From biopython-bugs at bioperl.org Thu Sep 5 06:30:25 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] Notification: incoming/84 Message-ID: <200209051030.g85AUPIn027385@pw600a.bioperl.org> JitterBug notification new message incoming/84 Message summary for PR#84 From: "Expatriate Retirement Plans and Education Plans" Subject: Expatriate Education & Retirement Plans Date: Thu, 5 Sep 2002 16:32:00 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From info@expatsh.com Thu Sep 5 06:30:24 2002 Received: from 550e ([61.172.43.172]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g85AUIIn027381 for ; Thu, 5 Sep 2002 06:30:22 -0400 x-esmtp: 0 0 1 Message-ID: <2904187-220029458320200@expatsh.com> X-EM-Version: 6, 0, 1, 0 X-EM-Registration: #00F06206106618006920 X-Priority: 3 Reply-To: info@expatsh.com Errors-to: info@expatsh.com Organization: Expatriate Retirement Plans and Education Plans From: "Expatriate Retirement Plans and Education Plans" To: "biopython-bugs@bioperl.org" Subject: Expatriate Education & Retirement Plans Date: Thu, 5 Sep 2002 16:32:00 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_84815C5ABAF209EF376268C8" X-SMTPExp-Version: 1, 0, 2, 13 X-SMTPExp-Registration: 00B0320C107602006905 ------=_NextPart_84815C5ABAF209EF376268C8 Content-type: text/plain; charset="US-ASCII" Expatriate Retirement Plans and Education Fee Planning For Your Children If you are an Expatriate, with over seven years to go until your retirement, it is increasingly unlikely that you will receive your State Pension Plan. Also, if you have children and are a responsible parent, you will be amazed at what you should be saving for their future education. We have been advising Expatriates all over the world about their own personal retirement and education plans for decades now and if you would like an independent, obligation-free quotation as to what you should be saving towards each of those financial goals, please ... Click Here for a Retirement Plan Calculation or ... Click Here for an Education Plan Calculation Remember, your retirement is the longest holiday of your life, with all monies going out and nothing coming in - can you afford not to plan ahead? The greatest gift you can give your children is, Knowledge! If you do not wish to receive these e-mails, please click Here to and send a blank e-mail to Unsubscribe ------=_NextPart_84815C5ABAF209EF376268C8 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Untitled Document

Expatriate Retirement Plans and Education Fee Planning For Your Ch= ildren

If you are an Expatriate, with over seven years to go until y= our=20 retirement, it is increasingly unlikely that you will receive= your=20 State Pension Plan=2E Also, if you have children and are a res= ponsible=20 parent, you will be amazed at what you should be sav= ing=20 for their future education=2E

We have been advising Expatriates all over the world about their own = personal=20 retirement and education plans for decades now and if you would like a= n independent,=20 obligation-free quotation as to what you should be saving towards each= of=20 those financial goals, please =2E=2E=2E

Click Here= for a Retirement=20 Plan Calculation or =2E=2E=2E

Click H= ere for=20 an Education Plan Calculation

Remember, your retirement is the longest holiday= of your=20 life, with all monies going out and nothing coming in - can you afford= not=20 to plan ahead?

The greatest gift you can give your children is,= Knowledge!

If you do not wish to receive these e-mails, ple= ase click=20 Here= to and send a=20 blank e-mail to Unsubscribe

