From cariaso at yahoo.com Fri Oct 1 20:18:55 2004 From: cariaso at yahoo.com (Mike Cariaso) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Missing windows installer on biopython.org/download Message-ID: <20041002001855.60451.qmail@web52703.mail.yahoo.com> 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 From MKC at Stowers-Institute.org Mon Oct 4 18:29:56 2004 From: MKC at Stowers-Institute.org (Coleman, Michael) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] bug in FormatRegistry.py Message-ID: <200410042229.i94MTDKr003235@portal.open-bio.org> 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 From Yves.Bastide at irisa.fr Tue Oct 5 08:30:10 2004 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Spam, again Message-ID: <416293D2.4000901@irisa.fr> 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 From Yves.Bastide at irisa.fr Tue Oct 5 08:34:36 2004 From: Yves.Bastide at irisa.fr (Yves Bastide) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Patch: data validation in Bio.Seq and Bio.MutableSeq Message-ID: <416294DC.5070202@irisa.fr> Attached patch adds a third parameter, "check", to Seq and MutableSeq's constructors. If set, the data is checked against the alphabet. Regards, yves -------------- next part -------------- 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 @@ -4,12 +4,36 @@ 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: + for ch in data: + if ch not in alphabet.letters: + return 0 + return 1 + class Seq: - def __init__(self, data, alphabet = Alphabet.generic_alphabet): + """Seq(data[, alphabet, [check]]) -> Seq object. + + Create a sequence. the alphabet describes how to interpret the + data's individual characters. Be default, no checking is done on + the data's validity. + """ + def __init__(self, data, alphabet=Alphabet.generic_alphabet, check=0): # Enforce string storage assert (type(data) == type("") or # must use a string type(data) == type(u"")) # but can be a unicode string + if check and not _check_data(data, alphabet): + raise TypeError, "invalid data" self.data = data # Seq API requirement self.alphabet = alphabet # Seq API requirement @@ -44,7 +68,7 @@ class Seq: elif other.alphabet.contains(self.alphabet): return self.__class__(self.data + other.data, other.alphabet) else: - raise TypeError, ("incompatable alphabets", str(self.alphabet), + raise TypeError, ("incompatible alphabets", str(self.alphabet), str(other.alphabet)) def __radd__(self, other): if self.alphabet.contains(other.alphabet): @@ -52,7 +76,7 @@ class Seq: elif other.alphabet.contains(self.alphabet): return self.__class__(other.data + self.data, other.alphabet) else: - raise TypeError, ("incompatable alphabets", str(self.alphabet), + raise TypeError, ("incompatible alphabets", str(self.alphabet), str(other.alphabet)) @@ -119,11 +143,13 @@ class Seq: class MutableSeq: - def __init__(self, data, alphabet = Alphabet.generic_alphabet): - if type(data) == type(""): - self.data = array.array("c", data) + def __init__(self, data, alphabet=Alphabet.generic_alphabet, check=0): + if check and not _check_data(data, alphabet): + raise TypeError, "invalid data" + if isinstance(data, array.array): + self.data = data else: - self.data = data # assumes the input is an array + self.data = array.array("c", data) # assume convertibility self.alphabet = alphabet def __repr__(self): return "%s(%s, %s)" % (self.__class__.__name__, @@ -176,7 +202,7 @@ class MutableSeq: elif other.alphabet.contains(self.alphabet): return self.__class__(self.data + other.data, other.alphabet) else: - raise TypeError, ("incompatable alphabets", str(self.alphabet), + raise TypeError, ("incompatible alphabets", str(self.alphabet), str(other.alphabet)) def __radd__(self, other): if self.alphabet.contains(other.alphabet): @@ -184,7 +210,7 @@ class MutableSeq: elif other.alphabet.contains(self.alphabet): return self.__class__(other.data + self.data, other.alphabet) else: - raise TypeError, ("incompatable alphabets", str(self.alphabet), + raise TypeError, ("incompatible alphabets", str(self.alphabet), str(other.alphabet)) def append(self, c): From jeffrey.chang at duke.edu Tue Oct 5 14:52:56 2004 From: jeffrey.chang at duke.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] bug in FormatRegistry.py In-Reply-To: <200410042229.i94MTDKr003235@portal.open-bio.org> References: <200410042229.i94MTDKr003235@portal.open-bio.org> Message-ID: 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 > 1000 E. 50th St., Kansas City, MO 64110 > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev From winselvam at hotmail.com Tue Oct 12 07:39:52 2004 From: winselvam at hotmail.com (selvam) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Proteins secondary structure using Python Message-ID: <416BC288.000003.98637@O3G4L7> Dear Sirs, I am a beginner in the field of Bioinformatics. When I was browsing the web, I found about your Python language. As a biologist, I am interested to know whether one can use Python to predict the secondary structure of proteins. If so, kindly send me the relevant details on how to do it as I am interested to work on this area for my projects. Thanking you in advance. With regards, R.Selvam. From hoffman at ebi.ac.uk Fri Oct 15 10:09:18 2004 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Restricting this list to subscribers only Message-ID: 