From biopython-bugs at bioperl.org Fri Feb 1 00:44:19 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Notification: incoming/57 Message-ID: <200202010544.g115iJEV002863@pw600a.bioperl.org> JitterBug notification new message incoming/57 Message summary for PR#57 From: "" Subject: Shanghai in February - So Much to See & Do Date: Fri, 1 Feb 2002 13:41:51 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From info@expatsh.com Fri Feb 1 00:44:18 2002 Received: from 550e ([61.171.94.171]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g115hxEV002857 for ; Fri, 1 Feb 2002 00:44:10 -0500 x-esmtp: 0 0 1 Message-ID: <614758-2200225154151456@expatsh.com> X-EM-Version: 6, 0, 1, 0 X-EM-Registration: #00F06206106618006920 X-Priority: 3 Reply-To: info@expatsh.com To: "Expat Shanghai" From: "" Subject: Shanghai in February - So Much to See & Do Date: Fri, 1 Feb 2002 13:41:51 +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" February in Shanghai It's Valentine's Day, it's Chinese New Year - it's February! Click Here to see Expat Shanghai's comprehensive list of what to see and do in February: Superbowl Live Brunch "Who Wants a Screw"? Party Rhythm of The Dance - Live Punchline Comedy Club Royal Drums Part II Shanghai Open 2002 - Snooker International Carpet Fair Women-Only Seminar from Triumph Bra's Swan Lake Saxophone & Catwalk Model Show China National Basketball Matches Fireworks Displays Discount Golf Days Health Foods Fair Mini Dress Evening Valentines Day Promotions Galoreto name but a few ..... Home Page|| Sitemap || A-Z Directory || OASIS Online || In Detail || Calendar of Events || Expat Links || Consulates || Emergency Contact Numbers || Clubs & Associations || Restaurants || Bars || Nightclubs|| Real Estate || Classifieds || Shopping || Art || Theatre || Golf Courses || Theme Parks || Newspapers from Home || Relocating to Shanghai?|| Online Help || Schools || Kindergarten || Universities|| |Markets || Latest Headlines || Newspapers || Live Cams || Lottery Results Please Click Here if you Do Not wish to Receive These E-Mails ------=_NextPart_84815C5ABAF209EF376268C8 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable =20 Shanghai Events
=20

February=20 in Shanghai

It's=20 Valentine's Day, it's Chinese New Year - it's February! Click Here=20 to see Expat Shanghai's comprehensive list of what to see and do in Februa= ry:=20

Superbowl=20 Live Brunch
<= B>"Who=20 Wants a Screw"? Party
Rhythm=20 of The Dance - Live
Punchline=20 Comedy Club
Royal=20 Drums Part II
Shanghai=20 Open 2002 - Snooker
International=20 Carpet Fair
<= B>Women-Only=20 Seminar from Triumph Bra's
Swan=20 Lake
Saxop= hone=20 & Catwalk Model Show
= China=20 National Basketball Matches
Fireworks=20 Displays
Discount=20 Golf Days
Health=20 Foods Fair
Mini=20 Dress Evening
Valentines=20 Day Promotions Galore
to=20 name but a few =2E=2E=2E=2E=2E
=20
= Home=20 Page|| Sitemap || A-Z=20 Directory || OASIS= Online=20 || In Detail ||=20 Calendar of Eve= nts || Expat=20 Links || Consulates=20 || Emergency=20 Contact Numbers || MESSAGE TRUNCATED AT 8192 <==== From katel at worldpath.net Fri Feb 1 22:15:08 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Dispath module Message-ID: <002101c1ab97$d2fd1fa0$010a0a0a@cadence.com> I've used Andrew's advice to rewrite the saf perser but I'm not sure how to hook it up to the Martel table. I've tried omitting the interest_tags and it just consumes the file without reaching the callbacks. If I specify the tags it wants handlers, without start and end, like with the old mechanism. I updated the latest Martel files. Looks like they were just uploaded.an hour ago. Cayte From adalke at mindspring.com Sat Feb 2 12:42:30 2002 From: adalke at mindspring.com (Andrew Dalke) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Fw: [ANN] HMM-0.1 Message-ID: <074301c1ac10$fd438780$0201a8c0@josiah.dalkescientific.com> I don't do HMMs but figured this might