From ecky.l at gmx.de Mon Nov 3 19:48:20 2003 From: ecky.l at gmx.de (Eckhard Lehmann) Date: Mon Nov 3 19:45:06 2003 Subject: [BioPython] how to set proxy for Bio.WWW Message-ID: <31155.1067906900@www3.gmx.net> Hi, I want to fetch protein entries from Swissprot, but therefore I need to tell BioPython my proxy server + proxy username and password. Has anyone an idea how to do this? Thanks much in advance, Eckhard From dalke at dalkescientific.com Tue Nov 4 01:38:32 2003 From: dalke at dalkescientific.com (Andrew Dalke) Date: Tue Nov 4 01:35:04 2003 Subject: [BioPython] how to set proxy for Bio.WWW In-Reply-To: <31155.1067906900@www3.gmx.net> Message-ID: <820A8B01-0E91-11D8-B7FA-000393C92466@dalkescientific.com> Eckhard Lehmann: > I want to fetch protein entries from Swissprot, but therefore I need > to tell > BioPython my proxy server + proxy username and password. > > Has anyone an idea how to do this? Bio.WWW uses the urllib module to fetch the entries. There's no provision to pass in a set of proxies (though that would be realtively easy to add). Instead, you'll need to change the default way it handles proxies, which is different for different OSes. See http://www.python.org/doc/current/lib/module-urllib.html For unix, set the environment variable 'http_proxy' to the proxy, as http://username:password@hostname/ ... I think. However, looking at the code I can't tell if it actually supports proxies which require an authenticated user name. It doesn't seem to, and the search of the back usenet posts suggests that it does not. It does seem that urllib2 supports proxies with passwords. I think you're going to have to experiment a bit. If setting the system proxy (eg, through an env variable) doesn't work then try having Bio.WWW.ExPASy first 'import urllib2' and replace the urllib.urlopen with urllib2.urlopen Andrew dalke@dalkescientific.com From sbassi at asalup.org Tue Nov 4 15:13:13 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Tue Nov 4 15:06:18 2003 Subject: [BioPython] Tm for BioPython Message-ID: <3FA80859.3030204@asalup.org> I want to write a DNA melting temperature (Tm) calculator function for BioPython. The problem is that different programs use diferent formulae to get the Tm. GCG uses: Proc.Natl. Acad. Sci. USA. 95; 1460-1465 (1986)): T(m)(oligo) = delta H / ((delta S' + R x ln(c/4)) - 273.15 where delta H is the enthalpy of helix formation, delta S' is the salt-adjusted entropy of helix formation (including helix initiation), R is the molar gas constant (1.987 cal/degree Celsius/mol), and c is the oligonucleotide concentration. The salt-adjusted delta S' is determined from the delta S at 1M salt according to the equation: delta S' = delta S + (0.368 x (oligo_length - 1) x ln[K(+)]) where [K(+)] is the potassium ion concentration. ACCCTTCAGCAGTTCCACAC = 54.3 C DAN (from EMBOSS) uses: Breslauer, K.J., Frank, R., Blocker, H., and Marky, L.A. (1986). "Predicting DNA Duplex Stability from the Base Sequence." Proceedings of the National Academy of Sciences USA 83, 3746-3750. from the source code: if(isproduct) { TmP1 = 81.5 + 16.6 * (float)log10((double)(salt/1000.0)) + 0.41 * cga[*np]; TmP2 = -(0.65 * formamide) - (675.0/fprodlen) - mismatch; tpa[*np] = TmP1 + TmP2; ACCCTTCAGCAGTTCCACAC = 59.2 C ggtaccgctggccgagcatc = 64.9 C Primer3 also has diferent numbers. I also have some working code on Python, but I'd like Brad, Jeff or somebody to tell me witch ecuation to use. All the thermodynamic constants seems to agree in diferent works, so the only problem is the main formaulae. -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From jeffrey.chang at duke.edu Tue Nov 4 17:02:31 2003 From: jeffrey.chang at duke.edu (Jeffrey Chang) Date: Tue Nov 4 16:55:54 2003 Subject: [BioPython] Tm for BioPython In-Reply-To: <3FA80859.3030204@asalup.org> References: <3FA80859.3030204@asalup.org> Message-ID: <20031104220231.GA2880@springfield.stanford.edu> On Tue, Nov 04, 2003 at 05:13:13PM -0300, Sebastian Bassi wrote: > I want to write a DNA melting temperature (Tm) calculator function for > BioPython. > The problem is that different programs use diferent formulae to get the Tm. > > GCG uses: [...] > > > DAN (from EMBOSS) uses: [...] > Primer3 also has diferent numbers. > > I also have some working code on Python, but I'd like Brad, Jeff or > somebody to tell me witch ecuation to use. All the thermodynamic > constants seems to agree in diferent works, so the only problem is the > main formaulae. Just pick any one you'd like! :) Having one function does not preclude any of the others. Since the answers are different, and presumably each has its advantages, I would not object to including multiple implementations in Biopython. We could have all 3 functions: Tm_gcg Tm_dan Tm_primer3 So just go ahead and pick your favorite one. Jeff From ecky.l at gmx.de Tue Nov 4 17:03:35 2003 From: ecky.l at gmx.de (Eckhard Lehmann) Date: Tue Nov 4 17:00:17 2003 Subject: [BioPython] how to set proxy for Bio.WWW References: <820A8B01-0E91-11D8-B7FA-000393C92466@dalkescientific.com> Message-ID: <4437.1067983415@www1.gmx.net> > Eckhard Lehmann: > > I want to fetch protein entries from Swissprot, but therefore I need > > to tell > > BioPython my proxy server + proxy username and password. > > > > Has anyone an idea how to do this? > > For unix, set the environment variable 'http_proxy' to the > proxy, as http://username:password@hostname/ ... I think. I have managed the auth proxy access by "installing" Jeff Epplers patch (http://mail.python.org/pipermail/python-list/2000-January/021435.html, and slightly modified it for Python 2.3, which I use). Now it works on windows too with a proxy variable setting like http://username:password@hostname:port/ But it's funny that this patch wasn't applied in the official source of python - it is in fact very easy to add proxy auth support in this way and it does not that big changes to urllib... > not. It does seem that urllib2 supports proxies with passwords. I had a look at urllib2 too, but