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 European Bioinformatics Institute From hawaii2005 at vreme.yubc.net Thu Oct 21 16:30:10 2004 From: hawaii2005 at vreme.yubc.net (IPSI-2005) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] Reminder, IPSI conferences, Hawaii and Amalfi (Italy), vip/bb Message-ID: <200410212030.i9LKUANf021653@vreme.yubc.net> 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: * Internet * Computer Science and Engineering * Management and Business Administration * Education * e-Medicine * Electrical Engineering * Bioengineering * Environmental Protection * e-Economy. * Social Impacts of e-World If you would like more information on either conference, please reply to this e-mail message (one can also find more information on the web). If you plan to submit an abstract and paper, please let us know immediately for planning purposes. Sincerely Yours, Prof. V. Milutinovic Chairman IPSI BgD Conferences * * * CONTROLLING OUR E-MAILS TO YOU * * * If you would like to continue to be informed about future IPSI BgD conferences, please reply to this e-mail message with a subject line of SUBSCRIBE. If you would like to be removed from our mailing list, please reply to this e-mail message with a subject line of REMOVE. From bugzilla-daemon at portal.open-bio.org Mon Oct 25 06:56:56 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1704] New: problem with Bio.Blast.NCBIStandalone Message-ID: <200410251056.i9PAuu3G007727@portal.open-bio.org> 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@biopython.org ReportedBy: gebauer-jung@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 ||||||||||||||||||| Sbjct: 85 accaacaaaaccaacatca 67 Subset of the database(s) listed below Number of letters searched: 562,618,960 Number of sequences searched: 228,924 Database: insects Posted date: Oct 17, 2004 10:00 PM Number of letters in database: 3,987,564,307 Number of sequences in database: 991,337 Database: /bio/blast/./nt.01 Posted date: Oct 17, 2004 11:04 PM Number of letters in database: 3,989,920,418 Number of sequences in database: 760,163 Database: /bio/blast/./nt.02 Posted date: Oct 18, 2004 2:00 AM Number of letters in database: 3,989,747,597 Number of sequences in database: 888,596 Database: /bio/blast/./nt.03 Posted date: Oct 15, 2004 1:00 AM Number of letters in database: 14,716,213 Number of sequences in database: 1558 Lambda K H 1.37 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 ... The 'Subset of the database(s) ...' line lets _Scanner._scan_database_report() crash. Even Bio.Blast.Record cannot keep such data. (If there was some need to do so.) As a work-around I suggest the following change in Bio.Blast.NCBIStandalone.py: 422,423c422,432 < while 1: < read_and_call(uhandle, consumer.database, start=' Database') --- > > while 1: > # read_and_call(uhandle, consumer.database, start=' Database') > # work-around to skip: > # Subset of the database(s) listed below > # Number of letters searched: 562,618,960 > # Number of sequences searched: 228,924 > # > # even Record.DatabaseRecord does not contain any structure to keep this stuff > read_and_call_until(uhandle, consumer.database, start=' Database') > ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Oct 25 14:19:03 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1706] New: Problem with the Swiss Prot parser Message-ID: <200410251819.i9PIJ3VN019302@portal.open-bio.org> 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@biopython.org ReportedBy: Biosql@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 _scan_sq self._scan_line('SQ', uhandle, consumer.sequence_header, exactly_one=1) File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 359, in _scan_line read_and_call(uhandle, event_fn, start=line_type) File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 300, in read_and_call raise SyntaxError, errmsg SyntaxError: Line does not start with 'SQ': RA Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S., ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Oct 25 14:47:55 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1706] Problem with the Swiss Prot parser Message-ID: <200410251847.i9PIltew019697@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1706 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Additional Comments From jchang@biopython.org 2004-10-25 14:47 ------- Try grabbing the latest Bio/SwissProt/SProt.py file from the CVS (cvs.biopython.org). There's been some fixes to the parser, which might fix your problem. If it does not, then please send some sample code and data file. Jeff ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Oct 25 14:51:49 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:54 2005 Subject: [Biopython-dev] [Bug 1704] problem with Bio.Blast.NCBIStandalone Message-ID: <200410251851.i9PIpneU019717@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1704 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- Additional Comments From jchang@biopython.org 2004-10-25 14:51 ------- There has been some fixes to the Database parsing code recently. Please try the Bio/Blast/ NCBIStandalone.py file from the CVS (cvs.biopython.org) and see if that works around your problem. If not, please send some sample BLAST output that is causing the problems. Jeff ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.