be useful, or at least interesting. Andrew -----Original Message----- From: Alexandre Fayolle Newsgroups: comp.lang.python Date: Thursday, January 31, 2002 8:30 AM Subject: [ANN] HMM-0.1 >hmm is a python module designed to work with Hidden Markov Models. >Usual algorithms (Viterbi, Baum-Welsh) are implemented using Numeric >Python. > >This module has been tested with Python 2.1 and NumPy-20.3, but it should >work with python 2.2. > >The home page of the project is http://www.logilab.org/hmm/ > >Discussions about hmm should take place on the ai-tools@logilab.org >mailing list. More information on the list can be found at >http://lists.logilab.org/mailman/listinfo/ai-tools/ > > >Alexandre Fayolle >-- >LOGILAB, Paris (France). >http://www.logilab.com http://www.logilab.fr http://www.logilab.org >Narval, the first software agent available as free software (GPL). From Y.Benita at pharm.uu.nl Tue Feb 5 09:42:50 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] GenBank parsing problem In-Reply-To: <20020130215309.88303.qmail@web20507.mail.yahoo.com> Message-ID: on 30/1/2002 22:53, Chunlei Wu at reillywu@yahoo.com wrote: > The current release of biopython 1.00a4 doesn't > include "Std.py" which needed by this new > genbank_format.py. Then I updated my biopython from > CVS including Martel and updated genbank_format.py to > 1.17. > 2. The code works fine under python shell This does not work for me. I updated genbank_format.py to 1.17 and also the __init__.py and Expression.py of Martel. Many attributes called from the init file are missing in the Expression.py file. What else do I need to update? Thanks, Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From reillywu at yahoo.com Tue Feb 5 11:18:09 2002 From: reillywu at yahoo.com (Chunlei Wu) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] GenBank parsing problem In-Reply-To: Message-ID: <20020205161809.80554.qmail@web20504.mail.yahoo.com> Hi, Yair, You may try a full update from CVS using a cvs tool. I use "cvs" under cygwin installed on win2000. hope it will help. Chunlei --- Yair Benita wrote: > on 30/1/2002 22:53, Chunlei Wu at reillywu@yahoo.com > wrote: > > > The current release of biopython 1.00a4 doesn't > > include "Std.py" which needed by this new > > genbank_format.py. Then I updated my biopython > from > > CVS including Martel and updated genbank_format.py > to > > 1.17. > > 2. The code works fine under python shell > > This does not work for me. I updated > genbank_format.py to 1.17 and also the > __init__.py and Expression.py of Martel. Many > attributes called from the > init file are missing in the Expression.py file. > What else do I need to > update? > Thanks, > Yair > -- > Yair Benita > Pharmaceutical Proteomics > Utrecht University > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev __________________________________________________ Do You Yahoo!? Send FREE Valentine eCards with Yahoo! Greetings! http://greetings.yahoo.com From scott at psel.uchc.edu Tue Feb 5 11:24:15 2002 From: scott at psel.uchc.edu (Scott Robson) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] GenBank parsing problem References: <20020205161809.80554.qmail@web20504.mail.yahoo.com> Message-ID: <3C6006DB.11FEFEA8@psel.uchc.edu> unsubscribe sweetsweet scott@psel.uchc.edu Chunlei Wu wrote: > Hi, Yair, > You may try a full update from CVS using a cvs > tool. I use "cvs" under cygwin installed on win2000. > > hope it will help. > > Chunlei > > --- Yair Benita wrote: > > on 30/1/2002 22:53, Chunlei Wu at reillywu@yahoo.com > > wrote: > > > > > The current release of biopython 1.00a4 doesn't > > > include "Std.py" which needed by this new > > > genbank_format.py. Then I updated my biopython > > from > > > CVS including Martel and updated genbank_format.py > > to > > > 1.17. > > > 2. The code works fine under python shell > > > > This does not work for me. I updated > > genbank_format.py to 1.17 and also the > > __init__.py and Expression.py of Martel. Many > > attributes called from the > > init file are missing in the Expression.py file. > > What else do I need to > > update? > > Thanks, > > Yair > > -- > > Yair Benita > > Pharmaceutical Proteomics > > Utrecht University > > > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > > __________________________________________________ > Do You Yahoo!? > Send FREE Valentine eCards with Yahoo! Greetings! > http://greetings.yahoo.com > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -- __________________________________ Scott Robson (PhD Student) Department of Biochemistry UConn Health Centre 263 Farmington Avenue Farmington, Connecticut 06032-3305 USA __________________________________ http://psel.uchc.edu/~scott for web page http://psel.uchc.edu/~scott/pubkey.txt for pgp key (in case you have something naughty to write to me) From scott at psel.uchc.edu Tue Feb 5 11:31:01 2002 From: scott at psel.uchc.edu (Scott Robson) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] No subject was specified. References: <20020205161809.80554.qmail@web20504.mail.yahoo.com> Message-ID: <3C600871.DD424007@psel.uchc.edu> unsubscribe sweetsweet scott@psel.uchc.edu Chunlei Wu wrote: > Hi, Yair, > You may try a full update from CVS using a cvs > tool. I use "cvs" under cygwin installed on win2000. > > hope it will help. > > Chunlei > > --- Yair Benita wrote: > > on 30/1/2002 22:53, Chunlei Wu at reillywu@yahoo.com > > wrote: > > > > > The current release of biopython 1.00a4 doesn't > > > include "Std.py" which needed by this new > > > genbank_format.py. Then I updated my biopython > > from > > > CVS including Martel and updated genbank_format.py > > to > > > 1.17. > > > 2. The code works fine under python shell > > > > This does not work for me. I updated > > genbank_format.py to 1.17 and also the > > __init__.py and Expression.py of Martel. Many > > attributes called from the > > init file are missing in the Expression.py file. > > What else do I need to > > update? > > Thanks, > > Yair > > -- > > Yair Benita > > Pharmaceutical Proteomics > > Utrecht University > > > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > > __________________________________________________ > Do You Yahoo!? > Send FREE Valentine eCards with Yahoo! Greetings! > http://greetings.yahoo.com > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -- __________________________________ Scott Robson (PhD Student) Department of Biochemistry UConn Health Centre 263 Farmington Avenue Farmington, Connecticut 06032-3305 USA __________________________________ http://psel.uchc.edu/~scott for web page http://psel.uchc.edu/~scott/pubkey.txt for pgp key (in case you have something naughty to write to me) From scott at psel.uchc.edu Tue Feb 5 11:33:24 2002 From: scott at psel.uchc.edu (Scott Robson) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] No subject was specified. References: <20020205161809.80554.qmail@web20504.mail.yahoo.com> <3C600871.DD424007@psel.uchc.edu> Message-ID: <3C6008FF.2414A3B@psel.uchc.edu> Sorry about the junk guys but how do I unsubscribe from this list? I can;t find out anywhere! Scott Robson wrote: > unsubscribe sweetsweet scott@psel.uchc.edu > > Chunlei Wu wrote: > > > Hi, Yair, > > You may try a full update from CVS using a cvs > > tool. I use "cvs" under cygwin installed on win2000. > > > > hope it will help. > > > > Chunlei > > > > --- Yair Benita wrote: > > > on 30/1/2002 22:53, Chunlei Wu at reillywu@yahoo.com > > > wrote: > > > > > > > The current release of biopython 1.00a4 doesn't > > > > include "Std.py" which needed by this new > > > > genbank_format.py. Then I updated my biopython > > > from > > > > CVS including Martel and updated genbank_format.py > > > to > > > > 1.17. > > > > 2. The code works fine under python shell > > > > > > This does not work for me. I updated > > > genbank_format.py to 1.17 and also the > > > __init__.py and Expression.py of Martel. Many > > > attributes called from the > > > init file are missing in the Expression.py file. > > > What else do I need to > > > update? > > > Thanks, > > > Yair > > > -- > > > Yair Benita > > > Pharmaceutical Proteomics > > > Utrecht University > > > > > > _______________________________________________ > > > Biopython-dev mailing list > > > Biopython-dev@biopython.org > > > http://biopython.org/mailman/listinfo/biopython-dev > > > > __________________________________________________ > > Do You Yahoo!? > > Send FREE Valentine eCards with Yahoo! Greetings! > > http://greetings.yahoo.com > > _______________________________________________ > > Biopython-dev mailing list > > Biopython-dev@biopython.org > > http://biopython.org/mailman/listinfo/biopython-dev > > -- > __________________________________ > Scott Robson (PhD Student) > Department of Biochemistry > UConn Health Centre > 263 Farmington Avenue > Farmington, Connecticut 06032-3305 USA > __________________________________ > > http://psel.uchc.edu/~scott for web page > http://psel.uchc.edu/~scott/pubkey.txt for pgp key > (in case you have something naughty to write to me) > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev -- __________________________________ Scott Robson (PhD Student) Department of Biochemistry UConn Health Centre 263 Farmington Avenue Farmington, Connecticut 06032-3305 USA __________________________________ http://psel.uchc.edu/~scott for web page http://psel.uchc.edu/~scott/pubkey.txt for pgp key (in case you have something naughty to write to me) From chapmanb at arches.uga.edu Tue Feb 5 11:37:14 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] No subject was specified. In-Reply-To: <3C6008FF.2414A3B@psel.uchc.edu> References: <20020205161809.80554.qmail@web20504.mail.yahoo.com> <3C600871.DD424007@psel.uchc.edu> <3C6008FF.2414A3B@psel.uchc.edu> Message-ID: <20020205113714.A678@ci350185-a.athen1.ga.home.com> > Sorry about the junk guys but how do I unsubscribe from this list? I > can;t find out anywhere! The easiest way is through the web interface at: http://biopython.org/mailman/listinfo/biopython-dev/ At the bottom of the page there is a place to get to your subscriber options, which will let you get your password and unsubscribe. HTH, Brad From katel at worldpath.net Tue Feb 5 19:51:40 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] ndb Message-ID: <003701c1aea8$fafe67c0$010a0a0a@cadence.com> I'd like to parse the output from the Nucleic Acid Database at rutgers. I'm still waiting for Ecell2 to answer a question I posted before I finish the documentation. Andrew, do you have any examples of using Dispatch? I don't understand the callback mechanism. Cayte From katel at worldpath.net Wed Feb 6 19:59:48 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] ECell Message-ID: <002401c1af72$bea06600$010a0a0a@cadence.com> I commited a new version because I fixed the documentation and added an explanation that the code . Cayte From katel at worldpath.net Wed Feb 6 20:49:52 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] jython Message-ID: <000901c1af79$bd6e2360$010a0a0a@cadence.com> jython is an open source java implementation of python that allows embedding and extending with java. I like java better than python when it comes to visualization and graphics. Cayte From reillywu at yahoo.com Wed Feb 6 19:22:39 2002 From: reillywu at yahoo.com (Chunlei Wu) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] GenBank parsing problem In-Reply-To: <20020130143917.A56849@ci350185-a.athen1.ga.home.com> Message-ID: <20020207002239.93057.qmail@web20503.mail.yahoo.com> Another GenBank parsing problem when parsing "S40706", which seems also related with "linear". >>> from Bio import GenBank >>> gi=GenBank.search_for('S40706')[0] >>> ncbi_dict=GenBank.NCBIDictionary(parser=GenBank.FeatureParser()) >>> ncbi_dict[gi] Traceback (most recent