receive the following error:

Would you like to build Bio.KDTree ? (y/N)
running build
running build_py
running build_ext
building 'Bio.clistfns' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC -I/usr/include/python2.5 -c Bio/clistfnsmodule.c
-o build/temp.linux-i686-2.5/Bio/clistfnsmodule.o
Bio/clistfnsmodule.c:10:20: error: Python.h: No such file or directory
Bio/clistfnsmodule.c:25: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
Bio/clistfnsmodule.c:80: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
Bio/clistfnsmodule.c:146: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'clistfnsMethods'
Bio/clistfnsmodule.c: In function 'initclistfns':
Bio/clistfnsmodule.c:160: warning: implicit declaration of function
'Py_InitModule3'
Bio/clistfnsmodule.c:160: error: 'clistfnsMethods' undeclared (first use in
this function)
Bio/clistfnsmodule.c:160: error: (Each undeclared identifier is reported
only once
Bio/clistfnsmodule.c:160: error: for each function it appears in.)
error: command 'gcc' failed with exit status 1


It seems a file Python.h is missing or mispelled.
Con you confirm that?

Cheers


-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it


From biopython at maubp.freeserve.co.uk  Fri Jul 18 13:36:25 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 18 Jul 2008 14:36:25 +0100
Subject: [BioPython] biopython 1.47 installation fails - and modified
	how to install instructions on wiki
In-Reply-To: <5aa3b3570807180620o224f4d53q812d15297a49d92e@mail.gmail.com>
References: <5aa3b3570807180620o224f4d53q812d15297a49d92e@mail.gmail.com>
Message-ID: <320fb6e00807180636y4d1b819dgd4ad68aa81178b39@mail.gmail.com>

Giovanni Marco Dall'Olio wrote:
> Second, I was trying to install biopython 1.47 using the tar/zip archives on
> http://biopython.org/DIST/biopython-1.47.tar.gz
>
> There it seems to be a problem with the installation; after running sudo
> python setup.py install, I receive the following error:
>
> Would you like to build Bio.KDTree ? (y/N)
> running build
> running build_py
> running build_ext
> building 'Bio.clistfns' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> -Wstrict-prototypes -fPIC -I/usr/include/python2.5 -c Bio/clistfnsmodule.c
> -o build/temp.linux-i686-2.5/Bio/clistfnsmodule.o
> Bio/clistfnsmodule.c:10:20: error: Python.h: No such file or directory
> ...
>
> It seems a file Python.h is missing or mispelled.
> Can you confirm that?

You are probably missing the python header files - you didn't say what
OS you are using but from the path names its some form of Unix I
think.  Under Debian Linux you can use apt-get to install the build
dependencies of the Biopython package, and then install the latest
Biopython from source (specifically I think you are missing the
equivalent of the Debian python-dev package).

Peter


From dalloliogm at gmail.com  Fri Jul 18 13:48:52 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Fri, 18 Jul 2008 15:48:52 +0200
Subject: [BioPython] biopython 1.47 installation fails - and modified
	how to install instructions on wiki
In-Reply-To: <320fb6e00807180636y4d1b819dgd4ad68aa81178b39@mail.gmail.com>
References: <5aa3b3570807180620o224f4d53q812d15297a49d92e@mail.gmail.com>
	<320fb6e00807180636y4d1b819dgd4ad68aa81178b39@mail.gmail.com>
Message-ID: <5aa3b3570807180648q292bb750u60197af8daffb493@mail.gmail.com>

On Fri, Jul 18, 2008 at 3:36 PM, Peter <biopython at maubp.freeserve.co.uk>
wrote:

> Giovanni Marco Dall'Olio wrote:
> > gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> > -Wstrict-prototypes -fPIC -I/usr/include/python2.5 -c
> Bio/clistfnsmodule.c
> > -o build/temp.linux-i686-2.5/Bio/clistfnsmodule.o
> > Bio/clistfnsmodule.c:10:20: error: Python.h: No such file or directory
> > ...
>
> You are probably missing the python header files - you didn't say what
> OS you are using but from the path names its some form of Unix I
> think.  Under Debian Linux you can use apt-get to install the build
> dependencies of the Biopython package, and then install the latest
> Biopython from source (specifically I think you are missing the
> equivalent of the Debian python-dev package).
>

it's true!
I was missing the python-dev package.
Now the compilation goes well.

Thanks!


>
> Peter
>



-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it


From biopython at maubp.freeserve.co.uk  Mon Jul 21 15:42:56 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 21 Jul 2008 16:42:56 +0100
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
Message-ID: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>

Dear all,

I've recently filed Bug 2547 about changing the behaviour of
Bio.Seq.translate() when given ambiguous codons like NNN or TAN which
could be either an amino acid OR a stop codon.

http://bugzilla.open-bio.org/show_bug.cgi?id=2547

In my opinion it would be nice if there was an established convention
for how to represent an ambiguous character meaning {X or stop}, for
the TAN example even {Y or stop}.  However, as far as I am aware,
people just use X to mean any amino acid OR a stop codon.  This is the
behaviour in both the EMBOSS transeq tool and in BioPerl.

I am proposing to change Bio.Seq.translate() be able to translate
codons like NNN and TAN as X (rather than throwing a translation error
as happens now).

Comments please?

[Any implementation suggestions on the development mailing list please.]

Peter


From bsouthey at gmail.com  Mon Jul 21 19:23:34 2008
From: bsouthey at gmail.com (Bruce Southey)
Date: Mon, 21 Jul 2008 14:23:34 -0500
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>
Message-ID: <4884E236.1090605@gmail.com>

Peter wrote:
> Dear all,
>
> I've recently filed Bug 2547 about changing the behaviour of
> Bio.Seq.translate() when given ambiguous codons like NNN or TAN which
> could be either an amino acid OR a stop codon.
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2547
>
> In my opinion it would be nice if there was an established convention
> for how to represent an ambiguous character meaning {X or stop}, for
> the TAN example even {Y or stop}.  However, as far as I am aware,
> people just use X to mean any amino acid OR a stop codon.  This is the
> behaviour in both the EMBOSS transeq tool and in BioPerl.
>
> I am proposing to change Bio.Seq.translate() be able to translate
> codons like NNN and TAN as X (rather than throwing a translation error
> as happens now).
>
> Comments please?
>
> [Any implementation suggestions on the development mailing list please.]
>
> Peter
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>   
The relevant document here is the IUPAC 'Nomenclature for Incompletely 
Specified Bases in Nucleic Acid Sequences'  
(http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html).

Table 4 provides some examples such as showing the correspondence 
between the triplet  'NNN' and the amino acid 'Unknown' with one letter 
code 'X'.  Consequently, here must also be a correspondence between 
triplet 'TAN' (or any other related triplet for that matter) and the 
amino acid 'X' because the triple 'NNN' must also include the stop 
codons which have no corresponding amino acid (okay ignoring 
selenocysteine etc.).

Bruce



From biopython at maubp.freeserve.co.uk  Mon Jul 21 21:04:34 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 21 Jul 2008 22:04:34 +0100
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <4884E236.1090605@gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>
	<4884E236.1090605@gmail.com>
Message-ID: <320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>

> The relevant document here is the IUPAC 'Nomenclature for Incompletely
> Specified Bases in Nucleic Acid Sequences'
>  (http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html).
>
> Table 4 provides some examples such as showing the correspondence between
> the triplet  'NNN' and the amino acid 'Unknown' with one letter code 'X'.
> Consequently, here must also be a correspondence between triplet 'TAN' (or
> any other related triplet for that matter) and the amino acid 'X' because
> the triple 'NNN' must also include the stop codons which have no
> corresponding amino acid (okay ignoring selenocysteine etc.).
>
> Bruce

I'd seen that table, but hadn't interpreted it in quite the same way
as you seem to have.  Table 4 shows a mapping from amino acids to
ambiguous codons - but it is not a bijection (it is NOT a reversible
mapping).  Or to put it another way, Table 4 just shows the narrowest
possible ambiguous codon which covers all possible codons for that
amino acid (or stop).  This does NOT mean that ambiguous codon will
allways translate to the given amino acid.

Here are two explicit examples to try and explain myself (using a
little set notation).  In the standard genetic code, stop codons are
{TAA, TGA, TAG} = {TAR, TGA} = {TAA, TRA}.  If you have to use a
single codon, the best you can do is TRR = {TAA, TAG, TGA, TGG} =
{stop codons}U{TGG}.  Table 4 maps "*" to "TRR".  While TRR does cover
all the possible stop codons, it also includes a codon for Trp (W).  I
would NOT want TRR translated as a stop!  It codes for a stop or a W.

Similarly, for Leucine (L) the possible codons are {TTA, TTG, CTT,
CTC, CTA, CTG} = {TTR, CTN}.  If you have to use a single codon then
YTN covers this - but it also covers CTA and CTG which code for Phe
(F).  I would NOT want YTN translated as L - it codes for L or F, so
would have to be translated as X.

So on the basis of Table 4, there is no reason to infer that IUPAC
explicitly suggest NNN should be translated as X.

Peter


From biopython at maubp.freeserve.co.uk  Tue Jul 22 08:51:26 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 22 Jul 2008 09:51:26 +0100
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>
	<4884E236.1090605@gmail.com>
	<320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>
Message-ID: <320fb6e00807220151r20a49511ue61fed8f244bc65@mail.gmail.com>

On Mon, Jul 21, 2008 at 10:04 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> The relevant document here is the IUPAC 'Nomenclature for Incompletely
>> Specified Bases in Nucleic Acid Sequences'
>>  (http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html).
>>
>> Table 4 ...
>
> I'd seen that table, but hadn't interpreted it in quite the same way
> as you seem to have.  ...
> So on the basis of Table 4, there is no reason to infer that IUPAC
> explicitly suggest NNN should be translated as X.

Re-reading that, I can be pedantic sometime, can't I?

Putting our differences of opinion about exactly what the IUPAC Table
4 is intended to convey, do you agree that Biopython's
Bio.Seq.translate() function should turn NNN and TAN into X?

