Mike Cariaso | 2 Oct 02:18 2004
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Missing windows installer on biopython.org/download

from http://www.biopython.org/files/ I can see that
there are precompiled binaries for windows. However
these are not linked to from the download page. Please
consider adding this.

=====
Mike Cariaso
Coleman, Michael | 5 Oct 00:29 2004

bug in FormatRegistry.py

Hi,

I ran into a bug in FormatRegistry.py just now.  In this function, the
reference to 'parent' is bogus.  I suspect it should be 'child'.

    def _build_child_path(self, format, visited=None):
        if visited is None:
            visited = {}
        if visited.has_key(format.name):
            return []
        format_list = [format]
        for child in getattr(format, 'objs', []):
            format_list.extend(self._build_child_path(parent, visited)) 
        return format_list

I ran into this while following this recipe

	http://www.biopython.org/docs/cookbook/genbank_to_fasta.html

Regards,
Mike

Mike Coleman, Scientific Programmer, +1 816 926 4419
Stowers Institute for Biomedical Research
1000 E. 50th St., Kansas City, MO  64110
Yves Bastide | 5 Oct 14:30 2004
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Spam, again

Hi all,

Seems there's been no thread recently on how unusable the list and its
archive are :-(... Either member-only posting and spam filtering are not
implemented or our community *is* the spammers

Regards,

yves
Yves Bastide | 5 Oct 14:34 2004
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Patch: data validation in Bio.Seq and Bio.MutableSeq

Attached patch adds a third parameter, "check", to Seq and MutableSeq's
constructors. If set, the data is checked against the alphabet.

Regards,

yves
Index: Bio/Seq.py
===================================================================
RCS file: /home/repository/biopython/biopython/Bio/Seq.py,v
retrieving revision 1.10
diff -u -p -r1.10 Seq.py
--- Bio/Seq.py	26 Aug 2004 13:22:58 -0000	1.10
+++ Bio/Seq.py	5 Oct 2004 12:28:10 -0000
 <at>  <at>  -4,12 +4,36  <at>  <at>  import Alphabet
 from Alphabet import IUPAC
 from Data.IUPACData import ambiguous_dna_complement, ambiguous_rna_complement

+def _check_data(data, alphabet):
+    """_check_data(data, alphabet) -> bool
+    
+    Check whether the data corresponds to the alphabet."""
+    if not data or not alphabet.letters:
+        return 1
+    if alphabet.size == 1:
+        import re
+        mo = re.match(r"^[%s]+$" % re.escape(alphabet.letters), data)
+        return mo is not None
+    else:
(Continue reading)

Jeffrey Chang | 5 Oct 20:52 2004

Re: bug in FormatRegistry.py

Good catch!  I've committed the fix in the CVS.

Jeff

On Oct 4, 2004, at 6:29 PM, Coleman, Michael wrote:

> Hi,
>
> I ran into a bug in FormatRegistry.py just now.  In this function, the
> reference to 'parent' is bogus.  I suspect it should be 'child'.
>
>     def _build_child_path(self, format, visited=None):
>         if visited is None:
>             visited = {}
>         if visited.has_key(format.name):
>             return []
>         format_list = [format]
>         for child in getattr(format, 'objs', []):
>             format_list.extend(self._build_child_path(parent, visited))
>         return format_list
>
> I ran into this while following this recipe
>
> 	http://www.biopython.org/docs/cookbook/genbank_to_fasta.html
>
> Regards,
> Mike
>
> Mike Coleman, Scientific Programmer, +1 816 926 4419
> Stowers Institute for Biomedical Research
(Continue reading)

selvam | 12 Oct 13:39 2004
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Proteins secondary structure using Python

Ø^OF¦
_______________________________________________
Biopython-dev mailing list
Biopython-dev <at> biopython.org
http://biopython.org/mailman/listinfo/biopython-dev
Michael Hoffman | 15 Oct 16:09 2004
Picon
Picon

Restricting this list to subscribers only

This has probably been asked before but can't we restrict submissions
to this list to subscribers only? The ham/spam ratio is pretty atrocious.
--

-- 
Michael Hoffman <hoffman <at> ebi.ac.uk>
European Bioinformatics Institute
IPSI-2005 | 21 Oct 22:30 2004
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Reminder, IPSI conferences, Hawaii and Amalfi (Italy), vip/bb

Dear potential speaker:

On behalf of the organizing committee, I would like to extend a cordial invitation for you to attend one or
both of the upcoming IPSI BgD Multidisciplinary (M.), Interdisciplinary (I.), and Transdisciplinary
(T.) conferences (the M.I.T. research approach).

Please note, all those who attended an IPSI conference once, always like to come back! If you have not
attended an IPSI conference so far, please check with those who did (you can find their names on our web).

The first will be in Hawaii:

IPSI-2005 HAWAII
Big Island Hawaii (arrival: 6 January 2005 / departure: 9 January 2005)
Deadlines: 20 October 2004 (abstract, only 100 words) / 20 November 2004 (full paper)

The second will be in Amalfi, Italy:

IPSI-2005 AMALFI
Amalfi, Italy (arrival: 17 February 2005 / departure: 20 February 2005.)
Deadlines: 30 October 2004 (abstract) / 10 December 2004 (full papers)

All IPSI BgD conferences are non-profit.  They bring together the elite of the world of science; so far, we
have had seven Nobel Laureates speaking at the opening ceremonies).  The conferences always take place in
some of the most attractive locations in the world.

These conferences are in line with the newest recommendations of the US National Science Foundation and
from the European Union to stress multidisciplinary, interdisciplinary, and transdisciplinary
research.  The speakers and activities at the conferences truly support this type of scientific interaction.

Topics of interest include, but are not limited to:
(Continue reading)

bugzilla-daemon | 25 Oct 12:56 2004

[Bug 1704] New: problem with Bio.Blast.NCBIStandalone

http://bugzilla.open-bio.org/show_bug.cgi?id=1704

           Summary: problem with Bio.Blast.NCBIStandalone
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: gebauer-jung <at> ice.mpg.de

If the blast database is generated using a GI-List via a *.nal file like that:

#
TITLE insects
#
DBLIST ./nr
#
GILIST insects.list
#

the database report at the end of the blast output file looks like that:

...

Query: 2656 accaacaaaaccaacatca 2674
            |||||||||||||||||||
(Continue reading)

bugzilla-daemon | 25 Oct 20:19 2004

[Bug 1706] New: Problem with the Swiss Prot parser

http://bugzilla.open-bio.org/show_bug.cgi?id=1706

           Summary: Problem with the Swiss Prot parser
           Product: Biopython
           Version: 1.24
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev <at> biopython.org
        ReportedBy: Biosql <at> hotmail.com

After installing the latest update of the Swiss Prot parser from cvs, I'm 
getting this error : 
Traceback (most recent call last):
  File "C:\Joe_script\Parser_Trembl.py", line 30, in ?
    cur_record = s_iterator.next()
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 166, in 
next  return self._parser.parse(File.StringHandle(data))
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 290, in 
parse  self._scanner.feed(handle, self._consumer)
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 332, in 
feed
    self._scan_record(uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 337, in 
_scan_record
    fn(self, uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 468, in 
(Continue reading)


Gmane