call last): File "", line 1, in ? File "C:\Python21\Bio\GenBank\__init__.py", line 1555, in __getitem__ return self.parser.parse(handle) File "C:\Python21\Bio\GenBank\__init__.py", line 268, in parse self._scanner.feed(handle, self._consumer) File "C:\Python21\Bio\GenBank\__init__.py", line 1250, in feed self._parser.parseFile(handle) File "C:\Python21\Martel\Parser.py", line 247, in parseFile self.parseString(fileobj.read()) File "C:\Python21\Martel\Parser.py", line 283, in parseString self._cont_handler.endDocument() File "C:\Python21\Bio\ParserSupport.py", line 311, in endDocument self._make_callback(self._previous_tag) File "C:\Python21\Bio\ParserSupport.py", line 300, in _make_callback callback_function(info_to_pass) File "C:\Python21\Bio\GenBank\__init__.py", line 984, in record_end raise ValueError("Could not determine alphabet for seq_type %s" ValueError: Could not determine alphabet for seq_type linear Chunlei --- Brad Chapman wrote: > Hi Chunlei; > > > Thank you for your fix. But it seems I can not > get > > the latest version of genbank_format.py from CVS. > The > > current one is still the old one ver. 1.16. Maybe > some > > delay of the server? > > Hmm, you're right. It still is 1.16. The anonymous > CVS normally syncs up > with the read/write access CVS in a few hours, so > maybe something is > wrong with anonymous CVS (most of the administrators > are having fun in > the sun in Arizona right now). > > Anyways, until the fix moves to anonymous CVS, you > can grab the changed > file from: > > http://www.bioinformatics.org/bradstuff/bp/genbank_format-1.17.py > > Sorry about the pain! > Brad > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev __________________________________________________ Do You Yahoo!? Send FREE Valentine eCards with Yahoo! Greetings! http://greetings.yahoo.com From katel at worldpath.net Thu Feb 7 19:06:11 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Ndb Message-ID: <005001c1b034$6b4d4aa0$010a0a0a@cadence.com> Ndb has a lot of sequences with more than 2 strands. Some of the sequences have 3 letter codes embedded in the ACGT alphabet. I wonder if these are annotation. One of these is YRR. After searching the internet I found that YRR and YRY are sometimes used to annotate parallel or antiparallel. There were other codes like D1T but I couldn't find any explanation. Should I assume these are annotation? Does anyone know what they are? Cayte From katel at worldpath.net Thu Feb 7 23:20:35 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Ndb References: <005001c1b034$6b4d4aa0$010a0a0a@cadence.com> Message-ID: <00a001c1b057$f5871ac0$010a0a0a@cadence.com> After checking further, I found that the codes were pdb hetero codes. But I still have the problem of representing mixed alphabets. Seq seems to assume equal sized elements. If all the letters are mashed together you won't be able to tell 3 letter codes from 1 letter codes. I'd appreciate your ideas on how to handle pdb mixins. One possibility is a hetero class with the pdb code plus its location on the sequence. Also I'm not sure if the mixin is treated as a residue a doc t I t the first or third residue? Cayte ----- Original Message ----- From: "Cayte" To: Sent: Thursday, February 07, 2002 4:06 PM Subject: [Biopython-dev] Ndb > Ndb has a lot of sequences with more than 2 strands. Some of the sequences > have 3 letter codes embedded in the ACGT alphabet. I wonder if these are > annotation. One of these is YRR. After searching the internet I found that > YRR and YRY are sometimes used to annotate parallel or antiparallel. There > were other codes like D1T but I couldn't find any explanation. Should I > assume these are annotation? Does anyone know what they are? > > Cayte > > _______________________________________________ From Y.Benita at pharm.uu.nl Fri Feb 8 09:12:37 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Bugs fixed in MacBiopython Message-ID: Hi guys, I have updated the MacPython version: 1. Some problems concerning urllib related to the Mac platform were fixed. 