Thanks

Peter


From bsouthey at gmail.com  Tue Jul 22 13:20:37 2008
From: bsouthey at gmail.com (Bruce Southey)
Date: Tue, 22 Jul 2008 08:20:37 -0500
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <320fb6e00807220151r20a49511ue61fed8f244bc65@mail.gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>	
	<4884E236.1090605@gmail.com>	
	<320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>
	<320fb6e00807220151r20a49511ue61fed8f244bc65@mail.gmail.com>
Message-ID: <4885DEA5.8070706@gmail.com>

Peter wrote:
> On Mon, Jul 21, 2008 at 10:04 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>   
>>> The relevant document here is the IUPAC 'Nomenclature for Incompletely
>>> Specified Bases in Nucleic Acid Sequences'
>>>  (http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html).
>>>
>>> Table 4 ...
>>>       
>> I'd seen that table, but hadn't interpreted it in quite the same way
>> as you seem to have.  ...
>> So on the basis of Table 4, there is no reason to infer that IUPAC
>> explicitly suggest NNN should be translated as X.
>>     
>
> Re-reading that, I can be pedantic sometime, can't I?
>   
Sure, why not? Some one must be pedantic otherwise all these corner 
cases get missed and lead to bigger problems.

> Putting our differences of opinion about exactly what the IUPAC Table
> 4 is intended to convey, do you agree that Biopython's
> Bio.Seq.translate() function should turn NNN and TAN into X?
>
> Thanks
>
> Peter
>
>   
Yes because if you accept that 'NNN should be translated as X' then, by 
the same reasoning, you must also accept 'TAN into X' as well as similar 
cases.

For Biopython, there could a be flag or similar that causes translate() 
to either return an error for any ambiguous codons or just continues on 
using 'X'.

Bruce


From mmokrejs at ribosome.natur.cuni.cz  Tue Jul 22 14:04:29 2008
From: mmokrejs at ribosome.natur.cuni.cz (=?UTF-8?B?TWFydGluIE1PS1JFSsWg?=)
Date: Tue, 22 Jul 2008 16:04:29 +0200
Subject: [BioPython] Translation of ambiguous codons like NNN and TAN
In-Reply-To: <4885DEA5.8070706@gmail.com>
References: <320fb6e00807210842m2a800caevf9534755aa897c8f@mail.gmail.com>		<4884E236.1090605@gmail.com>		<320fb6e00807211404s2888ef7tf39764b7b11faffb@mail.gmail.com>	<320fb6e00807220151r20a49511ue61fed8f244bc65@mail.gmail.com>
	<4885DEA5.8070706@gmail.com>
Message-ID: <4885E8ED.3010205@ribosome.natur.cuni.cz>

Bruce Southey wrote:
>>   
> Yes because if you accept that 'NNN should be translated as X' then, by 
> the same reasoning, you must also accept 'TAN into X' as well as similar 
> cases.
> 
> For Biopython, there could a be flag or similar that causes translate() 
> to either return an error for any ambiguous codons or just continues on 
> using 'X'.

Yes, I agree as well. When translating ESTs I don't to get my code bailing
out due to sequencing errors. But I agree that usually people would like to
get an error instead.

Martin


From biopython at maubp.freeserve.co.uk  Tue Jul 22 15:38:36 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Tue, 22 Jul 2008 16:38:36 +0100
Subject: [BioPython] Deprecating the HTML parser in Bio.Blast.NCBIWWW
In-Reply-To: <320fb6e00807120645u26321d71q30f72ed5808f700@mail.gmail.com>
References: <320fb6e00807120645u26321d71q30f72ed5808f700@mail.gmail.com>
Message-ID: <320fb6e00807220838x3aae8246w8a6e3108bf6feec8@mail.gmail.com>

For any Biopython and Blast users,

For some time now we've been discouraging the use of the HTML
and plain text Blast parsers in favour of the XML format.

I think it would be a good idea to now officially deprecate the
HTML parser in Bio.Blast.NCBIWWW with warning messages
when it is used.  I don't even know if it still works with the recent
big revision to the BLAST webpages, but I suspect not.

However, the plain text parser in Bio.Blast.NCBIStandalone still
has its uses - even if it doesn't support the current BLAST output
100%. In particular, right now the PSI-BLAST output in XML format
lacks some of the information found in the plain text output (new
vs reused entries) so it would be premature to deprecate our plain
text (PSI) BLAST parser.

Is anyone still using Biopython to parse the HTML output from BLAST?
If so, please speak up.

Peter


From winter at biotec.tu-dresden.de  Wed Jul 23 09:55:23 2008
From: winter at biotec.tu-dresden.de (Christof Winter)
Date: Wed, 23 Jul 2008 11:55:23 +0200
Subject: [BioPython] Deprecating the HTML parser in Bio.Blast.NCBIWWW
In-Reply-To: <320fb6e00807220838x3aae8246w8a6e3108bf6feec8@mail.gmail.com>
References: <320fb6e00807120645u26321d71q30f72ed5808f700@mail.gmail.com>
	<320fb6e00807220838x3aae8246w8a6e3108bf6feec8@mail.gmail.com>
Message-ID: <4887000B.1070409@biotec.tu-dresden.de>

Peter wrote, On 22.07.2008 17:38:
> For any Biopython and Blast users,
> 
> For some time now we've been discouraging the use of the HTML
> and plain text Blast parsers in favour of the XML format.
> 
> I think it would be a good idea to now officially deprecate the
> HTML parser in Bio.Blast.NCBIWWW with warning messages
> when it is used.

Full ack.

Christof



From jcigar at ulb.ac.be  Wed Jul 23 14:51:21 2008
From: jcigar at ulb.ac.be (Julien Cigar)
Date: Wed, 23 Jul 2008 16:51:21 +0200
Subject: [BioPython] blast
Message-ID: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>

Hello list,

I'm working on a project (on African rats) which has a "blast"
functionnality. In our (PostgreSQL) database sequences are linked to a
specimen. The sequence table contains the sequence itself (which is just
a text field) and additional things like the accession number (if
exists), etc.

The idea behind this is that a user can enter a part of DNA and see what
kind of specimen (taxonomy) it could be.

So I created a FASTA file with all the sequences, and then I used
formatdb to be able to BLAST on it.

It works quite well, you can see it in action on
http://projects.biodiversity.be/africanrodentia/search/dna 
In the output I use the score attribute to show how close the entered
sequence is (is it OK ?). The problem is that the users would prefer a
kind of percentage. This is a copy of a mail I received :

"Yet I have a question regarding the BLAST function: It works well but
the output is unclear. Could one not indicate the % similarity  of the
ranked sequences versus the pasted sequence instead of te rather
enigmatic scores that we see now?  Such an output would make the
interpretation clearer,  particularly in cases where we do not have the
sequence of the investigated species. In such a case the species with
the most similar sequence will be given as a potential species name, in
itself not a problem as long as one knows how different they are (e.g.
in rodents wthin species variability approx less <3%, between species
differences typically >4%). This provides a direct indication whether
the output is likely to be yield a correct species name."

I wondered how this "score" is calculated, and if there's already a
function to convert it to a percentage ? Otherwise, is it OK to take the
hsp.sbjct field as 100% and then compare it to hsp.query ?

For example if I have :

CCTATTCCTAGCTATACACTACACATCGGACACAACAAC
|||||||||||| ||||||||||||||||||||||||||
CCTATTCCTAGCCATACACTACACATCGGACACAACAAC

The score is shown as "35", is it OK if I do something like :

percentage = (100.0 / len(hsp.sbjct)) * hsp.match.count('|')

so with my example it will be: (100 / 39) * 38

Many thanks,
Julien

-- 
Julien Cigar
Belgian Biodiversity Platform
http://www.biodiversity.be
Universit? Libre de Bruxelles (ULB)
Campus de la Plaine CP 257
B?timent NO, Bureau 4 N4 115C (Niveau 4)
Boulevard du Triomphe, entr?e ULB 2
B-1050 Bruxelles
Mail: jcigar at ulb.ac.be
@biobel: http://biobel.biodiversity.be/person/show/471
Tel : 02 650 57 52



From lueck at ipk-gatersleben.de  Wed Jul 23 13:17:26 2008
From: lueck at ipk-gatersleben.de (=?UTF-8?Q?Stefanie_L=C3=BCck?=)
Date: Wed, 23 Jul 2008 15:17:26 +0200
Subject: [BioPython] blast
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
Message-ID: <00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>

Hi!

I calculated like this for my program (you blast against your own primer 
stock database and get % match per primers to your query sequence):

percent = float(100) * float(hsp.score) / float(alignment.length)

Regards
Stefanie 


From p.j.a.cock at googlemail.com  Wed Jul 23 13:53:50 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 14:53:50 +0100
Subject: [BioPython] blast
In-Reply-To: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
Message-ID: <320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>

On Wed, Jul 23, 2008 at 3:51 PM, Julien Cigar <jcigar at ulb.ac.be> wrote:
> Hello list,
>
> I'm working on a project (on African rats) which has a "blast"
> functionnality. In our (PostgreSQL) database sequences are linked to a
> specimen. The sequence table contains the sequence itself (which is just
> a text field) and additional things like the accession number (if
> exists), etc.
>
> The idea behind this is that a user can enter a part of DNA and see what
> kind of specimen (taxonomy) it could be.
>
> So I created a FASTA file with all the sequences, and then I used
> formatdb to be able to BLAST on it.
>
> It works quite well, you can see it in action on
> http://projects.biodiversity.be/africanrodentia/search/dna
> In the output I use the score attribute to show how close the entered
> sequence is (is it OK ?). The problem is that the users would prefer a
> kind of percentage. This is a copy of a mail I received :

It is pretty, but doesn't look like the BLAST output many biologists
will be used to, so I think I understand why the want some more
information to judge the similarity.

> "Yet I have a question regarding the BLAST function: It works well but
> the output is unclear. Could one not indicate the % similarity  of the
> ranked sequences versus the pasted sequence instead of te rather
> enigmatic scores that we see now?  Such an output would make the
> interpretation clearer,  particularly in cases where we do not have the
> sequence of the investigated species. In such a case the species with
> the most similar sequence will be given as a potential species name, in
> itself not a problem as long as one knows how different they are (e.g.
> in rodents wthin species variability approx less <3%, between species
> differences typically >4%). This provides a direct indication whether
> the output is likely to be yield a correct species name."