it seems a bit overcrowded for simply and only accessing an auth proxy. That is the first case, where I have to say that it is better arranged in perl and LWP. But its also the only case yet ;-). Ecky ;) From Cary.Miller at uchsc.edu Wed Nov 5 21:38:13 2003 From: Cary.Miller at uchsc.edu (Cary Miller) Date: Wed Nov 5 21:34:52 2003 Subject: [BioPython] connecting to biomoby Message-ID: Hi all, I am attempting to contact biomoby with xmlrpclib and SOAPpy. It's not totally clear where the server lives so I have tried 3 urls. http://mobycentral.cbr.nrc.ca/MOBY/Central http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl http://192.168.1.9/cgi-bin/MOBY-Central.pl Each of these seems to connect with my client but then fails when the request is sent. Do I have the wrong url, wrong function call or what? >>> import xmlrpclib >>> url = "http://mobycentral.cbr.nrc.ca/MOBY/Central" >>> server = xmlrpclib.ServerProxy(url) >>> foo = server.retrieveServiceNames() Traceback (most recent call last): File "", line 1, in ? File "/usr/local/lib/python2.3/xmlrpclib.py", line 1029, in __call__ return self.__send(self.__name, args) File "/usr/local/lib/python2.3/xmlrpclib.py", line 1316, in __request verbose=self.__verbose File "/usr/local/lib/python2.3/xmlrpclib.py", line 1070, in request headers xmlrpclib.ProtocolError: >>> from SOAPpy import SOAPProxy >>> url = "http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl" >>> server = SOAPProxy(url) >>> foo = server.retrieveServiceNames() Traceback (most recent call last): File "", line 1, in ? File "/usr/local/lib/python2.3/site-packages/SOAPpy/Client.py", line 363, in __call__ return self.__r_call(*args, **kw) File "/usr/local/lib/python2.3/site-packages/SOAPpy/Client.py", line 385, in __r_call self.__hd, self.__ma) File "/usr/local/lib/python2.3/site-packages/SOAPpy/Client.py", line 307, in __call raise p SOAPpy.Types.faultType: >>> ?????????? Thanks, cam -- //=\ Cary Miller //=\ \=// Center for Computational Pharmacology \=// //=\ University of Colorado Health Sciences Center //=\ \=// http://compbio.uchsc.edu/Hunter_lab/Miller \=// //=\ (303) 315-1584 //=\ From omid9dr18 at hotmail.com Fri Nov 7 01:16:47 2003 From: omid9dr18 at hotmail.com (Omid Khalouei) Date: Fri Nov 7 01:13:26 2003 Subject: [BioPython] Passing DNA sequence to CGI script Message-ID: Hello, I've had this problem for 2 weeks now and have tried everything that I could come up with, I would really appreciate your feedback. This is actually a very basic task that I want to perfom with HTML forms but for some reason it doesnt' seem to be working. I'm using apache on Windows XP. I'm trying to send a DNA sequence from an HTML form to a cgi script located in the cgi-bin of my apache server. Although I get to execute the cgi script after pressing the "submit" button of the form, the sequence or any other input doesn't seem to be passed to the script. I have simplified the files and enclosed them here. Thank you in advance for your reply. Sam Khalouei ******************************************

****************************************** #! C:\Python23\python.exe import sys, cgi, cgitb; cgitb.enable() print "Content-Type: text/html\n" form = cgi.FieldStorage() if (form.has_key("sequence")): print "sequence recieved!" print form["sequence"].value else: print "No sequence recieved!" ******************************************* _________________________________________________________________ STOP MORE SPAM with the new MSN 8 and get 2 months FREE* http://join.msn.com/?page=dept/bcomm&pgmarket=en-ca&RU=http%3a%2f%2fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgmarket%3den-ca From omid9dr18 at hotmail.com Fri Nov 7 01:26:49 2003 From: omid9dr18 at hotmail.com (Omid Khalouei) Date: Fri Nov 7 01:23:26 2003 Subject: [BioPython] Passing DNA sequence to CGI script_2 Message-ID: Hello again, I just noticed that if you checked my previous message by e-mail and not by mailing list on biopython web, the html code that I enclosed turns into an actual form. Here I skip the tags so hopefully that won't happen again! ************************************************** opening html tags

closing html tags ************************************************** Thanks Sam _________________________________________________________________ MSN 8 with e-mail virus protection service: 2 months FREE* http://join.msn.com/?page=features/virus&pgmarket=en-ca&RU=http%3a%2f%2fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgmarket%3den-ca From sbassi at asalup.org Fri Nov 7 09:31:03 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Fri Nov 7 11:32:44 2003 Subject: [BioPython] Passing DNA sequence to CGI script In-Reply-To: References: Message-ID: <3FABACA7.2000207@asalup.org> Omid Khalouei wrote: > Hello, > I've had this problem for 2 weeks now and have tried everything that I > could come up with, I would really appreciate your feedback. This is I don't see any obvious mistake, but here is the a working code of a program I did using cgi and Python (its a web gui for EMBOSS abiview:) Maybe you could use it as an example. It also took me a lot of time to make it works, so I post it here because it could help you. #! /usr/bin/python from HTMLgen import * from HTMLcolors import * import os import cgi import time os.chdir('/var/www/html/abiimg') #borro los pngs de la corrida anterior. lospng=os.listdir(str(os.getcwd())) for gdos in lospng: if gdos[-3:]=="png": # HACER LAS COSAS os.remove(gdos) else: pass formu=cgi.FieldStorage() doc= SimpleDocument(title="AbiView OUTPUT", bgcolor=WHITE, cgi=1) try: dname=formu["dname"].value except: dname = "defaultname.ab1" try: ffrom=formu["ffrom"].value except: ffrom = None try: fend=formu["tomax"].value except: fend= None try: fwsize=formu["wsize"].value fdisseq=formu["disseq"].value fdisaxis=formu["disyaxis"].value except: fwsize=40 fdisseq="Yes" fdisaxis="No" #EL DE ARRIBA TEMPORARIAMENTE SACADO cudir="/var/www/html/" if