2. GenBank parsing problem was fixed. Updated version can be downloaded from: http://homepage.mac.com/ybenita Please post that one on the web page. Thanks, Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From katel at worldpath.net Fri Feb 8 23:58:35 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Ndb Message-ID: <002301c1b126$6eff8e40$010a0a0a@cadence.com> My idea for representing DNA-RNA complexes is a nested structure. The top level class would contain a class called chain because Ndb decomposes the structures into chains, similar to strands except there may be more than 2.. Each chain would be composed of regions. A region could be a DNA or RNA sequence.or a hetero. A new class called Hetero would be required. If others have ideas I'd like to hear them. Cayte From biopython-bugs at bioperl.org Fri Feb 8 21:48:27 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Notification: incoming/58 Message-ID: <200202090248.g192mRkO026964@pw600a.bioperl.org> JitterBug notification new message incoming/58 Message summary for PR#58 From: "Expat Shanghai" Subject: Expat Shanghai - The Latest Information on Shanghai Date: Sat, 9 Feb 2002 10:53:08 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From info@expatsh.com Fri Feb 8 21:48:27 2002 Received: from 550e ([61.171.85.51]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g192m6kO026958 for ; Fri, 8 Feb 2002 21:48:19 -0500 x-esmtp: 0 0 1 Message-ID: <2943061-220022692538841@expatsh.com> X-EM-Version: 6, 0, 1, 0 X-EM-Registration: #00F06206106618006920 X-Priority: 3 Reply-To: info@expatsh.com To: "Shanghai" From: "Expat Shanghai" Subject: Expat Shanghai - The Latest Information on Shanghai Date: Sat, 9 Feb 2002 10:53:08 +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" Expat Shanghai - Classifieds & Online Ordering Our OASIS Online Ordering Section is a COMPLETELY FREE Section whereby you can order the following Online: Apartment Finder - Find The Latest Apartments for Rent in Shanghai - you tell us what you want and we will find it for you Reserve a Restaurant Table Online - Reserve a Restaurant Table Via Us - Free of Charge Book A Round of Golf Online - At any of Shanghai's 16 Golf Courses Relocation Information - Find Out Everything You Want To Ask Before You Arrive Financial Information - Find Our About Finance Before You Arrive Holiday Quotations Online - Get a variety of Holiday Quotations Online through us Free of Charge Car Finder - Tell Us Your Vehicle Rental/Sale needs and We Will Find One for You Get Help For ANYTHING Online - Got a question about Shanghai? - Let Us Solve It Our Classifieds Section is a COMPLETELY FREE Section whereby you can advertise any of the following free of charge to a weekly audience of over 150,000 in Shanghai: (Just Click on Any Below to See) Looking For Love - Find Love, Friendship or Even Marriage Here Jobs Wanted - Offer Your Resume/CV to Potential Employee's Jobs Offered - Let Shanghai Job-Seekers Know if You Have a Job Latest Apartments For Rent - Advertise Your Apartment/Villa For Rent - FREE of Charge Buy/Sell Something - Want to Sell Something or Buy Something - Advertise Here Tell Other Expats - Tell Others in Shanghai Anything Interesting They Might Want to Know Rehouse Your Ayi - Recommend a Good Ayi to Others if You Are Leaving Shanghai Home Page|| Sitemap || A-Z Directory || OASIS Online || In Detail || Calendar of Events || Expat Links || Consulates || Emergency Contact Numbers || Clubs & Associations || Restaurants || Bars || Nightclubs|| Real Estate || Classifieds || Shopping || Art || Theatre || Golf Courses || Theme Parks || Newspapers from Home || Relocating to Shanghai?|| Shanghai Chat || Online Help || Schools || Kindergarten || Universities|| |Markets || Latest Headlines || Newspapers || Live Cams || Lottery Results Please Click Here if you Do Not wish to Receive These E-Mails ------=_NextPart_84815C5ABAF209EF376268C8 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Expat Shanghai =20