I think they are asking for the percentage identify.  Another
possiblity is the bit-score which should be in the BLAST output as a
floating point number (hsp.score).

> I wondered how this "score" is calculated, and if there's already a
> function to convert it to a percentage ? Otherwise, is it OK to take the
> hsp.sbjct field as 100% and then compare it to hsp.query ?
>
> For example if I have :
>
> CCTATTCCTAGCTATACACTACACATCGGACACAACAAC
> |||||||||||| ||||||||||||||||||||||||||
> CCTATTCCTAGCCATACACTACACATCGGACACAACAAC
>
> The score is shown as "35", is it OK if I do something like :
>
> percentage = (100.0 / len(hsp.sbjct)) * hsp.match.count('|')
>
> so with my example it will be: (100 / 39) * 38

To get the percentage identify over the alignment, yes.  Watch out for
integer division, but because you multiplied by 100.0 it should be
fine.

I would also go directly from the relevant integer fields (which
should be the same).  Something like this (assuming you are using the
XML parser):

assert hsp.identities == hsp.match.count('|') #Only works on nucleotide blasts!
assert hsp.align_length == len(hsp.sbjct)
assert hsp.align_length == len(hsp.match)
assert hsp.align_length == len(hsp.query)
percentage_identity = (100.0 * hsp.identities) / hsp.align_length

Have you considered actually showing the blast alignment too?

Peter


From p.j.a.cock at googlemail.com  Wed Jul 23 14:05:14 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 15:05:14 +0100
Subject: [BioPython] blast
In-Reply-To: <00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
Message-ID: <320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>

I wrote:
> I think they are asking for the percentage identify.  Another
> possiblity is the bit-score which should be in the BLAST output as a
> floating point number (hsp.score).

I should have said raw score (hsp.score) or bit score (hsp.bits), both
of which might be of interest to your users.

Steganie wrote:
> Hi!
>
> I calculated like this for my program (you blast against your own primer
> stock database and get % match per primers to your query sequence):
>
> percent = float(100) * float(hsp.score) / float(alignment.length)
>

Using hsp.score gives the raw score, which you are then scaling by the
length and 100.  I'm not sure offhand what you've calculated, but if
you want the percentage identity, I think its just the number of
identically match letters divided by the alignment length:

percentage_identity = (100.0 * hsp.identities) / hsp.align_length

In the plain text output BLAST gives this number explicitly, e.g.
Identities = 112/146 (76%), Positives = 127/146 (86%), Gaps = 2/146 (1%)

There is also hsp.bits which gives the bit score.

Peter


From p.j.a.cock at googlemail.com  Wed Jul 23 14:18:08 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 15:18:08 +0100
Subject: [BioPython] blast
In-Reply-To: <1216830021.2612.65.camel@frodon.be-bif.ulb.ac.be>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>
	<1216830021.2612.65.camel@frodon.be-bif.ulb.ac.be>
Message-ID: <320fb6e00807230718v4edbe5f1x707ece2608e05582@mail.gmail.com>

> Thanks, I got another formula which seems to work well too (and which
> seems cleaner than counting the number of '|') :
>
> float(100) * float(hsp.score) / float(alignment.length)

I don't think that gives you the same thing as the percentage identify
(see my other email).

>> Have you considered actually showing the blast alignment too?
>>
> Yes, it's in the output, I just replaced the '|' with a red background
> and the ' ' with a green background, so they see directly where it
> doesn't match

Since the graphical representation of the match/mismatch string is
done using the colours red and green, it is useless for anyone who is
colour blind.

Also the user can't cut and paste the alignment into an email or other
document (electronic lab book?), which seems like an obvious thing to
want to do.

Personally, I would try and keep the output looking more similar to
traditional blast, as then its easier to understand (assuming you
already know BLAST!).

Peter


From jcigar at ulb.ac.be  Wed Jul 23 16:20:21 2008
From: jcigar at ulb.ac.be (Julien Cigar)
Date: Wed, 23 Jul 2008 18:20:21 +0200
Subject: [BioPython] blast
In-Reply-To: <320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>
Message-ID: <1216830021.2612.65.camel@frodon.be-bif.ulb.ac.be>

On Wed, 2008-07-23 at 14:53 +0100, Peter Cock wrote:
> On Wed, Jul 23, 2008 at 3:51 PM, Julien Cigar <jcigar at ulb.ac.be> wrote:
> > Hello list,
> >
> > I'm working on a project (on African rats) which has a "blast"
> > functionnality. In our (PostgreSQL) database sequences are linked to a
> > specimen. The sequence table contains the sequence itself (which is just
> > a text field) and additional things like the accession number (if
> > exists), etc.
> >
> > The idea behind this is that a user can enter a part of DNA and see what
> > kind of specimen (taxonomy) it could be.
> >
> > So I created a FASTA file with all the sequences, and then I used
> > formatdb to be able to BLAST on it.
> >
> > It works quite well, you can see it in action on
> > http://projects.biodiversity.be/africanrodentia/search/dna
> > In the output I use the score attribute to show how close the entered
> > sequence is (is it OK ?). The problem is that the users would prefer a
> > kind of percentage. This is a copy of a mail I received :
> 
> It is pretty, but doesn't look like the BLAST output many biologists
> will be used to, so I think I understand why the want some more
> information to judge the similarity.
> 

Yes, I'm not a biologist, I'm learning on the job .. so that explains
it :) (but it's interresting to learn)

> > "Yet I have a question regarding the BLAST function: It works well but
> > the output is unclear. Could one not indicate the % similarity  of the
> > ranked sequences versus the pasted sequence instead of te rather
> > enigmatic scores that we see now?  Such an output would make the
> > interpretation clearer,  particularly in cases where we do not have the
> > sequence of the investigated species. In such a case the species with
> > the most similar sequence will be given as a potential species name, in
> > itself not a problem as long as one knows how different they are (e.g.
> > in rodents wthin species variability approx less <3%, between species
> > differences typically >4%). This provides a direct indication whether
> > the output is likely to be yield a correct species name."
> 
> I think they are asking for the percentage identify.  Another
> possiblity is the bit-score which should be in the BLAST output as a
> floating point number (hsp.score).
> 

Yes, it's should be that, I forgot to take the alignement length into
account. I already showed the bit-score, but apparently it's not too
usefull for them.

> > I wondered how this "score" is calculated, and if there's already a
> > function to convert it to a percentage ? Otherwise, is it OK to take the
> > hsp.sbjct field as 100% and then compare it to hsp.query ?
> >
> > For example if I have :
> >
> > CCTATTCCTAGCTATACACTACACATCGGACACAACAAC
> > |||||||||||| ||||||||||||||||||||||||||
> > CCTATTCCTAGCCATACACTACACATCGGACACAACAAC
> >
> > The score is shown as "35", is it OK if I do something like :
> >
> > percentage = (100.0 / len(hsp.sbjct)) * hsp.match.count('|')
> >
> > so with my example it will be: (100 / 39) * 38
> 
> To get the percentage identify over the alignment, yes.  Watch out for
> integer division, but because you multiplied by 100.0 it should be
> fine.
> 
> I would also go directly from the relevant integer fields (which
> should be the same).  Something like this (assuming you are using the
> XML parser):
> 
> assert hsp.identities == hsp.match.count('|') #Only works on nucleotide blasts!
> assert hsp.align_length == len(hsp.sbjct)
> assert hsp.align_length == len(hsp.match)
> assert hsp.align_length == len(hsp.query)
> percentage_identity = (100.0 * hsp.identities) / hsp.align_length
> 

Thanks, I got another formula which seems to work well too (and which
seems cleaner than counting the number of '|') :

float(100) * float(hsp.score) / float(alignment.length)

> Have you considered actually showing the blast alignment too?
> 

Yes, it's in the output, I just replaced the '|' with a red background
and the ' ' with a green background, so they see directly where it
doesn't match

> Peter

Thanks,
Julien

-- 
Julien Cigar
Belgian Biodiversity Platform
http://www.biodiversity.be
Universit? Libre de Bruxelles (ULB)
Campus de la Plaine CP 257
B?timent NO, Bureau 4 N4 115C (Niveau 4)
Boulevard du Triomphe, entr?e ULB 2
B-1050 Bruxelles
Mail: jcigar at ulb.ac.be
@biobel: http://biobel.biodiversity.be/person/show/471
Tel : 02 650 57 52



From lueck at ipk-gatersleben.de  Wed Jul 23 14:30:10 2008
From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=)
Date: Wed, 23 Jul 2008 16:30:10 +0200
Subject: [BioPython] blast
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
Message-ID: <010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>

 >Peter wrote:
> Using hsp.score gives the raw score, which you are then scaling by the
> length and 100.  I'm not sure offhand what you've calculated, but if
> you want the percentage identity, I think its just the number of
> identically match letters divided by the alignment length:
> 
> percentage_identity = (100.0 * hsp.identities) / hsp.align_length


I tried and it dosen't work in my case. It's gives me wrong percentage. 

 

I need to know at which % my primer match to the query part:

 

query          --------taggcctcgcgcgcc-------

               ||||||||||||||||||||||||||||||

primer         tagcgctataggcctcgcgcgccatatagc

 

Here 50 %. 



From jcigar at ulb.ac.be  Wed Jul 23 16:46:34 2008
From: jcigar at ulb.ac.be (Julien Cigar)
Date: Wed, 23 Jul 2008 18:46:34 +0200
Subject: [BioPython] blast
In-Reply-To: <320fb6e00807230718v4edbe5f1x707ece2608e05582@mail.gmail.com>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<320fb6e00807230653k289d74e1v550503bac8bc98a8@mail.gmail.com>
	<1216830021.2612.65.camel@frodon.be-bif.ulb.ac.be>
	<320fb6e00807230718v4edbe5f1x707ece2608e05582@mail.gmail.com>
Message-ID: <1216831594.2612.85.camel@frodon.be-bif.ulb.ac.be>

On Wed, 2008-07-23 at 15:18 +0100, Peter Cock wrote:
> > Thanks, I got another formula which seems to work well too (and which
> > seems cleaner than counting the number of '|') :
> >
> > float(100) * float(hsp.score) / float(alignment.length)
> 
> I don't think that gives you the same thing as the percentage identify
> (see my other email).
> 

Indeed..! (sorry I sended my last mail before reading yours).