------=_NextPart_84815C5ABAF209EF376268C8-- From katel at worldpath.net Sat Sep 7 17:04:22 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] LocusLink Message-ID: <3D7A69D6.9050308@worldpath.net> Just added the parser for Locus webfiles. Cayte From jchang at smi.stanford.edu Tue Sep 10 02:39:16 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:15 2005 Subject: [Biopython-dev] large updates in CVS Message-ID: <20020909233916.D28155@springfield.stanford.edu> Hello everybody, I have just committed into CVS a reworking of the registry framework. That's the stuff that gets loaded into the Bio namespace. As before, you can do: krusty:~] jchang% python Python 2.2.1 (#1, 09/06/02, 17:02:21) [GCC Apple cpp-precomp 6.14] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Bio >>> Bio.formats Bio.dformats, exporting 'blast', 'blastn', 'blastp', 'blastx', 'embl', 'embl/65', 'empty', 'fasta', 'genbank', 'genbank-records', 'genbank-release', 'ncbi-blastn', 'ncbi-blastp', 'ncbi-blastx', 'ncbi-tblastn', 'ncbi-tblastx', 'search', 'sequence', 'swissprot', 'swissprot/38', 'swissprot/40', 'tblastn', 'tblastx', 'wu-blastn', 'wu-blastp', 'wu-blastx' >>> Bio.db db, exporting 'embl', 'embl-dbfetch-cgi', 'embl-ebi-cgi', 'embl-fast', 'embl-xembl-cgi', 'interpro-ebi-cgi', 'nucleotide-dbfetch-cgi', 'nucleotide-genbank-cgi', 'pdb', 'pdb-ebi-cgi', 'pdb-rcsb-cgi', 'prodoc-expasy-cgi', 'prosite-expasy-cgi', 'protein-genbank-cgi', 'swissprot', 'swissprot-expasy-cgi' >>> print Bio.db['swissprot']["P50105"].read()[:200] ID MPT1_YEAST STANDARD; PRT; 388 AA. AC P50105; DT 01-OCT-1996 (Rel. 34, Created) DT 01-OCT-1996 (Rel. 34, Last sequence update) DT 01-OCT-1996 (Rel. 34, Last annotation update) D >>> The differences are mostly internal. The Registry code has now been pulled out to make it easier to add new registries and new entries to registries. The DBRegistry has been slightly reworked from before, though. Similarly as before, the DBRegistry implements a dictionary-like interface to different kinds of databases. Now, the __getitem__ function will return a type native to the kind of database it is. For example, CGI databases return handles to the data and BioSQL will return a SeqRecord object. However, the DBRegistry objects now export a method: get_as(key, to_io) that will automatically convert the data to a specific type. >>> seq = Bio.db['swissprot'].get_as("P50105", SeqRecord.io) >>> print seq.seq Seq('MANSPKKPSDGTGVSASDTPKYQHTVPETKPAFNLSPGKASELSHSLPSPSQIKSTAHVS ...', SingleLetterAlphabet()) >>> This standardizes the data access across different kinds of databases. Please update your repositores with cvs update -P -d Please play around with this and let me know if anything has broken. One known issue is that some of the dbdefs need to be updated, due to changes in external web servers. Jeff From katel at worldpath.net Wed Sep 11 00:03:54 2002 From: katel at worldpath.net (katel@worldpath.net) Date: Sat Mar 5 14:43:16 2005 Subject: [Biopython-dev] LocusLink Message-ID: <174210-2200293114354247@M2W044.mail2web.com> I made some changes to fix bugs that further testing uncovered. Cayte -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From dyoo at acoma.Stanford.EDU Wed Sep 11 13:19:59 2002 From: dyoo at acoma.Stanford.EDU (Danny Yoo) Date: Sat Mar 5 14:43:16 2005 Subject: [Biopython-dev] Missing line in setup.py Message-ID: Hello! Since the registry changes, we need to add one more line to setup.py to get the bio.config installed. Here's the diff: ### [dyoo@tesuque biopython]$ cvs diff -u setup.py Index: setup.py =================================================================== RCS file: /home/repository/biopython/biopython/setup.py,v retrieving revision 1.49 diff -u -r1.49 setup.py --- setup.py 2002/08/21 20:05:21 1.49 +++ setup.py 2002/09/11 17:17:52 @@ -220,6 +220,7 @@ 'Bio.WWW', 'Bio.builders', 'Bio.builders.SeqRecord', + 'Bio.config', 'Bio.dbdefs', 'Bio.expressions', 'Bio.expressions.embl', ### Hope this helps! From biopython-bugs at bioperl.org Mon Sep 16 21:09:34 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:16 2005 Subject: [Biopython-dev] Notification: incoming/85 Message-ID: <200209170109.g8H19YIn014432@pw600a.bioperl.org> JitterBug notification new message incoming/85 Message summary for PR#85 From: "" Subject: Retirement & Education Fee Planning Date: Mon, 16 Sep 2002 16:47:39 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From info@expatsh.com Mon Sep 16 21:09:33 2002 Received: from 550e ([61.172.42.133]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g8H19KIn014428 for ; Mon, 16 Sep 2002 21:09:31 -0400 x-esmtp: 0 0 1 Message-ID: <1420592-22002911684739928@expatsh.com> X-EM-Version: 6, 0, 1, 0 X-EM-Registration: #00F06206106618006920 X-Priority: 3 Reply-To: info@expatsh.com Errors-to: info@expatsh.com Organization: Expatriate Finances From: "" To: "biopython-bugs@bioperl.org" Subject: Retirement & Education Fee Planning Date: Mon, 16 Sep 2002 16:47:39 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_84815C5ABAF209EF376268C8" X-SMTPExp-Version: 1, 0, 2, 13 X-SMTPExp-Registration: 00B0320C107602006905 ------=_NextPart_84815C5ABAF209EF376268C8 Content-type: text/plain; charset="US-ASCII" Expatriate Retirement Plans and Education Fee Planning For Your Children If you are an Expatriate, with over seven years to go until your retirement, it is increasingly unlikely that you will receive your State Pension Plan. Also, if you have children and are a responsible parent, you will be amazed at what you should be saving for their future education. We have been advising Expatriates all over the world about their own personal retirement and education plans for decades now and if you would like an independent, obligation-free quotation as to what you should be saving towards each of those financial goals, please ... Click Here for a Retirement Plan Calculation or ... Click Here for an Education Plan Calculation Remember, your retirement is the longest holiday of your life, with all monies going out and nothing coming in - can you afford not to plan ahead? The greatest gift you can give your children is, Knowledge! If you do not wish to receive these e-mails, please click Here to and send a blank e-mail to Unsubscribe ------=_NextPart_84815C5ABAF209EF376268C8 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Untitled Document

