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Bio.Seq and alphabets

I've been working on a complement() and reverse_complement() function for 
Bio.Seq's Seq and MutableSeq classes. Previously, similar functions existed in 
various places in Biopython. I am not sure though how to deal with the alphabet 
associated with a Seq or MutableSeq object. For example, a Seq can be created 
where the sequence is inconsistent with the alphabet:

 >>> from Bio.Alphabet import IUPAC
 >>> from Bio.Seq import Seq
 >>> Seq('GATCGACXYSMDG_or_any_funny_char_u_like_eg_*&$%', IUPAC.unambiguous_dna)
Seq('GATCGACXYSMDG_or_any_funny_char_u_like_eg_*&$%', IUPACUnambiguousDNA())

With a MutableSeq, one can change the sequence regardless of the alphabet:
 >>> from Bio.Seq import MutableSeq
 >>> s = MutableSeq('ACTGCCATCGT', IUPAC.unambiguous_dna)
 >>> s[9] = 'X'
 >>> s
MutableSeq(array('c', 'ACTGCCATCXT'), IUPACUnambiguousDNA())

Anyway, my immediate concern is how to deal with uppercase and lowercase 
characters. The reverse_complement function in Bio.GFF.easy converts lowercase 
characters to uppercase before taking the complement:

def _forward_complement_list_with_table(table, seq):
     return [table[x] for x in seq.tostring().upper()]

However, the complement and antiparallel functions in Bio.SeqUtils are not 
implemented for lowercase sequences:

_before = ''.join(IUPACData.ambiguous_dna_complement.keys())
_after = ''.join(IUPACData.ambiguous_dna_complement.values())
(Continue reading)

Shapkin, Michail | 6 Jul 08:57 2004

test

test
Cristian S. Rocha | 6 Jul 19:52 2004
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hmmpfam parser

Hi,

While I was searching for a hmmsearch output parser for biopython, I had
found a mail from you to the biopython-dev list with a source code. I'm
interesting to use it to parse a lot of hmm results but I would like to
know if exists a mature version and if you can append it to the
Bio-python CVS. If I can help you to testing and appending code to your
parser will be a pleasure. I really need these code. I was learning
Martel to write a parser, but I prefer help you than write one alone.

Thanks,
Cristian.

PD: Sorry about my bad english... :)

--

-- 
Lic. Cristian S. Rocha.
<crocha <at> dc.uba.ar>
Departamento de Computacin. FCEyN. UBA.
Pabellon I. Cuarto 9.
Ciudad Universitaria.
(1428) Buenos Aires. Argentina.
Tel: +54-11-4576-3390/96 int 714
Tel/Fax: +54-11-4576-3359
Cel: 15-5-607-9192
Thomas C. Williams | 6 Jul 03:35 2004
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http://www.reportlab.org/rl_toolkit.html


_______________________________________________
Biopython-dev mailing list
Biopython-dev <at> biopython.org
http://biopython.org/mailman/listinfo/biopython-dev
Shapkin, Michail | 12 Jul 11:52 2004

RE: Обзор арбитражной практики.

Привет !
Прошу отписать меня, по-хорошему!	

Best Regards, Mickle.
mailto:michail_shapkin <at> nuron.uz



-----Original Message-----
From: alok [mailto:terri <at> seznam.cz]
Sent: Saturday, July 10, 2004 12:00 PM
To: Shapkin, Michail
Subject: Обзор арбитражной практики.