> >> Have you considered actually showing the blast alignment too?
> >>
> > Yes, it's in the output, I just replaced the '|' with a red background
> > and the ' ' with a green background, so they see directly where it
> > doesn't match
> 
> Since the graphical representation of the match/mismatch string is
> done using the colours red and green, it is useless for anyone who is
> colour blind.
> 

You're right .. I haven't thought about this

> Also the user can't cut and paste the alignment into an email or other
> document (electronic lab book?), which seems like an obvious thing to
> want to do.
> 
> Personally, I would try and keep the output looking more similar to
> traditional blast, as then its easier to understand (assuming you
> already know BLAST!).
> 

ok, I'll ask them what they prefer.

> Peter

Thanks,
Julien

-- 
Julien Cigar
Belgian Biodiversity Platform
http://www.biodiversity.be
Universit? Libre de Bruxelles (ULB)
Campus de la Plaine CP 257
B?timent NO, Bureau 4 N4 115C (Niveau 4)
Boulevard du Triomphe, entr?e ULB 2
B-1050 Bruxelles
Mail: jcigar at ulb.ac.be
@biobel: http://biobel.biodiversity.be/person/show/471
Tel : 02 650 57 52



From p.j.a.cock at googlemail.com  Wed Jul 23 14:49:39 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 15:49:39 +0100
Subject: [BioPython] blast
In-Reply-To: <010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
Message-ID: <320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>

On Wed, Jul 23, 2008 at 3:30 PM, Stefanie L?ck <lueck at ipk-gatersleben.de> wrote:
>>Peter wrote:
>>
>> Using hsp.score gives the raw score, which you are then scaling by the
>> length and 100.  I'm not sure offhand what you've calculated, but if
>> you want the percentage identity, I think its just the number of
>> identically match letters divided by the alignment length:
>>
>> percentage_identity = (100.0 * hsp.identities) / hsp.align_length
>
> I tried and it dosen't work in my case. It's gives me wrong percentage.
>
> I need to know at which % my primer match to the query part:
>
>
> query          --------taggcctcgcgcgcc-------
>              ||||||||||||||||||||||||||||||
> primer         tagcgctataggcctcgcgcgccatatagc
>
> Here 50 %.

Your query match region has an un-gapped length of 15, and gapped length of 30
Your subject match region has a length of 30
Your query and subject have 15 identical matches
The alignment length is 30, therefore 100*15/30 = 50%

Using my suggested formula correctly gives the percentage identies
relative to the alignment length:
percentage_identity = (100.0 * hsp.identities) / hsp.align_length

It seems what you want to calculate is 100*15/15 = 100%  i.e. The
percentage identites relative to the ungapped query length?  This
would probably work but isn't very elegant:

percentage_identity_ref_matched_query = (100.0 * hsp.identities) /
(hsp.align_length - hsp.query.count("-"))

Or even relative to the full original query?  If record is the blast
record object that the hsp cam from,

percentage_identity_ref_full_query = (100.0 * hsp.identities) /
record.query_letters)

(For a short query sequence like a probe, these may be the same)

Peter



From p.j.a.cock at googlemail.com  Wed Jul 23 14:54:42 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 15:54:42 +0100
Subject: [BioPython] blast
In-Reply-To: <320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
Message-ID: <320fb6e00807230754k52bebba4v453933ef0a215351@mail.gmail.com>

>> I need to know at which % my primer match to the query part:
>>
>>
>> query          --------taggcctcgcgcgcc-------
>>              ||||||||||||||||||||||||||||||
>> primer         tagcgctataggcctcgcgcgccatatagc
>>
>> Here 50 %.

How did you get this example?  NCBI Blast doesn't include the leading
and trailing gaps (in plain text, XML or HTML), e.g.

 Features in this part of subject sequence:
   transcription elongation factor protein, GreA/GreB family

 Score = 30.2 bits (15),  Expect =    39
 Identities = 15/15 (100%), Gaps = 0/15 (0%)
 Strand=Plus/Plus

Query  1        TAGGCCTCGCGCGCC  15
                |||||||||||||||
Sbjct  2614347  TAGGCCTCGCGCGCC  2614361


Peter


From lueck at ipk-gatersleben.de  Wed Jul 23 15:20:04 2008
From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=)
Date: Wed, 23 Jul 2008 17:20:04 +0200
Subject: [BioPython] blast
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
	<320fb6e00807230754k52bebba4v453933ef0a215351@mail.gmail.com>
Message-ID: <013e01c8ecd7$95731490$1022a8c0@ipkgatersleben.de>

Sorry, I forgot to say that I do the alignment myself. It's was just for 
demonstration.

Yes. I have a 30 bp primer. 15 bp from the primer bind to my query sequence. 
The percentage would be 50 %.
percent = match * 100 / full length primer

>
percentage_identity = (100.0 * hsp.identities) / hsp.align_length
percentage_identity_ref_matched_query = (100.0 * hsp.identities) / 
(hsp.align_length - hsp.query.count("-"))
>

Sorry, both give me wrong percentage if I try on my database.

Look here, compare alignment and percentage:

http://picasaweb.google.de/luecks/Python02/photo#5226228430697476754

e.g Hit 13 should give 60 %

What you recommend to use instead of hsp.score?

Nice quitting time
Stefanie




From p.j.a.cock at googlemail.com  Wed Jul 23 15:36:40 2008
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Jul 2008 16:36:40 +0100
Subject: [BioPython] blast
In-Reply-To: <013e01c8ecd7$95731490$1022a8c0@ipkgatersleben.de>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
	<320fb6e00807230754k52bebba4v453933ef0a215351@mail.gmail.com>
	<013e01c8ecd7$95731490$1022a8c0@ipkgatersleben.de>
Message-ID: <320fb6e00807230836j1196ad41s303927af1c1645c3@mail.gmail.com>

> Sorry, both give me wrong percentage if I try on my database.
>
> Look here, compare alignment and percentage:
>
> http://picasaweb.google.de/luecks/Python02/photo#5226228430697476754
>
> e.g Hit 13 should give 60 %
>
> What you recommend to use instead of hsp.score?

I am assuming you want to parse some BLAST output in order to populate
this database.  How about something based on this:

from Bio.Blast import NCBIXML
for record in NCBIXML.parse(open("test.xml")) :
    print "Query %i length %i" % (record.query_id, record.query_letters)
    for alignment in record.alignments :
        for hsp in alignment.hsps :
            percentage_identities_versus_full_query = (100.0 *
hsp.identities) / record.query_letters
            print " vs %s gives %0.1f%% identities" \
              % (alignment.hit_id, percentage_identities_versus_full_query)

This uses the fact the the original query length is recorded in the
record object as the "query_letters" property (this name was a
historical choice based on the plain text blast output).

For the example you gave, then then I would expect hsp.identities ==
12 (and hsp.alignment_length == 12) while record.query_letters == 60
which will give you the desired output of 60%.

Peter


From biopython at maubp.freeserve.co.uk  Wed Jul 23 22:12:34 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Jul 2008 23:12:34 +0100
Subject: [BioPython] Deprecating Bio.Saf (PredictProtein Simple Alignment
	Format)
Message-ID: <320fb6e00807231512s507d2652jc0f26764a62b01d5@mail.gmail.com>

Is anyone using Bio.Saf or PredictProtein's "Simple Alignment Format" (SAF)?

Bio.Saf is one of the older parsers in Biopython.  It parses the
PredictProtein "Simple Alignment Format" (SAF), a fairly free-format
multiple sequence alignment file format described here:
http://www.predictprotein.org/Dexa/optin_saf.html

Potentially we could support this file format within Bio.AlignIO (if
there was any demand).  However, as far as I can tell, this file
format is ONLY used for PredictProtein, and they will accept several
other more mainstream alignment file formats as alternatives.

Bio.Saf uses Martel for parsing, which is not entirely compatible with
mxTextTools 3.0.  If we did want to integrate SAF support into
Bio.AlignIO it might be best to reimplement the parser in plain
python.

If no one is using it, I would like to deprecate Bio.Saf in the next
release of Biopython.

Peter


From biopython at maubp.freeserve.co.uk  Wed Jul 23 22:29:37 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 23 Jul 2008 23:29:37 +0100
Subject: [BioPython] Deprecating the HTML parser in Bio.Blast.NCBIWWW
In-Reply-To: <4887000B.1070409@biotec.tu-dresden.de>
References: <320fb6e00807120645u26321d71q30f72ed5808f700@mail.gmail.com>
	<320fb6e00807220838x3aae8246w8a6e3108bf6feec8@mail.gmail.com>
	<4887000B.1070409@biotec.tu-dresden.de>
Message-ID: <320fb6e00807231529w5a6d4ee0n9d595234764eea02@mail.gmail.com>

Christof Winter wrote:
> Peter wrote:
>>
>> For any Biopython and Blast users,
>>
>> For some time now we've been discouraging the use of the HTML
>> and plain text Blast parsers in favour of the XML format.
>>
>> I think it would be a good idea to now officially deprecate the
>> HTML parser in Bio.Blast.NCBIWWW with warning messages
>> when it is used.
>
> Full ack.
>
> Christof

This is now deprecated in CVS, and I'll update the tutorial shortly.
For the next couple of releases of Biopython the parser will still be
there, but will now issue a warning message. if you try and use it.
If there is anyone out there still using the HTML BLAST parser, it
isn't too late to undo this change.

Peter


From alexl at users.sourceforge.net  Thu Jul 24 08:23:21 2008
From: alexl at users.sourceforge.net (Alex Lancaster)
Date: Thu, 24 Jul 2008 01:23:21 -0700
Subject: [BioPython] Fedora biopython packages updated for 1.47
Message-ID: <xvmyk7y9l2.fsf@allele2.eebweb.arizona.edu>

Hi there,

For all Fedora users, new packages for biopython 1.47 are now
available the "updates-testing" repository for F-8 and F-9

To test them out simply run (as root):

yum --enablerepo=updates-testing install python-biopython

You can provide feedback on packages here:

For F-9:

https://admin.fedoraproject.org/updates/F9/FEDORA-2008-6235

For F-8:

https://admin.fedoraproject.org/updates/F8/FEDORA-2008-6243

(You can leave feedback anonymously, or using your Fedora account name
if you happen to be a Fedora contributor)

The more positive feedback from testing, the faster the packages can
go into the stable "updates" repo (or conversely if there are any
problems, they can be fixed before being pushed).