Expatriate Retirement Plans and Education Fee Planning For Your Ch= ildren

If you are an Expatriate, with over seven years to go until y= our=20 retirement, it is increasingly unlikely that you will receive= your=20 State Pension Plan=2E Also, if you have children and are a res= ponsible=20 parent, you will be amazed at what you should be sav= ing=20 for their future education=2E

We have been advising Expatriates all over the world about their own = personal=20 retirement and education plans for decades now and if you would like a= n independent,=20 obligation-free quotation as to what you should be saving towards each= of=20 those financial goals, please =2E=2E=2E

Click Here= for a Retirement=20 Plan Calculation or =2E=2E=2E

Click H= ere for=20 an Education Plan Calculation

Remember, your retirement is the longest holiday= of your=20 life, with all monies going out and nothing coming in - can you afford= not=20 to plan ahead?

The greatest gift you can give your children is,= Knowledge!

If you do not wish to receive these e-mails, ple= ase click=20 Here= to and send a=20 blank e-mail to Unsubscribe

------=_NextPart_84815C5ABAF209EF376268C8-- From jchang at smi.stanford.edu Sun Sep 22 03:32:28 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:16 2005 Subject: [Biopython-dev] updated db definitions Message-ID: <20020922003228.A68503@springfield.stanford.edu> Some of the database definitions in the db registry were out of date. For example, the prosite scripts were returning HTML rather than raw text. I have just fixed these and a few others and committed the fixes into the CVS. Please let me know if anything looks like out of whack. Jeff From jchang at smi.stanford.edu Sun Sep 22 03:33:34 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:16 2005 Subject: [Biopython-dev] Re: [BioPython] Blast/NCBIWWW parser Problems In-Reply-To: <200209200739.g8K7d9WB012893@mail1.dreamwiz.com>; from picxenk@dreamwiz.com on Fri, Sep 20, 2002 at 04:39:08PM +0900 References: <200209200739.g8K7d9WB012893@mail1.dreamwiz.com> Message-ID: <20020922003334.B68503@springfield.stanford.edu> This turned out to be because NCBI changed their format. The parser is fixed and committed. Jeff On Fri, Sep 20, 2002 at 04:39:08PM +0900, ?????? wrote: > Hi. > > Maybe.. Blast format changed again. > > I think, in NCBIWWW/_scan_one_pairwise_alignment method > "read_and_call_until(uhandle, consumer.noevent, contain='
')" is needed before read_and_call(....
).
> 
> and in NCBIWWW/_scan_alignment_header method
> alignment header can be three lines.
> so Parser can not find "Length =" string.
> 
> check it please.
> 
> I used Python 2.2 and biopython-1.00a4, of course with a updated NCBIWWW.py in CVS
> 
> 
> # by picxenk
> # picxenk@dreamwiz.com
> # picxenk@xenbio.net
> # http://xenbio.net
> # http://squeak.wo.to
>    
> 
> -------------------------------------------------
> DreamWiz Free Mail @ http://www.dreamwiz.com/
> DreamSearch Click the world!!! http://search.dreamwiz.com/
> 