formu["upfile"].value<>"": #arch=open(cudir+"filenuevo.ab1","w") #arch=open("filenuevo.ab1","w") arch=open(dname,"w") arch.write(formu["upfile"].value) arch.close() if fend=="end": #pass #os.system('abiview -fname filenuevo.ab1 -outseq fileout.txt -graph png -yticks '+fdisaxis+' -window '+fwsize+' -startbase '+ffrom) #doc.append(os.system('pwd')) os.system('/BioServer/EMBOSS-2.5.0/emboss/.libs/abiview -auto -fname '+dname+' -outseq fileout.txt -graph png -yticks '+fdisaxis+' -window '+fwsize+' -startbase '+ffrom+' >malo.txt') #os.system('abiview -fname filenuevo.ab1 -outseq fileout.txt -graph png') #doc.append("ENTRA al END") #el problema es que no estan saliendo los graficos!!!!! else: #pass os.system('/BioServer/EMBOSS-2.5.0/emboss/.libs/abiview -auto -fname '+dname+' -outseq fileout.txt -graph png -yticks '+fdisaxis+' -window '+fwsize+' -startbase '+ffrom+' -endbase '+fend+' >malo.txt') #la dif es que este si tiene un FIN #Escribir la secuencia time.sleep(3) doc.append(Paragraph("La secuencia es:")) archtext=open("fileout.txt","r") # VER COMO SACAR LA SECUENCIA DE ACA!!!! lineas=archtext.read() #seq=lineas[1][:-1] seq=lineas archtext.close() doc.append('
')
	doc.append(Paragraph(seq))
	doc.append('
') # AHORA VIENEN LOS GRAFICOS doc.append(Paragraph(os.curdir)) lospng=os.listdir(os.curdir) for g in lospng: if g[-3:]=="png": # HACER LAS COSAS #doc.append(Image(os.curdir+"/"+g)) doc.append(Image('abiimg/'+g)) doc.append(HR()) else: pass else: doc.append(Heading(2),"You must UPLOAD a file") print doc os.remove(dname) -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From jeffrey_chang at stanfordalumni.org Tue Nov 11 14:34:48 2003 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Tue Nov 11 14:31:20 2003 Subject: [BioPython] Future Leadership for the Biopython Project Message-ID: <1C80715C-147E-11D8-BA9B-000A956845CE@stanfordalumni.org> Hello Biopythonistas, After 4 years on the Biopython project, I am turning leadership responsibilities over to Brad Chapman. While I've enjoyed working on Biopython, my responsibilities at my day job has grown considerably over the last year, reducing the amount of time I can afford to spend. While I will no longer be the point person on the project, I will still stay involved and help out where I can. Please do not send inquiries about the project or its organization directly to me any longer. Instead, please send them to biopython-dev@biopython.org. What does this mean for the project? Probably good things, since Biopython is in great hands! :) I imagine that for the short term, things will likely continue the same way. In the long run, however, Brad has some exciting ideas about the direction of the project. Also, I'd like to thank everyone who has helped out with Biopython and have become part of the community. Although I, and now Brad, have been nominally "in charge," Biopython is really a community-driven project. It would not have been as successful if not for people who have put in hours of their "free" time in part for altruistic reasons. Let's keep up the good work! I, for one, am eager to see where Biopython goes, and how it supports biology research in the future. Jeff From letondal at pasteur.fr Wed Nov 12 08:18:54 2003 From: letondal at pasteur.fr (Catherine Letondal) Date: Wed Nov 12 08:15:23 2003 Subject: [BioPython] connecting to biomoby In-Reply-To: Your message of "Wed, 05 Nov 2003 19:38:13 MST." Message-ID: <200311121318.hACDIsbs330788@electre.pasteur.fr> Cary Miller wrote: > Hi all, > I am attempting to contact biomoby with xmlrpclib and SOAPpy. BTW, has someone started to develop a biomoby python client? > It's not > totally clear where the server lives so I have tried 3 urls. > http://mobycentral.cbr.nrc.ca/MOBY/Central > http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl > http://192.168.1.9/cgi-bin/MOBY-Central.pl > Each of these seems to connect with my client but then fails when the > request is sent. Do I have the wrong url, wrong function call or what? > > >>> import xmlrpclib > >>> url = "http://mobycentral.cbr.nrc.ca/MOBY/Central" > >>> server = xmlrpclib.ServerProxy(url) > >>> foo = server.retrieveServiceNames() > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/local/lib/python2.3/xmlrpclib.py", line 1029, in __call__ > return self.__send(self.__name, args) > File "/usr/local/lib/python2.3/xmlrpclib.py", line 1316, in __request > verbose=self.__verbose > File "/usr/local/lib/python2.3/xmlrpclib.py", line 1070, in request > headers > xmlrpclib.ProtocolError: mobycentral.cbr.nrc.ca/MOBY/Central: 404 Not Found> > > > >>> from SOAPpy import SOAPProxy > >>> url = "http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl" > >>> server = SOAPProxy(url) > >>> foo = server.retrieveServiceNames() > class > (main) at /usr/local/lib/perl5/site_perl/5.8.0/SOAP/Lite.pm line 2128. > > > Traceback (most recent call last): > File "", line 1, in ? > File "/usr/local/lib/python2.3/site-packages/SOAPpy/Client.py", line > 363, in __call__ > return self.__r_call(*args, **kw) > File "/usr/local/lib/python2.3/site-packages/SOAPpy/Client.py", line > 385, in __r_call > self.__hd, self.__ma) > File "/usr/local/lib/python2.3/site-packages/SOAPpy/Client.py", line > 307, in __call > raise p > SOAPpy.Types.faultType: (retrieveServiceNames) in class (main) at > /usr/local/lib/perl5/site_perl/5.8.0/SOAP/Lite.pm line 2128. > > > >>> > > ?????????? > Thanks, > cam > > -- > //=\ Cary Miller //=\ > \=// Center for Computational Pharmacology \=// > //=\ University of Colorado Health Sciences Center //=\ > \=// http://compbio.uchsc.edu/Hunter_lab/Miller \=// > //=\ (303) 315-1584 //=\ > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython -- Catherine Letondal -- Pasteur Institute Computing Center From jko1 at cdc.gov Sun Nov 16 20:31:51 2003 From: jko1 at cdc.gov (Osborne, John) Date: Sun Nov 16 20:43:38 2003 Subject: [BioPython] Blast 2.2 or better Message-ID: Hi, I just started learning python last week, hoping to use some general purpose blast parsing code with little effort on my part and I ran into trouble using the standalone blast parser. It looks like it was written for only blast 2.0 about 3 or 4 years ago. Is this an area that needs contribution or is there something else I should be using other than this for fast blast parsing? I'm using NCBI's 2.2 blast locally. -John From idoerg at burnham.org Sun Nov 16 22:49:26 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sun Nov 16 22:46:10 2003 Subject: [BioPython] Blast 2.2 or better In-Reply-To: Message-ID: Although the docs may not be up to date, the blast parser is. I think the -m8 and the XML outputs are not supported, but the 0m9 and the rest of the formats are. If you run into an actual BLAST parsing bug, give a holler, and don't forget to add the output. Of course, if you want to write a parser for the unsupported formats, then that will be great! Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo On Sun, 16 Nov 2003, Osborne, John wrote: > Hi, > > I just started learning python last week, hoping to use some general > purpose blast parsing code with little effort on my part and I ran into > trouble using the standalone blast parser. It looks like it was written > for only blast 2.0 about 3 or 4 years ago. Is this an area that needs > contribution or is there something else I should be using other than > this for fast blast parsing? I'm using NCBI's 2.2 blast locally. > > > > -John > > > > From jko1 at cdc.gov Mon Nov 17 11:39:07 2003 From: jko1 at cdc.gov (Osborne, John) Date: Mon Nov 17 12:20:57 2003 Subject: [BioPython] Blast 2.2 or better Message-ID: Hi Jeff, Thanks for your quick response, I took a look at the biopython blast code and it appears to me that the problem is that the blast result description headers are slightly different in the version of blast I am using. As it turns out I now recognize the results I gave it to parse as being from mpiblast 1.1 wherein lies the rub... mpiblast gives the first sequence description of a hit prefixed with a '>' and if there are identical hits it just lists them out after the initial one with no leading '>'. I think this is causing the problem, scan_alignments does look for a '>' and start to process an alignment which is not there. I've included the blast output and the error file, I have tried debugging this myself but I have run into some odd behaviour. I tried adding a print statement (print "boo") to NCBIStandalone.py and as output I got 'print "boo"' ie) it included the word print and quotes?! I just started with python last week and found this odd to say the least. I also am also confused by read_and_call functions? Is this biopython or python? I tried grepping for "def read_and_call" in the biopython directory but can't find it, how would I go about finding this (and similar) function? Any help appreciated for a potential python convert, -John I -----Original Message----- From: Jeffrey Chang [mailto:jchang@jeffchang.com] Sent: Sunday, November 16, 2003 9:18 PM To: Osborne, John Subject: Re: [BioPython] Blast 2.2 or better Hi John, The parser was started on Blast 2.0, but we have tried to keep it up to date with Blast. It does work with some flavors of Blast 2.2, but unfortunately, the format changes very fast. Sometimes it changes faster than the parser. So, yes, a patch that updates it with your current version is best. Next best would be to send email to the list, with a description of the problem and a sample of the output that breaks the parser. Good luck! Jeff On Nov 16, 2003, at 8:31 PM, Osborne, John wrote: > Hi, > > I just started learning python last week, hoping to use some general > purpose blast parsing code with little effort on my part and I ran into > trouble using the standalone blast parser. It looks like it was > written > for only blast 2.0 about 3 or 4 years ago. Is this an area that needs > contribution or is there something else I should be using other than > this for fast blast parsing? I'm using NCBI's 2.2 blast locally. > > > > -John > > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython -------------- next part -------------- A non-text attachment was scrubbed... Name: error Type: application/octet-stream Size: 1943 bytes Desc: error Url : http://portal.open-bio.org/pipermail/biopython/attachments/20031117/aa86cef8/error-0001.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: oneresult Type: application/octet-stream Size: 143825 bytes Desc: oneresult Url : http://portal.open-bio.org/pipermail/biopython/attachments/20031117/aa86cef8/oneresult-0001.obj From lee at epigenomix.com Mon Nov 17 14:48:22 2003 From: lee at epigenomix.com (Lee R. Shekter) Date: Mon Nov 17 14:48:24 2003 Subject: [BioPython] GenBank file parsing question Message-ID: <1069098670.4594.75.camel@precision2.epivax-lan.com> All - I have been using BioPython to parse GenBank files. The fields that I have been parsing include the accession number, the date, and the sequence. I have then output these into Fasta format for input into a sequence analysis program. I also want to grab the country of origin and the strain. I think these are available to be parsed as they are documented in Bio/GenBank/genbank_format.py under a section called: feature_key_names however I can't figure out the syntax to call this part after having loaded in my file and parsed it like this: #!