Thanks!
Alex


From matzke at berkeley.edu  Fri Jul 25 05:27:55 2008
From: matzke at berkeley.edu (Nick Matzke)
Date: Thu, 24 Jul 2008 22:27:55 -0700
Subject: [BioPython] problem installing mxTextTools
Message-ID: <4889645B.9080400@berkeley.edu>

Hi all,

I am trying to install biopython and am carefully following the 
directions at:

http://biopython.org/DIST/docs/install/Installation.html

...as instructed, here are the steps I took:


1. I start by successfully installing Python2.4.4 on my Mac OSX 10.4.  I 
set the environment variable so that Python2.4.4 is the default version 
of Python at the terminal.

2. Then, as instructed I try to install mxTextTools.  Downloaded:
egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt

...from here:
http://www.egenix.com/products/python/mxBase/


3. However, none of these (the official instructions, or several 
alternatives proposed in various online fora) work for installing 
mxTextTools.  Here are the results:

3a. instructions here:
http://biopython.org/DIST/docs/install/Installation.html#htoc9

======================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
root# python -V
Python 2.4.4

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
root# python setup.py build
running build
running mx_autoconf
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
-L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
macros to define: [('HAVE_STRPTIME', '1')]
macros to undefine: []
running build_ext

building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
building 'mx.DateTime.mxDateTime.mxDateTime' extension
creating build/temp.macosx-10.3-fat-2.4_ucs2
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime
creating 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
-DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
mx/DateTime/mxDateTime/mxDateTime.c -o 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o
i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
i686-apple-darwin8-gcc-4.0.1: no input files
powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
powerpc-apple-darwin8-gcc-4.0.1: no input files
lipo: can't figure out the architecture type of: /var/tmp//cch9pAof.out
error: command 'gcc' failed with exit status 1

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
root#
======================


3b. Instructions here:
http://www.egenix.com/products/python/mxBase/

sudo python setup.py install

==================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ python -V
Python 2.4.4

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py install
running install
running build
running mx_autoconf
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
-L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
macros to define: [('HAVE_STRPTIME', '1')]
macros to undefine: []
running build_ext

building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
building 'mx.DateTime.mxDateTime.mxDateTime' extension
gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
-fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
-DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
-I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
-I/usr/local/include -I/opt/local/include 
-I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
mx/DateTime/mxDateTime/mxDateTime.c -o 
build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o
i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
i686-apple-darwin8-gcc-4.0.1: no input files
powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
such file or directory
powerpc-apple-darwin8-gcc-4.0.1: no input files
lipo: can't figure out the architecture type of: /var/tmp//ccGUEnk3.out
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

==================




3c. Instructions here:
http://www.egenix.com/mailman-archives/egenix-users/2007-October/114291.html

sudo python setup.py build --skip install
================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ python -V
Python 2.4.4
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py build --skip install
running build
skipping the build process and reusing the existing build files and data
error: build/build-macosx-10.3-fat-py2.4_ucs2.pck: No such file or directory
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ ls
COPYRIGHT               PKG-INFO                build 
installer.bmp           mxSetup.pyc             wininst.bat
LICENSE                 README                  egenix_mx_base.py 
mx                      setup.cfg
MANIFEST                bdist_zope.bat          egenix_mx_base.pyc 
mxSetup.py              setup.py
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ ls ./build
build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
temp.darwin-8.11.1-i386-2.3_ucs2
lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 
temp.macosx-10.3-fat-2.4_ucs2
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$
================


4. Give up and email the biopython list.  Help!!  Please!!


5. Ask existential questions about why, oh why, all useful software 
comes with dependencies that you have to compile yourself and which 
never, ever compile correctly when the instructions are followed even on 
utterly standard systems like Mac OSX 10.4.


Thanks very very much,
Nick







-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab website: http://ib.berkeley.edu/people/lab_detail.php?lab=54
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: 
http://fisher.berkeley.edu/~edna/lab_test/members/matzke.html
Lab phone: 510-643-6299
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Office hours for Bio1B: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================


From matzke at berkeley.edu  Fri Jul 25 05:46:20 2008
From: matzke at berkeley.edu (Nick Matzke)
Date: Thu, 24 Jul 2008 22:46:20 -0700
Subject: [BioPython] problem installing mxTextTools
In-Reply-To: <4889645B.9080400@berkeley.edu>
References: <4889645B.9080400@berkeley.edu>
Message-ID: <488968AC.4000303@berkeley.edu>

Hi all,

An update -- I found a solution by copying the .pck file the download 
actually gave me to the filename that the install was apparently looking 
for.  This was not exactly obvious (!!!!) but apparently it worked:

<snipping output of solution which made the email too long for the 
auto-moderator>

==============================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ cd build

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ ls
build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
temp.darwin-8.11.1-i386-2.3_ucs2
lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 temp.macosx-10.3-fat-2.4_ucs2

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ cp build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
build-macosx-10.3-fat-py2.4_ucs2.pck

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ cd ..

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py build --skip installPassword:
running build
skipping the build process and reusing the existing build files and data
restoring build data from a previous build run
running install
running install_lib
running build_ext
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating

[...]

writing byte-compilation script '/tmp/tmpIfqFr6.py'
/Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/Python 
-O /tmp/tmpIfqFr6.py
removing /tmp/tmpIfqFr6.py
running install_data


wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ more README
=============================================================================
eGenix mx Base Distribution for Python
-----------------------------------------------------------------------------

Source Installation
-------------------

In order to build and install the distribution, run

     python setup.py install

Then change to some other directory and try to import the packages:

$ cd ~
$ python
Python 2.4.3 (#1, May  9 2007, 00:48:21)
[GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> from mx.DateTime import now
 >>> print now()
2007-05-30 11:00:03.24
 >>>

Note that trying this from the installation directory will cause
Python to pick up the source tree packages which do not contain the
compiled binaries.  This will likely fail with strange error messages.


Prebuilt Installation
---------------------

If you have downloaded a prebuilt distribution archive, the
installation is slightly different. You have to run

     python setup.py build --skip install

Then follow the same instructions as for the source installation.


Copyrights & Licenses
---------------------

The software in this distribution is copyrighted and protected by
international, EU and German copyright law. Please see the COPYRIGHT
file for details.

The software is licensed to you under the eGenix.com Public License as
stated in the LICENSE file of the distribution directory.  Some
subpackages may contain third-party software which is licensed under
different conditions. Please see the documentation and/or LICENSE
files of the subpackages for details.

If in doubt, please check the web-site at http://www.egenix.com or
contact sales at egenix.com for more information on copyright, licensing
conditions and authorized use.


-----------------------------------------------------------------------------
eGenix.com GmbH
Pastor-Loeh-Str. 48
D-40764 Langenfeld
Germany
info at egenix.com

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ cd ..

wright:/bioinformatics/pythonstuff nick$ ls
egenix python_notes.rtf
egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt

wright:/bioinformatics/pythonstuff nick$ python
Python 2.4.4 (#1, Oct 18 2006, 10:34:39)
[GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

 >>> from mx.DateTime import now
 >>>

 >>> print now()
2008-07-24 22:39:17.66
 >>>
==============================

Several hours of my life gone, but yay!

Cheers,
Nick


From matzke at berkeley.edu  Fri Jul 25 07:37:15 2008
From: matzke at berkeley.edu (Nick Matzke)
Date: Fri, 25 Jul 2008 00:37:15 -0700
Subject: [BioPython] problem installing mxTextTools
In-Reply-To: <488968AC.4000303@berkeley.edu>
References: <4889645B.9080400@berkeley.edu> <488968AC.4000303@berkeley.edu>
Message-ID: <488982AB.8000209@berkeley.edu>

Or, even better, version 2 of mxTextTools should be downloaded and used, 
it installs easily, and is supposed to work better anyway, however you 
can only find this from this page:

http://biopython.org/wiki/Download#Optional_Software
http://www.egenix.com/www2002/python/eGenix-mx-Extensions-v2.x.html/

...but not the "complete instructions" page:
http://biopython.org/DIST/docs/install/Installation.html#htoc9

(Sorry if this stuff is annoying but probably someone else naive will 
have these same problems in the future.)