From dlrubin at yahoo.com  Tue Sep 24 01:19:35 2002
From: dlrubin at yahoo.com (Daniel Rubin)
Date: Sat Mar  5 14:43:16 2005
Subject: [Biopython-dev] comile bug in _KDTree
Message-ID: <20020924051935.23062.qmail@web13908.mail.yahoo.com>

 I got a compile error (below) that seems to be from
the fact that a default 
 parameter is declared in both the header file &
implementation file for _KDTree
 (illegal). I fixed this by removing the default
assignment in the .h file, 
 and then the build worked. Who do I report this to?
 
 Thanks,
 Daniel
 
 gcc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC 
 -I/home/rubin/include/python2.2 -c
Bio/KDTree/_KDTree.C -o 
 build/temp.solaris-2.8-sun4u-2.2/_KDTree.o
 Bio/KDTree/_KDTree.C:277: default argument given for
parameter 2 of `int
     Region::test_intersection(Region*, float = 0)'
 Bio/KDTree/_KDTree.h:71: after previous specification
in `int
     Region::test_intersection(Region*, float = 0)'
 Bio/KDTree/_KDTree.C: In member function `void
     KDTree::neighbor_simple_search(float)':
 Bio/KDTree/_KDTree.C:912: warning: comparison between
signed and unsigned
     integer expressions
 Bio/KDTree/_KDTree.C:921: warning: comparison between
signed and unsigned
     integer expressions
 error: command 'gcc' failed with exit status 1

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From thamelry at vub.ac.be  Tue Sep 24 02:25:27 2002
From: thamelry at vub.ac.be (Thomas Hamelryck)
Date: Sat Mar  5 14:43:16 2005
Subject: [Biopython-dev] comile bug in _KDTree
In-Reply-To: <20020924051935.23062.qmail@web13908.mail.yahoo.com>
References: <20020924051935.23062.qmail@web13908.mail.yahoo.com>
Message-ID: <200209240620.g8O6KL702744@c3po.skynet.be>

>  I got a compile error (below) that seems to be from
> the fact that a default
>  parameter is declared in both the header file &
> implementation file for _KDTree
>  (illegal). I fixed this by removing the default
> assignment in the .h file,
>  and then the build worked. Who do I report this to?

Hi Daniel,

Thanks for the info. I'll take a look at it.

-Thomas

---
Thomas Hamelryck      Vrije Universiteit Brussel (VUB)
Intitute for Molecular Biology           ULTR Department
Paardenstraat 65   1640 Sint-Gensius-Rode    Belgium
              http://ultr.vub.ac.be/~thomas

From jchang at smi.stanford.edu  Tue Sep 24 02:31:35 2002
From: jchang at smi.stanford.edu (Jeffrey Chang)
Date: Sat Mar  5 14:43:16 2005
Subject: [Biopython-dev] NCBI scripts now using e-utils
Message-ID: <20020923233135.B73992@springfield.stanford.edu>

Hello everyone,

I've migrated all out libraries hitting NCBI (namely PubMed and
GenBank) to the new e-utils system.  This was necessary because
they're deprecating and removing the old scripts at the end of the
year.  The new stuff is supposed to be much more powerful, and support
more fancy queries such as restriction by date.  However, I cannot get
the date stuff on esearch.fcgi to work.  Has anyone had any experience
with this?

Jeff

From biopython-bugs at bioperl.org  Mon Sep 30 10:22:15 2002
From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org)
Date: Sat Mar  5 14:43:16 2005
Subject: [Biopython-dev] Notification: incoming/86
Message-ID: <200209301422.g8UEMFIn027341@pw600a.bioperl.org>

JitterBug notification

new message incoming/86

Message summary for PR#86
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