Образовательный Центр,
приглашает руководителей организаций, юристов,
финансовых директоров, а также
их помощников и заместителей на программы открытых семинаров-практикумов


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

19 июля 2004 года
«Обзор арбитражной практики по рассмотрению 
отдельных категорий споров»

При обращении в арбитражный суд важно не только
знать, как написать исковое заявление, но и
немаловажно знать практику применения той или иной
(Continue reading)

h.j.tipney@stud.man.ac.uk | 13 Jul 15:56 2004
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python newbies blast problem

Hi
I posted this to the other mailing list and got no response so I'm 
hoping you guys can help me. I'm very new to programming and 
even newer to python, so I apologise in advance if this is a simple
problem with an obvious solution but there are no python 
programmers
near to help me. Anyway, I inherited the script below and have been
using it on and off as part of a larger workflow. It has been running
fine, but I ran it again last week and it didn't give the output I
expected - it returned the 'your results will be updated in X seconds'
page rather than the actual results. It has been a while since I had
used this program and both blast and biopython had been updated 
so
I've now got the new biopython release (1.30) but I still get the
'wrong' output. I'm using python 2.3.3 on solaris, if that helps. Any
help would be greatly appreciated! Thank you in advance Hannah 
Tipney

    #!/opt/cs/bin/python
    from Bio import Fasta
    from Bio.Blast import NCBIWWW
    import sys
    import getopt

    opts, args =
    getopt.getopt(sys.argv[1:],"",['program=','database=','format=','e
    ntrez_query='])

    print sys.argv
    print opts
(Continue reading)

Jeffrey Chang | 14 Jul 05:47 2004

Re: python newbies blast problem

Hello,

This is because the NCBI website is not really meant to be queried by 
computer scripts.  It looks like a recent change has broken the 
NCBIWWW.blast function.  Fortunately, NCBI does have a computer 
friendly BLAST API called QBLAST.  I added an interface to QBLAST into 
biopython called NCBIWWW.qblast.  Please get the updated version of the 
NCBIWWW.py from CVS, and replace NCBIWWW.blast with NCBIWWW.qblast in 
your script, and see if that fixes things.

The anonymous CVS is at:
http://cvs.biopython.org/

Jeff

On Jul 13, 2004, at 9:56 AM, h.j.tipney <at> stud.man.ac.uk wrote:

> Hi
> I posted this to the other mailing list and got no response so I'm
> hoping you guys can help me. I'm very new to programming and
> even newer to python, so I apologise in advance if this is a simple
> problem with an obvious solution but there are no python
> programmers
> near to help me. Anyway, I inherited the script below and have been
> using it on and off as part of a larger workflow. It has been running
> fine, but I ran it again last week and it didn't give the output I
> expected - it returned the 'your results will be updated in X seconds'
> page rather than the actual results. It has been a while since I had
> used this program and both blast and biopython had been updated
> so
(Continue reading)

bugzilla-daemon | 14 Jul 06:35 2004

[Bug 1667] New: PUBMED key collision in dbxref table

http://bugzilla.open-bio.org/show_bug.cgi?id=1667

           Summary: PUBMED key collision in dbxref table
           Product: Biopython
           Version: Not Applicable
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: BioSQL
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: open-bio <at> zesty.ca

I am using BioPython 1.30.

While loading records from the human genome into a MySQL database, BioSQL
causes the error: "Duplicate entry PUBMED-0 for key 2".

PUBMED appears in the dbxref table.  I looked at the code that inserts entries
into the dbxref table: the method _add_dbxref at line 97 of BioSQL/Loader.py.

_add_dbxref is called twice, at lines 333 and 336.  I believe the second call
has a bug, since both calls supply "reference.medline_id" as an argument.

            if reference.medline_id:
                dbxref_id = self._add_dbxref("MEDLINE",
                                             reference.medline_id, 0)
            elif reference.pubmed_id:
                dbxref_id = self._add_dbxref("PUBMED",
(Continue reading)

Hegedus, Tamas . | 15 Jul 20:58 2004

ModBioSQL release 0.12

Dear All,

Since I used Python and BioPython in my Modular BioSQL packege, my site would be interesting for you:
http://www.biomembrane.hu/~hegedus/modbiosql/

Best regards,
Tamas

--
Tamas Hegedus, Research Fellow | phone: 480-301-6041
Mayo Clinic Scottsdale         | fax:   480-301-7017
13000 E. Shea Blvd             | mailto:hegedus.tamas <at> mayo.edu
Scottsdale, AZ, 85259          | http://www.biomembrane.hu/~hegedus

Gmane