Cheers,
Nick




Nick Matzke wrote:
> Hi all,
> 
> An update -- I found a solution by copying the .pck file the download 
> actually gave me to the filename that the install was apparently looking 
> for.  This was not exactly obvious (!!!!) but apparently it worked:
> 
> <snipping output of solution which made the email too long for the 
> auto-moderator>
> 
> ==============================
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ cd build
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
> nick$ ls
> build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
> temp.darwin-8.11.1-i386-2.3_ucs2
> lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 temp.macosx-10.3-fat-2.4_ucs2
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
> nick$ cp build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
> build-macosx-10.3-fat-py2.4_ucs2.pck
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
> nick$ cd ..
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ sudo python setup.py build --skip installPassword:
> running build
> skipping the build process and reusing the existing build files and data
> restoring build data from a previous build run
> running install
> running install_lib
> running build_ext
> creating 
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx 
> 
> copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/__init__.py 
> -> 
> /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx 
> 
> creating
> 
> [...]
> 
> writing byte-compilation script '/tmp/tmpIfqFr6.py'
> /Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/Python 
> -O /tmp/tmpIfqFr6.py
> removing /tmp/tmpIfqFr6.py
> running install_data
> 
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ more README
> ============================================================================= 
> 
> eGenix mx Base Distribution for Python
> ----------------------------------------------------------------------------- 
> 
> 
> Source Installation
> -------------------
> 
> In order to build and install the distribution, run
> 
>     python setup.py install
> 
> Then change to some other directory and try to import the packages:
> 
> $ cd ~
> $ python
> Python 2.4.3 (#1, May  9 2007, 00:48:21)
> [GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>  >>> from mx.DateTime import now
>  >>> print now()
> 2007-05-30 11:00:03.24
>  >>>
> 
> Note that trying this from the installation directory will cause
> Python to pick up the source tree packages which do not contain the
> compiled binaries.  This will likely fail with strange error messages.
> 
> 
> Prebuilt Installation
> ---------------------
> 
> If you have downloaded a prebuilt distribution archive, the
> installation is slightly different. You have to run
> 
>     python setup.py build --skip install
> 
> Then follow the same instructions as for the source installation.
> 
> 
> Copyrights & Licenses
> ---------------------
> 
> The software in this distribution is copyrighted and protected by
> international, EU and German copyright law. Please see the COPYRIGHT
> file for details.
> 
> The software is licensed to you under the eGenix.com Public License as
> stated in the LICENSE file of the distribution directory.  Some
> subpackages may contain third-party software which is licensed under
> different conditions. Please see the documentation and/or LICENSE
> files of the subpackages for details.
> 
> If in doubt, please check the web-site at http://www.egenix.com or
> contact sales at egenix.com for more information on copyright, licensing
> conditions and authorized use.
> 
> 
> ----------------------------------------------------------------------------- 
> 
> eGenix.com GmbH
> Pastor-Loeh-Str. 48
> D-40764 Langenfeld
> Germany
> info at egenix.com
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ cd ..
> 
> wright:/bioinformatics/pythonstuff nick$ ls
> egenix python_notes.rtf
> egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> 
> wright:/bioinformatics/pythonstuff nick$ python
> Python 2.4.4 (#1, Oct 18 2006, 10:34:39)
> [GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> 
>  >>> from mx.DateTime import now
>  >>>
> 
>  >>> print now()
> 2008-07-24 22:39:17.66
>  >>>
> ==============================
> 
> Several hours of my life gone, but yay!
> 
> Cheers,
> Nick
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab website: http://ib.berkeley.edu/people/lab_detail.php?lab=54
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: 
http://fisher.berkeley.edu/~edna/lab_test/members/matzke.html
Lab phone: 510-643-6299
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Office hours for Bio1B: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================


From biopython at maubp.freeserve.co.uk  Fri Jul 25 09:11:29 2008
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 25 Jul 2008 10:11:29 +0100
Subject: [BioPython] problem installing mxTextTools
In-Reply-To: <488982AB.8000209@berkeley.edu>
References: <4889645B.9080400@berkeley.edu> <488968AC.4000303@berkeley.edu>
	<488982AB.8000209@berkeley.edu>
Message-ID: <320fb6e00807250211x4a9cdd31jfdaf4762204e522e@mail.gmail.com>

On Fri, Jul 25, 2008 at 8:37 AM, Nick Matzke <matzke at berkeley.edu> wrote:
> Or, even better, version 2 of mxTextTools should be downloaded and used, it
> installs easily, and is supposed to work better anyway, however you can only
> find this from this page:
>
> http://biopython.org/wiki/Download#Optional_Software
> http://www.egenix.com/www2002/python/eGenix-mx-Extensions-v2.x.html/
>
> ...but not the "complete instructions" page:
> http://biopython.org/DIST/docs/install/Installation.html#htoc9
>
> (Sorry if this stuff is annoying but probably someone else naive will have
> these same problems in the future.)

As you have discovered the wiki is more up to date, but we should
update that document too.

On the wiki we do explicitly recommend mxTextTools 2.0 rather than 3.0
(there were some unicode related API changes), but in any case
mxTextTools is now optional as it is only needed for a few less used
parsers.  As the install script says, you can delay installing
mxTextTools until when using Biopython you see an import error
relating to it.

At least you've succeeded in the installation now :)

Peter


From dalke at dalkescientific.com  Mon Jul 28 21:58:22 2008
From: dalke at dalkescientific.com (Andrew Dalke)
Date: Mon, 28 Jul 2008 23:58:22 +0200
Subject: [BioPython] training in Python for cheminformatics
Message-ID: <B20E21E1-166C-4631-95B7-6843E6878261@dalkescientific.com>

Hi all,

   This isn't quite bioinformatics, but maybe if you squint
hard enough you might see the purines and pyrimidines in DNA. :)

   I'm going to teach a two-day intensive course in Python
programming, focusing on cheminformatics/small molecules.
The target audience is computational chemists who want to
be more effective at doing science by learning more about
how to program.  Most of my examples will be directly
based on problems that come up in a normal research
environment.

   The course is scheduled for 6-7 October in Leipzig, Germany.

   More details are at:
      http://dalkescientific.com/training/

				Andrew
				dalke at dalkescientific.com




From shulin.zhuang at gmail.com  Wed Jul 30 00:34:23 2008
From: shulin.zhuang at gmail.com (Shulin Zhuang)
Date: Tue, 29 Jul 2008 17:34:23 -0700
Subject: [BioPython] how to using python to multiply call a program for
	caculation
Message-ID: <4f1a9e210807291734t6d7c7e9fq6d34df63e3e172d6@mail.gmail.com>

Dear All,

Here just disturb you a question.

I make a simple script to execute one program, the script content:

import string, re, sys, os, time, math
calc = '/usr/local/bin/resc 1bmp.pdb 8 A > 8.txt '
os.system(calc)

I can sucessfully execute this script and get the result file"8.txt.


In the calc column,  8 is a residue number,  resc is a program. The aim is
to use resc to calculate residue 8 and get the output 8.txt.


 I want to calculate the whole residues from 1, 2, 3, ..... to 100, if I use
above simple script, I should execute 100 times. Therefore, I want to write
a script to let the python do all the calculations at one time.

Then I write the script as following:

import string, re, sys, os, time, math
i = 1
while i <=100:
       calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + abc
       i = i +1
os.system(calc)


However, when I execute the script and get an error:"The first argument
should bu numerical"

Would you like to tell me how to write a good script to tackle this problem.
great thanks

Best regards


From shulin.zhuang at gmail.com  Wed Jul 30 01:35:51 2008
From: shulin.zhuang at gmail.com (Shulin Zhuang)
Date: Tue, 29 Jul 2008 18:35:51 -0700
Subject: [BioPython] how to using python to multiply call a program for
	caculation
In-Reply-To: <4f1a9e210807291734t6d7c7e9fq6d34df63e3e172d6@mail.gmail.com>
References: <4f1a9e210807291734t6d7c7e9fq6d34df63e3e172d6@mail.gmail.com>
Message-ID: <4f1a9e210807291835l929aeebs4035d312bc0809a7@mail.gmail.com>

Dear All,

Sorry to disturb you again.
If I edit the sentence to:
import string, re, sys, os, time, math
i = 1
while i <=100:
         calc = "/usr/local/bin/resc 1bmp.pdb %d  A >%d.txt"%(i,i)
         os.system(calc)

in above A is the chain name of 1bmp.pdb.


Now I can execute it and get the result.

Thanks for your notice.  It is because that I am just a beginner and not
familiar with the string and value.
Best regards
Shulin





On Tue, Jul 29, 2008 at 5:34 PM, Shulin Zhuang <shulin.zhuang at gmail.com>wrote:

> Dear All,
>
> Here just disturb you a question.
>
> I make a simple script to execute one program, the script content:
>
> import string, re, sys, os, time, math
> calc = '/usr/local/bin/resc 1bmp.pdb 8 A > 8.txt '
> os.system(calc)
>
> I can sucessfully execute this script and get the result file"8.txt.
>
>
> In the calc column,  8 is a residue number,  resc is a program. The aim is
> to use resc to calculate residue 8 and get the output 8.txt.
>
>
>  I want to calculate the whole residues from 1, 2, 3, ..... to 100, if I
> use above simple script, I should execute 100 times. Therefore, I want to
> write a script to let the python do all the calculations at one time.
>
> Then I write the script as following:
>
> import string, re, sys, os, time, math
> i = 1
> while i <=100:
>        calc = '/home/shulin/program/rescP/resc 1bmp.pdb  ' + abc
>        i = i +1
> os.system(calc)
>
>
> However, when I execute the script and get an error:"The first argument
> should bu numerical"
>
> Would you like to tell me how to write a good script to tackle this
> problem. great thanks
>
> Best regards
>
>
>


From lpritc at scri.ac.uk  Wed Jul 30 08:00:50 2008
From: lpritc at scri.ac.uk (Leighton Pritchard)
Date: Wed, 30 Jul 2008 09:00:50 +0100
Subject: [BioPython] how to using python to multiply call a program for
 caculation
In-Reply-To: <4f1a9e210807291734t6d7c7e9fq6d34df63e3e172d6@mail.gmail.com>
Message-ID: <C4B5DE42.13CC7%lpritc@scri.ac.uk>

Hi Shulin,

I can't see in your code with the while condition where you are specifying
the residue on the command-line string: the variable 'abc' appears to be
undefined in your code:

calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + abc

So the above should throw an error.

>From your code, the variable containing the residue number you want to use
in the command line appears to be 'i', and there are a number of ways you
can get your variable 'i' into the command-line string from there,
including:

calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + str(i)
calc = '/home/shulin/program/rescP/resc 1PGA.pdb %d' % i
calc = ' '.join(['/home/shulin/program/rescP/resc 1PGA.pdb', str(i)])


I've not tested the following code, but it may be the sort of thing you're
looking for:

# For this code you only need to import os
import os
# Define the command-line string components once
cmdexe = "/home/shulkin/program/rescP/resc"    # executable location
cmdstructure = "1PGA.pdb"                      # structure for analysis
# Then loop over the residue numbers, building a new command line
# and calling each time
for residue in range(1, 101):
    cmdstr = "%s %s %d > %d.txt" % (cmdexe, cmdstructure, residue, residue)
    #print cmdstr                 # does the command-line look right?
    os.system(cmdstr)             # make the system call
    
Sections of the Python documentation you might find useful here are:

string formatting
http://docs.python.org/lib/typesseq-strings.html

subprocess (which is favoured over os.system):
http://docs.python.org/lib/module-subprocess.html

And you may also be interested in the Python Tutor mailing list:
http://mail.python.org/mailman/listinfo/tutor

I hope this is useful,

L.