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= Home=20 Page|| Sitemap || A-Z=20 Directory || OASIS= Online=20 || In Detail ||=20 Calendar of Eve= nts || Expat=20 Links || ====> MESSAGE TRUNCATED AT 8192 <==== From biopython-bugs at bioperl.org Thu Feb 14 05:06:33 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Notification: incoming/59 Message-ID: <200202141006.g1EA6XkO031780@pw600a.bioperl.org> JitterBug notification new message incoming/59 Message summary for PR#59 From: stephan@proceryon.at Subject: IndentationError Date: Thu, 14 Feb 2002 05:06:29 -0500 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From stephan@proceryon.at Thu Feb 14 05:06:33 2002 Received: from localhost (localhost [127.0.0.1]) by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g1EA6TkO031776 for ; Thu, 14 Feb 2002 05:06:33 -0500 Date: Thu, 14 Feb 2002 05:06:29 -0500 Message-Id: <200202141006.g1EA6TkO031776@pw600a.bioperl.org> From: stephan@proceryon.at To: biopython-bugs@bioperl.org Subject: IndentationError Full_Name: stephan Module: SProt.py Version: biopython-1.00a4 OS: linux Submission from: ns.proceryon.at (195.70.106.242) Traceback (most recent call last): File "sprot.py", line 3, in ? from Bio.SwissProt import SProt File "/home/people/share/sw/external/src/biopython-1.00a4/Bio/SwissProt/SProt.py", line 554 self.data.annotation_update = cols[1], int(self._chomp(cols[3])) #<= ^ IndentationError: expected an indented block Note: why don't you just use all-tabs for indentation? We do this since some time as it just makes life so much easier!! From chapmanb at arches.uga.edu Thu Feb 14 08:55:55 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Notification: incoming/59 In-Reply-To: <200202141006.g1EA6XkO031780@pw600a.bioperl.org> References: <200202141006.g1EA6XkO031780@pw600a.bioperl.org> Message-ID: <20020214085555.A67225@ci350185-a.athen1.ga.home.com> Hi Stephan; > JitterBug notification > new message incoming/59 [...] > Traceback (most recent call last): > File "sprot.py", line 3, in ? > from Bio.SwissProt import SProt > File "/home/people/share/sw/external/src/biopython-1.00a4/Bio/SwissProt/SProt.py", > line 554 > self.data.annotation_update = cols[1], int(self._chomp(cols[3])) #<= > ^ > IndentationError: expected an indented block I'm confused. I can't reproduce this error with release 1.00a4 on either UNIX (FreeBSD) or Windows. It looks like the line that causes the problem is on 534 in the original file, so I guess you have been modifying this file? > Note: why don't you just use all-tabs for indentation? > We do this since some time as it just makes life so much > easier!! As far as I know, we all tend to use the all-spaces style. This has the advantage of looking exactly the same in all editors, and I think is the way code in the main python distribution is being written. The more popular unix editors like emacs and vim do the 4 spaces indentation automagically. Anyways, it's all a matter of preference. If you have been mixing spaces and tabs in the code that is going to cause the indentation problems. You can do: python -t to look for tab/space mixing problems. Python comes with Tools/scripts/untabify.py, which can convert tabs and spaces, and you can also do this in text editors, etc. Hope this helps! Brad From biopython-bugs at bioperl.org Mon Feb 18 20:20:21 2002 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Notification: incoming/60 Message-ID: <200202190120.g1J1KLkO013300@pw600a.bioperl.org> JitterBug notification new message incoming/60 Message summary for PR#60 From: "International Financial Services Shanghai" Subject: Financial Services in Shanghai Date: Tue, 19 Feb 2002 09:23:55 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From apage@online.sh.cn Mon