/usr/bin/env python from Bio import GenBank,Writer import sys,string def GenBank2FASTA(): parser = GenBank.RecordParser() genbankfile = open(sys.argv[1],'r') iterator = GenBank.Iterator(genbankfile,parser) while 1: cur_record = iterator.next() if cur_record is None: break outfile = open(sys.argv[2],'a') cur_record.accession = " ".join(cur_record.accession) outfile.write('>%s|%s\n' %(cur_record.accession,cur_record.date)) seqwidth = 60 for i in range(0,len(cur_record.sequence),seqwidth): outfile.write('%s\n' % cur_record.sequence[i:i+seqwidth]) etc.,etc., This results in a file that looks like this: >AAQ10924|24-SEP-2003 MAGRSGDDDKELLKAVKIIKILYQSNPYPEPKGSRQARKNRRRRWRARQRQIDSISERIL STCLGRPTEPVPLQLPPLERLHLDSREDCGTSGTQQSQGVETGVGRPQISVESSGVLGSR TET >AAQ10915|24-SEP-2003 MAGRSGDNDEELLKAVRIIKILYKSNPYPEPKGSRQARKNRRRRWRARQRQIDSISERIL STYLGRSTEPVPLQLPPLERLHLDCREDCGTSGTQQSQGVETGVGRPQISVESPVILGSR TKN >AAQ10906|24-SEP-2003 MAGRSGDGDEGILPTVKIIQILYPSHPYPEPKGSRQARKNRRRRWRARQKQIDSISERIL STCLGRPAEPVPLQLPPLERLHLDSREDCGTSGTQQSQGVETGVGRPQISVESSGVLGSR TET What I'd like is have this plus: >AAQ10906|24-SEP-2003 | country | strain MAGRSGDGDEGILPTVKIIQILYPSHPYPEPKGSRQARKNRRRRWRARQKQIDSISERIL STCLGRPAEPVPLQLPPLERLHLDSREDCGTSGTQQSQGVETGVGRPQISVESSGVLGSR TET I'm sure there's a pretty simple solution to my problem. Any help would be appreciated either in terms of using BioPython to parse the country of origin and strain fields. Lee Shekter From jeffrey_chang at stanfordalumni.org Mon Nov 17 16:34:45 2003 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Mon Nov 17 16:31:02 2003 Subject: [BioPython] Blast 2.2 or better In-Reply-To: References: Message-ID: On Nov 17, 2003, at 11:39 AM, Osborne, John wrote: > Hi Jeff, > [...] > I've included the blast output and the error file, On the blast output file you sent, the parser seems to be working correctly, except that the file ends prematurely! It is raising an "Unexpected end of stream" error because the file ends abruptly in the middle of a hit: Query: 19 AIVDNEII-IAGGYNFNNPSLNKVYKINIENKIHVELPPMIMN---RCRFSLAVIDNTIY 74 A+V+ I+ + GGY FN+ N V ++ ++ + L + N R SLA+ + IY Sbjct: 346 AVVNGNIMWVVGGYMFNHSDYNMVLAYDLASREWLPLNRSVNNVVVRYGHSLALYKDKIY 405 Query: 75 AIGGQ 79 GG+ Sbjct: 406 MYGGK 410 The rest of the file with the database and statistics is missing, which confuses the parser. Did BLAST crash in the middle of the search? > I have tried > debugging this myself but I have run into some odd behaviour. I tried > adding a print statement (print "boo") to NCBIStandalone.py and as > output I got 'print "boo"' ie) it included the word print and quotes?! > I just started with python last week and found this odd to say the > least. I've been using python for 5 years, and I find it odd. ;) Where did you add it? I don't understand how that can happen. > I also am also confused by read_and_call functions? Is this > biopython or python? I tried grepping for "def read_and_call" in the > biopython directory but can't find it, how would I go about finding > this > (and similar) function? This is being imported from ParserSupport with the line: from Bio.ParserSupport import * grepping in biopython/Bio for "def read_and_call" should have identified the function as being defined in ParserSupport. Jeff From bertrand.frottier at free.fr Tue Nov 18 14:49:40 2003 From: bertrand.frottier at free.fr (Bertrand FROTTIER) Date: Tue Nov 18 14:46:17 2003 Subject: [BioPython] GenBank feature proprotein Message-ID: <3FBA77D4.3060007@free.fr> Hello everyone ! I recently wrote a simple program to get sequences from GenBank. It's working fine for most of the sequences but failed for 5 of them (NM_001565, NM_001710, NM_006332, NM_000245 and NM_000212 if you're curious). After having a look at the records, I discovered that they all have in common a new *undocumented* feature: "proprotein". Fortunately, the fix is rather simple: simply add a key "proprotein" in Bio.GenBank.genbank_format feature_key_names, and everything is working fine ! Hope this helps. Cheers, Bertrand From Peter.Bienstman at UGent.be Tue Nov 18 15:37:12 2003 From: Peter.Bienstman at UGent.be (Peter Bienstman) Date: Tue Nov 18 15:33:30 2003 Subject: [BioPython] GenBank feature proprotein In-Reply-To: <3FBA77D4.3060007@free.fr> References: <3FBA77D4.3060007@free.fr> Message-ID: <200311182137.12729.Peter.Bienstman@UGent.be> On Tuesday 18 November 2003 20:49, Bertrand FROTTIER wrote: > Hello everyone ! > > I recently wrote a simple program to get sequences from GenBank. > It's working fine for most of the sequences but failed for 5 of them > (NM_001565, NM_001710, NM_006332, NM_000245 and NM_000212 if you're > curious). > After having a look at the records, I discovered that they all have in > common a new *undocumented* feature: "proprotein". > Fortunately, the fix is rather simple: simply add a key "proprotein" in > Bio.GenBank.genbank_format feature_key_names, and everything is working > fine ! The fix is in CVs now. Thanks! Peter -- ------------------------------------------------ Peter Bienstman Ghent University, Dep. of Information Technology Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium tel: +32 9 264 34 45, fax: +32 9 264 35 93 WWW: http://photonics.intec.UGent.be email: Peter.Bienstman@UGent.be ------------------------------------------------ From dag at sonsorol.org Thu Nov 20 10:38:23 2003 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu Nov 20 10:43:06 2003 Subject: [BioPython] Total OBF server shutdown Saturday November 22nd (all day EDT timezone) Message-ID: <3FBCDFEF.1010807@sonsorol.org> Hi folks, Apologies for the massive cross-posting. Our CVS, mailing list and web servers are located in a Cambridge, MA USA datacenter belonging to Wyeth Resarch. Genetics Institute (which became part of Wyeth) has supported our signficant internet bandwidth and hosting needs for many years since the earliest versions of our open source efforts. Since I have to do this massive cross-post anyway I figured it was a good time to thank them again in public. The real reason for this message is to announce a 1-day period of significant server downtime. The office floor & datacenter in the building where our servers are hosted is going to have a planned electrical shutdown (including emergency and backup power circuits) from 10am - 6pm on Saturday November 22nd. I'll be manually bringing down our servers sometime before the 10am deadline. The time estimate is conservative. In the event that the facilty work takes less time than expected I'll probably take advantage of the window to perform some server upgrades and failed disk replacements. For any questions/concerns or if you notice a server or service that is still not available after the 22nd please contact