On 30/07/2008 01:34, "Shulin Zhuang" <shulin.zhuang at gmail.com> wrote:

> Dear All,
> 
> Here just disturb you a question.
> 
> I make a simple script to execute one program, the script content:
> 
> import string, re, sys, os, time, math
> calc = '/usr/local/bin/resc 1bmp.pdb 8 A > 8.txt '
> os.system(calc)
> 
> I can sucessfully execute this script and get the result file"8.txt.
> 
> 
> In the calc column,  8 is a residue number,  resc is a program. The aim is
> to use resc to calculate residue 8 and get the output 8.txt.
> 
> 
>  I want to calculate the whole residues from 1, 2, 3, ..... to 100, if I use
> above simple script, I should execute 100 times. Therefore, I want to write
> a script to let the python do all the calculations at one time.
> 
> Then I write the script as following:
> 
> import string, re, sys, os, time, math
> i = 1
> while i <=100:
>        calc = '/home/shulin/program/rescP/resc 1PGA.pdb  ' + abc
>        i = i +1
> os.system(calc)
> 
> 
> However, when I execute the script and get an error:"The first argument
> should bu numerical"
> 
> Would you like to tell me how to write a good script to tackle this problem.
> great thanks
> 
> Best regards
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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From jcigar at ulb.ac.be  Wed Jul 23 18:02:48 2008
From: jcigar at ulb.ac.be (Julien Cigar)
Date: Wed, 23 Jul 2008 18:02:48 -0000
Subject: [BioPython] blast
In-Reply-To: <320fb6e00807230836j1196ad41s303927af1c1645c3@mail.gmail.com>
References: <1216824681.2612.50.camel@frodon.be-bif.ulb.ac.be>
	<00a501c8ecc6$73973bf0$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230705l31f8bffsad95ca1cd27524ba@mail.gmail.com>
	<010301c8ecd0$9ca01a30$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230749yfb53ffem7410aed028b73e2@mail.gmail.com>
	<320fb6e00807230754k52bebba4v453933ef0a215351@mail.gmail.com>
	<013e01c8ecd7$95731490$1022a8c0@ipkgatersleben.de>
	<320fb6e00807230836j1196ad41s303927af1c1645c3@mail.gmail.com>
Message-ID: <1216830497.1019.2.camel@rivendell.lan>

Just FYI and another point of view (?), I asked one of the user about
which method is the best and he said that "one should not depend on the
length of the sequence to know how different/similar the use fragment
is", so it's really percentage identity which is needed

Julien

On Wed, 2008-07-23 at 16:36 +0100, Peter Cock wrote:
> > Sorry, both give me wrong percentage if I try on my database.
> >
> > Look here, compare alignment and percentage:
> >
> > http://picasaweb.google.de/luecks/Python02/photo#5226228430697476754
> >
> > e.g Hit 13 should give 60 %
> >
> > What you recommend to use instead of hsp.score?
> 
> I am assuming you want to parse some BLAST output in order to populate
> this database.  How about something based on this:
> 
> from Bio.Blast import NCBIXML
> for record in NCBIXML.parse(open("test.xml")) :
>     print "Query %i length %i" % (record.query_id, record.query_letters)
>     for alignment in record.alignments :
>         for hsp in alignment.hsps :
>             percentage_identities_versus_full_query = (100.0 *
> hsp.identities) / record.query_letters
>             print " vs %s gives %0.1f%% identities" \
>               % (alignment.hit_id, percentage_identities_versus_full_query)
> 
> This uses the fact the the original query length is recorded in the
> record object as the "query_letters" property (this name was a
> historical choice based on the plain text blast output).
> 
> For the example you gave, then then I would expect hsp.identities ==
> 12 (and hsp.alignment_length == 12) while record.query_letters == 60
> which will give you the desired output of 60%.
> 
> Peter
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython



From matzke at berkeley.edu  Fri Jul 25 05:44:01 2008
From: matzke at berkeley.edu (Nick Matzke)
Date: Fri, 25 Jul 2008 05:44:01 -0000
Subject: [BioPython] problem installing mxTextTools
In-Reply-To: <4889645B.9080400@berkeley.edu>
References: <4889645B.9080400@berkeley.edu>
Message-ID: <48896815.10104@berkeley.edu>

Hi all,

An update -- I found a solution by copying the .pck file the download 
actually gave me to the filename that the install was apparently looking 
for.  This was not exactly obvious (!!!!) but apparently it worked:


==============================
wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ cd build

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ ls
build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
temp.darwin-8.11.1-i386-2.3_ucs2
lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 
temp.macosx-10.3-fat-2.4_ucs2

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ cp build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
build-macosx-10.3-fat-py2.4_ucs2.pck

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt/build 
nick$ cd ..

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ sudo python setup.py build --skip installPassword:
running build
skipping the build process and reusing the existing build files and data
restoring build data from a previous build run
running install
running install_lib
running build_ext
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/BeeBase.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/BeeDict.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/BeeIndex.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/BeeStorage.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/Cache.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/Doc/mxBeeBase.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/ExitFunctions.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/FileLock.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/btr.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/mxBeeBase.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/mxBeeBase.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/mxBeeBase/testjohn.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/README -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/BeeBase/showBeeDict.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/ARPA.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/COPYRIGHT 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/DateTime.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Doc/mxDateTime.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Doc
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/alarm.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/AtomicClock.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/CommandLine.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/lifespan.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/numdate.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Examples/Y2000.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Feasts.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/ISO.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/LazyModule.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Locale.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/mxDateTime.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/mxDateTime.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/mxDateTime_Python.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testcmp.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testcoerce.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testcomdates.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testnow.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testpydatetime.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testrichard.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testroundoff.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/teststrftime.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testsubclassing.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/mxDateTime/testticks.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/NIST.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/ODMG.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Parser.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/README -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/timegm.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/DateTime/Timezone.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/eGenix-mx-Extensions.html 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxBeeBase.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxDateTime.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxProxy.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxQueue.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxStack.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxTextTools.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxTools.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxUID.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Doc/mxURL.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Doc
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Log.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/Cache.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/CommandLine.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/ConfigFile.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/Cookie.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/CSV.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/ExitFunctions.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/FileLock.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/LazyModule.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/LICENSE 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/Namespace.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/OrderedMapping.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Misc/PackageTools.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/NewBuiltins.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/Doc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/Doc/mxProxy.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/mxProxy/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/mxProxy/mxh.h 
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/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/mxProxy/mxProxy.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/mxProxy/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/mxProxy/testvlad.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/mxProxy/weakreftest.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/Proxy.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Proxy/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy
creating 
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copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/Doc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/Doc/mxQueue.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/Doc
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/LICENSE -> 
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creating 
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-> 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/mxQueue/mxh.h 
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-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue
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-> 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/mxQueue/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/queuebench.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Queue/UserQueue.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue
creating 
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copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/Doc/mxStack.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/mxStack/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack
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-> 
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-> 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/mxStack/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/stackbench.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Stack/UserStack.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack
creating 
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copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Constants/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Constants/Sets.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Constants/TagTables.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/COPYRIGHT 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Doc/mxTextTools.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Doc
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/altRTF.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/HTML.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/Loop.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/mysplit.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/pytag.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/Python.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/RegExp.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/RTF.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/Tim.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/Examples/Words.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
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-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/mxTextTools.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
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-> 
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/testHTML.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/testkj.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/testPickleSegFault.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/mxTextTools/testSegFault.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/README -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/TextTools/TextTools.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools
creating 
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copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/Doc/mxTools.pdf 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Doc
creating 
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copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/Examples/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Examples
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/Examples/Acquisition.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Examples
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/LICENSE -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
creating 
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copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/bench1.py 
-> 
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copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/bench2.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/hack.py 
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/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
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build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/mxh.h 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
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-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
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copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/test.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/mxTools/test_safecall.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/NewBuiltins.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/Tools/Tools.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/Doc/mxUID.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/Doc
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/LICENSE 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/mxh.h -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/mxUID.h -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/mxUID.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/mxUID/test.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/UID/UID.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/__init__.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/COPYRIGHT -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/Doc/mxURL.pdf -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/Doc
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/LazyModule.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/LICENSE 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/Listing.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
creating 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/__init__.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/mxh.h -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/mxURL.h -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/mxURL.so 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying 
build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/mxURL/test.py -> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/README 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
copying build/lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4/mx/URL/URL.py 
-> 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/BeeBase.py 
to BeeBase.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/BeeDict.py 
to BeeDict.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/BeeIndex.py 
to BeeIndex.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/BeeStorage.py 
to BeeStorage.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/Cache.py 
to Cache.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/ExitFunctions.py 
to ExitFunctions.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/FileLock.py 
to FileLock.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/mxBeeBase/testjohn.py 
to testjohn.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/BeeBase/showBeeDict.py 
to showBeeDict.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/ARPA.py 
to ARPA.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/DateTime.py 
to DateTime.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/alarm.py 
to alarm.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/AtomicClock.py 
to AtomicClock.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/CommandLine.py 
to CommandLine.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/lifespan.py 
to lifespan.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/numdate.py 
to numdate.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Examples/Y2000.py 
to Y2000.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Feasts.py 
to Feasts.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/ISO.py 
to ISO.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/LazyModule.py 
to LazyModule.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Locale.py 
to Locale.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/mxDateTime_Python.py 
to mxDateTime_Python.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testcmp.py 
to testcmp.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testcoerce.py 
to testcoerce.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testcomdates.py 
to testcomdates.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testnow.py 
to testnow.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testpydatetime.py 
to testpydatetime.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testrichard.py 
to testrichard.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testroundoff.py 
to testroundoff.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/teststrftime.py 
to teststrftime.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testsubclassing.py 
to testsubclassing.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/mxDateTime/testticks.py 
to testticks.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/NIST.py 
to NIST.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/ODMG.py 
to ODMG.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Parser.py 
to Parser.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/timegm.py 
to timegm.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/DateTime/Timezone.py 
to Timezone.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Log.py 
to Log.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/Cache.py 
to Cache.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/CommandLine.py 
to CommandLine.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/ConfigFile.py 
to ConfigFile.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/Cookie.py 
to Cookie.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/CSV.py 
to CSV.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/ExitFunctions.py 
to ExitFunctions.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/FileLock.py 
to FileLock.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/LazyModule.py 
to LazyModule.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/Namespace.py 
to Namespace.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/OrderedMapping.py 
to OrderedMapping.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Misc/PackageTools.py 
to PackageTools.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/NewBuiltins.py 
to NewBuiltins.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy/testvlad.py 
to testvlad.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/mxProxy/weakreftest.py 
to weakreftest.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Proxy/Proxy.py 
to Proxy.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/mxQueue/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/queuebench.py 
to queuebench.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Queue/UserQueue.py 
to UserQueue.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/mxStack/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/stackbench.py 
to stackbench.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Stack/UserStack.py 
to UserStack.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants/Sets.py 
to Sets.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Constants/TagTables.py 
to TagTables.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/altRTF.py 
to altRTF.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/HTML.py 
to HTML.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/Loop.py 
to Loop.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/mysplit.py 
to mysplit.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/pytag.py 
to pytag.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/Python.py 
to Python.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/RegExp.py 
to RegExp.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/RTF.py 
to RTF.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/Tim.py 
to Tim.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/Examples/Words.py 
to Words.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/testHTML.py 
to testHTML.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/testkj.py 
to testkj.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/testPickleSegFault.py 
to testPickleSegFault.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/mxTextTools/testSegFault.py 
to testSegFault.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/TextTools/TextTools.py 
to TextTools.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Examples/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Examples/Acquisition.py 
to Acquisition.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/bench1.py 
to bench1.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/bench2.py 
to bench2.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/hack.py 
to hack.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/mxTools/test_safecall.py 
to test_safecall.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/NewBuiltins.py 
to NewBuiltins.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/Tools/Tools.py 
to Tools.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/mxUID/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/UID/UID.py 
to UID.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/LazyModule.py 
to LazyModule.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/Listing.py 
to Listing.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL/__init__.py 
to __init__.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/mxURL/test.py 
to test.pyc
byte-compiling 
/Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages/mx/URL/URL.py 
to URL.pyc
writing byte-compilation script '/tmp/tmpIfqFr6.py'
/Library/Frameworks/Python.framework/Versions/2.4/Resources/Python.app/Contents/MacOS/Python 
-O /tmp/tmpIfqFr6.py
removing /tmp/tmpIfqFr6.py
running install_data


wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ more README
=============================================================================
eGenix mx Base Distribution for Python
-----------------------------------------------------------------------------

Source Installation
-------------------

In order to build and install the distribution, run

     python setup.py install

Then change to some other directory and try to import the packages:

$ cd ~
$ python
Python 2.4.3 (#1, May  9 2007, 00:48:21)
[GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> from mx.DateTime import now
 >>> print now()
2007-05-30 11:00:03.24
 >>>

Note that trying this from the installation directory will cause
Python to pick up the source tree packages which do not contain the
compiled binaries.  This will likely fail with strange error messages.


Prebuilt Installation
---------------------

If you have downloaded a prebuilt distribution archive, the
installation is slightly different. You have to run

     python setup.py build --skip install

Then follow the same instructions as for the source installation.


Copyrights & Licenses
---------------------

The software in this distribution is copyrighted and protected by
international, EU and German copyright law. Please see the COPYRIGHT
file for details.

The software is licensed to you under the eGenix.com Public License as
stated in the LICENSE file of the distribution directory.  Some
subpackages may contain third-party software which is licensed under
different conditions. Please see the documentation and/or LICENSE
files of the subpackages for details.

If in doubt, please check the web-site at http://www.egenix.com or
contact sales at egenix.com for more information on copyright, licensing
conditions and authorized use.


-----------------------------------------------------------------------------
eGenix.com GmbH
Pastor-Loeh-Str. 48
D-40764 Langenfeld
Germany
info at egenix.com

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$

wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
nick$ cd ..

wright:/bioinformatics/pythonstuff nick$ ls
egenix 
python_notes.rtf
egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt

wright:/bioinformatics/pythonstuff nick$ python
Python 2.4.4 (#1, Oct 18 2006, 10:34:39)
[GCC 4.0.1 (Apple Computer, Inc. build 5341)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

 >>> from mx.DateTime import now
 >>>

 >>> print now()
2008-07-24 22:39:17.66
 >>>
==============================

Several hours of my life gone, but yay!

Cheers,
Nick




Nick Matzke wrote:
> Hi all,
> 
> I am trying to install biopython and am carefully following the 
> directions at:
> 
> http://biopython.org/DIST/docs/install/Installation.html
> 
> ...as instructed, here are the steps I took:
> 
> 
> 1. I start by successfully installing Python2.4.4 on my Mac OSX 10.4.  I 
> set the environment variable so that Python2.4.4 is the default version 
> of Python at the terminal.
> 
> 2. Then, as instructed I try to install mxTextTools.  Downloaded:
> egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt
> 
> ...from here:
> http://www.egenix.com/products/python/mxBase/
> 
> 
> 3. However, none of these (the official instructions, or several 
> alternatives proposed in various online fora) work for installing 
> mxTextTools.  Here are the results:
> 
> 3a. instructions here:
> http://biopython.org/DIST/docs/install/Installation.html#htoc9
> 
> ======================
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> root# python -V
> Python 2.4.4
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> root# python setup.py build
> running build
> running mx_autoconf
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> _configtest.c -o _configtest.o
> gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
> -L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
> success!
> removing: _configtest.c _configtest.o _configtest
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> _configtest.c -o _configtest.o
> success!
> removing: _configtest.c _configtest.o
> macros to define: [('HAVE_STRPTIME', '1')]
> macros to undefine: []
> running build_ext
> 
> building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
> building 'mx.DateTime.mxDateTime.mxDateTime' extension
> creating build/temp.macosx-10.3-fat-2.4_ucs2
> creating 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime
> creating 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx
> creating 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime 
> 
> creating 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime 
> 
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
> -DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> mx/DateTime/mxDateTime/mxDateTime.c -o 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o 
> 
> i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
> such file or directory
> i686-apple-darwin8-gcc-4.0.1: no input files
> powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
> such file or directory
> powerpc-apple-darwin8-gcc-4.0.1: no input files
> lipo: can't figure out the architecture type of: /var/tmp//cch9pAof.out
> error: command 'gcc' failed with exit status 1
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> root#
> ======================
> 
> 
> 3b. Instructions here:
> http://www.egenix.com/products/python/mxBase/
> 
> sudo python setup.py install
> 
> ==================
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ python -V
> Python 2.4.4
> 
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ sudo python setup.py install
> running install
> running build
> running mx_autoconf
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> _configtest.c -o _configtest.o
> gcc _configtest.o -L/usr/local/lib -L/opt/local/lib 
> -L/Library/Frameworks/Python.framework/Versions/2.4/lib -o _configtest
> success!
> removing: _configtest.c _configtest.o _configtest
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -D_GNU_SOURCE=1 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> _configtest.c -o _configtest.o
> success!
> removing: _configtest.c _configtest.o
> macros to define: [('HAVE_STRPTIME', '1')]
> macros to undefine: []
> running build_ext
> 
> building extension "mx.DateTime.mxDateTime.mxDateTime" (required)
> building 'mx.DateTime.mxDateTime.mxDateTime' extension
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk 
> -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd 
> -fno-common -dynamic -DNDEBUG -g -O3 -DUSE_FAST_GETCURRENTTIME 
> -DHAVE_STRPTIME=1 -Imx/DateTime/mxDateTime 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
> -I/usr/local/include -I/opt/local/include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include -c 
> mx/DateTime/mxDateTime/mxDateTime.c -o 
> build/temp.macosx-10.3-fat-2.4_ucs2/mx-DateTime-mxDateTime-mxDateTime/mx/DateTime/mxDateTime/mxDateTime.o 
> 
> i686-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
> such file or directory
> i686-apple-darwin8-gcc-4.0.1: no input files
> powerpc-apple-darwin8-gcc-4.0.1: mx/DateTime/mxDateTime/mxDateTime.c: No 
> such file or directory
> powerpc-apple-darwin8-gcc-4.0.1: no input files
> lipo: can't figure out the architecture type of: /var/tmp//ccGUEnk3.out
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> 
> ==================
> 
> 
> 
> 
> 3c. Instructions here:
> http://www.egenix.com/mailman-archives/egenix-users/2007-October/114291.html 
> 
> 
> sudo python setup.py build --skip install
> ================
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ python -V
> Python 2.4.4
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ sudo python setup.py build --skip install
> running build
> skipping the build process and reusing the existing build files and data
> error: build/build-macosx-10.3-fat-py2.4_ucs2.pck: No such file or 
> directory
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ ls
> COPYRIGHT               PKG-INFO                build 
> installer.bmp           mxSetup.pyc             wininst.bat
> LICENSE                 README                  egenix_mx_base.py 
> mx                      setup.cfg
> MANIFEST                bdist_zope.bat          egenix_mx_base.pyc 
> mxSetup.py              setup.py
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$ ls ./build
> build-darwin-8.11.0-Power_Macintosh-py2.4_ucs4.pck 
> temp.darwin-8.11.1-i386-2.3_ucs2
> lib.darwin-8.11.0-Power_Macintosh-2.4_ucs4 temp.macosx-10.3-fat-2.4_ucs2
> wright:/bioinformatics/pythonstuff/egenix-mx-base-3.1.0.darwin-8.11.0-Power_Macintosh-py2.4_ucs4.prebuilt 
> nick$
> ================
> 
> 
> 4. Give up and email the biopython list.  Help!!  Please!!
> 
> 
> 5. Ask existential questions about why, oh why, all useful software 
> comes with dependencies that you have to compile yourself and which 
> never, ever compile correctly when the instructions are followed even on 
> utterly standard systems like Mac OSX 10.4.
> 
> 
> Thanks very very much,
> Nick
> 
> 
> 
> 
> 
> 
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. student, Graduate Student Researcher
Huelsenbeck Lab
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab website: http://ib.berkeley.edu/people/lab_detail.php?lab=54
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: 
http://fisher.berkeley.edu/~edna/lab_test/members/matzke.html
Lab phone: 510-643-6299
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Office hours for Bio1B: Biology: Plants, Evolution, Ecology
VLSB 2013, Monday 1-1:30 (some TA there for all hours during work week)

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
====================================================