Feb 18 20:20:21 2002 Received: from 550e ([61.171.85.219]) by pw600a.bioperl.org (8.12.2/8.12.2) with SMTP id g1J1KGkO013296 for ; Mon, 18 Feb 2002 20:20:19 -0500 x-esmtp: 0 0 1 Message-ID: <1044690-22002221912355315@online.sh.cn> X-EM-Version: 6, 0, 1, 0 X-EM-Registration: #00F06206106618006920 X-Priority: 3 Reply-To: apage@online.sh.cn To: "Shanghai" From: "International Financial Services Shanghai" Subject: Financial Services in Shanghai Date: Tue, 19 Feb 2002 09:23:55 +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" This leaflet is designed using Macromedia Flash, If you cannot see the leaflet below, please click Here Home Page|| Sitemap || A-Z Directory || OASIS Online || In Detail || Calendar of Events || Expat Links || Consulates || Emergency Contact Numbers || Clubs & Associations || Restaurants || Bars || Nightclubs|| Real Estate || Classifieds || Shopping || Art || Theatre || Golf Courses || Theme Parks || Newspapers from Home || Relocating to Shanghai?|| Shanghai Chat || Online Help || Schools || Kindergarten || Universities|| |Markets || Latest Headlines || Newspapers || Live Cams || Lottery Results ------=_NextPart_84815C5ABAF209EF376268C8 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Financial Services in Shanghai =20

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Home=20 Page|| Sitemap || A-Z=20 Directory || OASIS= Online=20 || In Detail ||=20 Calendar of Eve= nts || Expat=20 Links || Consulates=20 || Emergency=20 Contact Numbers || Clubs=20 & Associations || Restaurants=20 || Bars<= /A>=20 || Nightclubs||=20 Real=20 Estate || Classif= ieds ||=20 Shopping=20 || Art=20 ||=20 Theatre=20 ||=20 Golf Courses=20 || Theme Parks=20 || Newspapers=20 from Home || Relocating=20 to Shanghai?|| Shanghai=20 Chat || Onl= ine Help=20 || Schools=20 || Kindergarten=20 || Universities||=20 |Markets=20 || Latest=20 Headlines ||=20 New= spapers=20 ||= =20 Live=20 Cams=20 ||=20 MESSAGE TRUNCATED AT 8192 <==== From katel at worldpath.net Wed Feb 20 19:39:23 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Ndb support Message-ID: <001e01c1ba70$369c4900$010a0a0a@cadence.com> To support Ndb, I added some modules that represent structures with a mix of DNA, RNA, amino acids and pdb hetero codes. I encourage suggestions to make the modules more useful and general purpose. Cayte From Y.Benita at pharm.uu.nl Mon Feb 25 03:11:48 2002 From: Y.Benita at pharm.uu.nl (Yair Benita) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] Neural Networks Message-ID: Dear Brad, I see you added a new Neural Network module. Do you have some documentation for it? Yair -- Yair Benita Pharmaceutical Proteomics Utrecht University From katel at worldpath.net Wed Feb 27 00:21:53 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] CVS tree Message-ID: <003701c1bf4e$abaed2c0$010a0a0a@cadence.com> Is the tree automatically updated? I don't see my newest commits. Cayte From jchang at smi.stanford.edu Wed Feb 27 00:43:11 2002 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] CVS tree In-Reply-To: <003701c1bf4e$abaed2c0$010a0a0a@cadence.com> References: <003701c1bf4e$abaed2c0$010a0a0a@cadence.com> Message-ID: <20020226214311.A932@krusty.stanford.edu> Your changes should be reflected in the read/write tree immediately. The anonymous one gets sync'd once a day, I think. Jeff On Tue, Feb 26, 2002 at 09:21:53PM -0800, Cayte wrote: > Is the tree automatically updated? I don't see my newest commits. > > Cayte > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From katel at worldpath.net Wed Feb 27 16:51:04 2002 From: katel at worldpath.net (Cayte) Date: Sat Mar 5 14:43:11 2005 Subject: [Biopython-dev] GEO Message-ID: <000b01c1bfd8$dd47dcc0$010a0a0a@cadence.com> My next plan is to write a parser for Gene Expression Omnibus. GEO is used for microarrays, a hot new technology If anyone has started the same project, now is the time to let me know, to avoid duplication Cayte