me directly at 'chris@bioteam.net' or 1-617-877-5498. Regards, Chris From anewgene at hotpop.com Sun Nov 23 01:19:30 2003 From: anewgene at hotpop.com (CL WU) Date: Sun Nov 23 13:42:50 2003 Subject: [BioPython] suggestion on Fasta.index_file() Message-ID: <3FC05172.8060308@hotpop.com> Hi, group, Biopython's Fasta module provides a convenient way to generate a index file for a large fasta file. However, the generated index file stores the absolute path for fasta_seq_file, thus, the generated index file can not be used once the fasta_seq_file was moved. For my case, I store fasta_seq_file and its index file at a network drive and I need to access it from both windows and linux server. The original index file can not be used for both environments. To solve this problem, I modified two lines of Bio/Fasta/__init__.py as below. As the result, it require the index file is placed at the same directory of fasta_seq_file. class Dictionary: ... def __init__(self, indexname, parser=None): ... #self._handle = open(self._index[Dictionary.__filename_key]) self._handle = open(os.path.join(os.path.split(indexname)[0],self._index[Dictionary.__filename_key])) ... def index_file(filename, indexname, rec2key=None): ... #index[Dictionary._Dictionary__filename_key] = filename index[Dictionary._Dictionary__filename_key] = os.path.split(filename)[1] Do you it's worth to make this modification? Or, any better solution? Please discuss. Thanks. Chunlei Wu From chapmanb at uga.edu Mon Nov 24 11:53:50 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Mon Nov 24 12:05:20 2003 Subject: [BioPython] suggestion on Fasta.index_file() In-Reply-To: <3FC05172.8060308@hotpop.com> References: <3FC05172.8060308@hotpop.com> Message-ID: <20031124165350.GB27502@evostick.agtec.uga.edu> Hi Chunlei; > However, the generated index file stores the absolute path for > fasta_seq_file, It should just store the filename for whatever you pass to the index_file function. The relevant code from Bio/Fasta/__init__.py is: def index_file(filename, indexname, rec2key=None): [...] index[Dictionary._Dictionary__filename_key] = filename So, if you just pass relative paths, you shouldn't have any problem with absolute file names. A solution you could use in your code without needing to modify Biopython is to do: start_dir = os.getcwd() os.chdir("whatever/the/directory/is") index_file("the_file.fasta", "the_index.idx") os.chdir(start_dir) Then you would have an index with a relative path and you could change into this directory later to open the index. os.chdir("whatever/the/directory/is") dict = Fasta.Dictionary("the_index.idx") > For my case, I store fasta_seq_file and its index file at a network > drive and I need to access it from both windows and linux server. The > original index file can not be used for both environments. To solve this > problem, I modified two lines of Bio/Fasta/__init__.py as below. As the > result, it require the index file is placed at the same directory of > fasta_seq_file. [...] > Do you it's worth to make this modification? Or, any better solution? I'm not a big fan of restricting the index file and fasta file to the same directory. A backwards compatible solution would be to allow Dictionary to take a filename the index points to as an optional argument. def __init__(self, indexname, parser=None, filename = None): self._index = Index.Index(indexname) if filename: self._handle = open(filename) else: self._handle = open(self._index[Dictionary.__filename_key]) self._parser = parser Does this solution seem reasonable? Or will the os.chdir solution work for you? Hope this helps. Brad From chapmanb at uga.edu Mon Nov 24 12:15:03 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Mon Nov 24 12:26:28 2003 Subject: [BioPython] GenBank file parsing question In-Reply-To: <1069098670.4594.75.camel@precision2.epivax-lan.com> References: <1069098670.4594.75.camel@precision2.epivax-lan.com> Message-ID: <20031124171503.GD27502@evostick.agtec.uga.edu> Hi Lee; Sorry for the delay in getting back with you. > I also want to grab the country of origin and > the strain. I think these are available to be parsed as they are Yes, they definitely are parsed. To get them you will need to go into the feature tables of the GenBank Record object. I'm not sure exactly where country and strain are always stored as I don't normally look at bacterial GenBank entries but they look to be in the "source" feature from a quick glance. If this is true generally then the following code should work: def get_country_and_strain(record): country = "No country" strain = "No strain" for feature in record.features: if feature.key == "source": for qualifier in feature.qualifiers: if qualifier.key == "country": country = qualifier.value elif qualifier.key == "strain": strain = qualifier.value return country, strain Then you should be able to modify your code to something like (I also modified it to use Fasta Records which write the sequences prettily for you automatically: #!/usr/bin/env python from Bio import GenBank,Writer import sys,string def GenBank2FASTA(): parser = GenBank.RecordParser() genbankfile = open(sys.argv[1],'r') iterator = GenBank.Iterator(genbankfile,parser) while 1: cur_record = iterator.next() if cur_record is None: break outfile = open(sys.argv[2],'a') accession = " ".join(cur_record.accession) country, strain = get_country_and_strain(cur_record) fasta_rec = Fasta.Record() fasta_rec.title = "%s|%s|%s|%s" % (accession, cur_record.date, country, strain) fasta_rec.sequence = cur_record.sequence outfile.write(str(fasta_rec) + "\n") Hopefully this makes sense and helps. Sorry again about the delay in responding. Brad From anewgene at hotpop.com Mon Nov 24 12:59:09 2003 From: anewgene at hotpop.com (CL WU) Date: Mon Nov 24 13:02:08 2003 Subject: [BioPython] suggestion on Fasta.index_file() In-Reply-To: <20031124165350.GB27502@evostick.agtec.uga.edu> References: <3FC05172.8060308@hotpop.com> <20031124165350.GB27502@evostick.agtec.uga.edu> Message-ID: <3FC246ED.4090101@hotpop.com> I see. I think giving a optional filename argument is more flexible. Thanks, Brad. Chunlei Brad Chapman wrote: >Hi Chunlei; > > > >>However, the generated index file stores the absolute path for >>fasta_seq_file, >> >> > >It should just store the filename for whatever you pass to the >index_file function. The relevant code from Bio/Fasta/__init__.py >is: > >def index_file(filename, indexname, rec2key=None): > [...] > index[Dictionary._Dictionary__filename_key] = filename > >So, if you just pass relative paths, you shouldn't have any problem >with absolute file names. A solution you could use in your code >without needing to modify Biopython is to do: > >start_dir = os.getcwd() >os.chdir("whatever/the/directory/is") >index_file("the_file.fasta", "the_index.idx") >os.chdir(start_dir) > >Then you would have an index with a relative path and you could >change into this directory later to open the index. > >os.chdir("whatever/the/directory/is") >dict = Fasta.Dictionary("the_index.idx") > > > >>For my case, I store fasta_seq_file and its index file at a network >>drive and I need to access it from both windows and linux server. The >>original index file can not be used for both environments. To solve this >>problem, I modified two lines of Bio/Fasta/__init__.py as below. As the >>result, it require the index file is placed at the same directory of >>fasta_seq_file. >> >> >[...] > > >>Do you it's worth to make this modification? Or, any better solution? >> >> > >I'm not a big fan of restricting the index file and fasta file to >the same directory. A backwards compatible solution would be to >allow Dictionary to take a filename the index points to as an >optional argument. > > def __init__(self, indexname, parser=None, filename = None): > self._index = Index.Index(indexname) > if filename: > self._handle = open(filename) > else: > self._handle = open(self._index[Dictionary.__filename_key]) > self._parser = parser > >Does this solution seem reasonable? Or will the os.chdir solution >work for you? > >Hope this helps. >Brad >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython > > > From acobb at northwestern.edu Mon Nov 24 13:05:19 2003 From: acobb at northwestern.edu (Albert Chan On Bon) Date: Mon Nov 24 13:33:59 2003 Subject: [BioPython] Help on extracting title from description (Protein file parsing) Message-ID: <008b01c3b2b5$86c6dc30$d24d4ac7@Laptop> Hello, I just got into Biopython and I hope someone can help me on this matter. I'm trying to compare the blast result of various proteins against each other by (hopefully) extracting the alignment.title (which can be done) and putting it side by side against description title and then the corresponding e-value. However I am not able to extract the description.title by simply doing [print description.title] as biopython says that title argument is not defined but I can do it for [print alignment.title]. I am still trying to find out why. Sincerely, Albert p.s. I am following the instructions in the Biopython Cookbook about parsing information locally. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biopython/attachments/20031124/6bea6b59/attachment-0001.htm From chapmanb at uga.edu Mon Nov 24 17:07:23 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Mon Nov 24 17:18:47 2003 Subject: [BioPython] suggestion on Fasta.index_file() In-Reply-To: <3FC246ED.4090101@hotpop.com> References: <3FC05172.8060308@hotpop.com> <20031124165350.GB27502@evostick.agtec.uga.edu> <3FC246ED.4090101@hotpop.com> Message-ID: <20031124220723.GB28440@evostick.agtec.uga.edu> Hi Chunlei; > I see. I think giving a optional filename argument is more flexible. Okay -- I've checked the change in CVS as I described below. Thanks for the feedback! Brad > Brad Chapman wrote: > > >Hi Chunlei; > > > > > > > >>However, the generated index file stores the absolute path for > >>fasta_seq_file, > >> > >> > > > >It should just store the filename for whatever you pass to the > >index_file function. The relevant code from Bio/Fasta/__init__.py > >is: > > > >def index_file(filename, indexname, rec2key=None): > > [...] > > index[Dictionary._Dictionary__filename_key] = filename > > > >So, if you just pass relative paths, you shouldn't have any problem > >with absolute file names. A solution you could use in your code > >without needing to modify Biopython is to do: > > > >start_dir = os.getcwd() > >os.chdir("whatever/the/directory/is") > >index_file("the_file.fasta", "the_index.idx") > >os.chdir(start_dir) > > > >Then you would have an index with a relative path and you could > >change into this directory later to open the index. > > > >os.chdir("whatever/the/directory/is") > >dict = Fasta.Dictionary("the_index.idx") > > > > > > > >>For my case, I store fasta_seq_file and its index file at a network > >>drive and I need to access it from both windows and linux server. The > >>original index file can not be used for both environments. To solve this > >>problem, I modified two lines of Bio/Fasta/__init__.py as below. As the > >>result, it require the index file is placed at the same directory of > >>fasta_seq_file. > >> > >> > >[...] > > > > > >>Do you it's worth to make this modification? Or, any better solution? > >> > >> > > > >I'm not a big fan of restricting the index file and fasta file to > >the same directory. A backwards compatible solution would be to > >allow Dictionary to take a filename the index points to as an > >optional argument. > > > > def __init__(self, indexname, parser=None, filename = None): > > self._index = Index.Index(indexname) > > if filename: > > self._handle = open(filename) > > else: > > self._handle = open(self._index[Dictionary.__filename_key]) > > self._parser = parser > > > >Does this solution seem reasonable? Or will the os.chdir solution > >work for you? > > > >Hope this helps. > >Brad > >_______________________________________________ > >BioPython mailing list - BioPython@biopython.org > >http://biopython.org/mailman/listinfo/biopython > > > > > > > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From chapmanb at uga.edu Mon Nov 24 17:16:06 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Mon Nov 24 17:27:30 2003 Subject: [BioPython] Help on extracting title from description (Protein file parsing) In-Reply-To: <008b01c3b2b5$86c6dc30$d24d4ac7@Laptop> References: <008b01c3b2b5$86c6dc30$d24d4ac7@Laptop> Message-ID: <20031124221606.GC28440@evostick.agtec.uga.edu> Hi Albert; > Hello, I just got into Biopython and I hope someone can help me on > this matter. I'm trying to compare the blast result of various proteins > against each other by (hopefully) extracting the alignment.title (which > can be done) and putting it side by side against description title > and then the corresponding e-value. I guess I'm not exactly sure what you want to do here. The description title and the alignment title should be the same thing, except that the description title is shortened to fit into the description table. So from the start I don't think I understand what you're trying to accomplish. > However I am not able to extract the description.title by > simply doing [print description.title] as biopython says that > title argument is not defined but I can do it for [print > alignment.title]. I am still trying to find out why. You can get the title for all of the descriptions (as well as score and e-value) with code of the following type: for description in blast_record.descriptions: print description.title, description.score, description.e Similar to how you would get the information for alignments: for alignment in blast_record.alignments: print alignment.title, alignment.length I don't know if this helps answer your questions. If you supply some code or a better description of your problem I or someone else on the list may be able to help more. Hope this helps some. Brad From thamelry at vub.ac.be Tue Nov 25 08:26:58 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Tue Nov 25 08:39:50 2003 Subject: [BioPython] Bio.PDB article in Bioinformatics In-Reply-To: References: Message-ID: <200311251426.58578.thamelry@vub.ac.be> Hi everybody, An application note describing Bio.PDB (the Biopython PDB parser and related code dealing with crystal structures) just appeared in Bioinformatics. For reference and abstract see below. Regards, -Thomas ---- Bioinformatics. 2003 Nov 22;19(17):2308-10. PDB file parser and structure class implemented in Python. Hamelryck T, Manderick B. Department of Cellular and Molecular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB) and Computational Modeling Lab (COMO), Department of Computer Science, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium. SUMMARY: The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. AVAILABILITY: The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org --- Thomas Hamelryck Computational modeling lab (COMO) Vrije Universiteit Brussel (VUB) Belgium http://homepages.vub.ac.be/~thamelry From mr_buba88gana at post.cz Tue Nov 25 13:07:51 2003 From: mr_buba88gana at post.cz (Mr Buba Gana) Date: Tue Nov 25 13:15:35 2003 Subject: [BioPython] Urgent message from Mr Buba Gana Message-ID: <200311251814.hAPIELg0025860@portal.open-bio.org> MR BUBA GANA BRANCH MANAGER, UNITED BANK FOR AFRICA PLC ATTN:Dear I am pleased to get across to you for a very urgent and profitable business proposal, though I don't know you neither have I seen you before but my confidence was reposed on you when the Chief Executive of Lagos Chamber of Commerce and Industry handed me your contact for a confidential business interest. I am a UNITED BANK FOR AFRICA(UBA), Branch Manager, located at Victoria Island , Lagos, Republic Of Nigeria also currently with the bank up to date. The intended business is thus; We had a customer, a foriegner from your country, resident in Nigeria. He runs and maintained a Corporate Account in my branchand had the sum of US$27,623.400(TWENTY SEVEN MILLION SIX HUNDRED AND TWENTY THREE THOUSAND, FOUR HUNDRED UNITED STATES DOLLAR ONLY NO CENTS) as his lastbalance before he died as a result of auto crash. The customer died two years ago and uptil today non of his relative has come to claim his money from the UBA hence the deceased Customer, MR. G.OSBORN died along with whom he filled in the bank's form as his NEXT OF KIN while opening his account with us. Having noticed this, I in collabration with two other top officials of the bank covered up the account all this while. Now we want you as our foreign partner since you are from the same country with the deceased customer to be fronted as his Next Of Kin and forward an APPLICATION LETTER OF CLAIM FOR INHERITANCE of theabove amount. We will use our position to delete and insert your name as the beneficiary of the NEXT OF KIN to his file in the bank for a smooth claims into youraccount for our disbursements. Your response is only what we are waiting for to commence the action as we have animously agreed to give you 25% of the total sum at the end of this transaction into your possession while 70% would be for I and my colleagues and the remaining 5% would be for any form of expenses that may be incurred during the course of this transaction in the both side. Your indication of interest and your urgent reply is being awaited. Please reply me through my private email address:(mr_buba88gana@yahoo.com) Best regards, MR BUBA GANA. From mr_buba88gana at post.cz Tue Nov 25 13:11:18 2003 From: mr_buba88gana at post.cz (Mr Buba Gana) Date: Tue Nov 25 13:18:40 2003 Subject: [BioPython] Urgent message from Mr Buba Gana Message-ID: <200311251817.hAPIEmg0025870@portal.open-bio.org> MR BUBA GANA BRANCH MANAGER, UNITED BANK FOR AFRICA PLC ATTN:Dear I am pleased to get across to you for a very urgent and profitable business proposal, though I don't know you neither have I seen you before but my confidence was reposed on you when the Chief Executive of Lagos Chamber of Commerce and Industry handed me your contact for a confidential business interest. I am a UNITED BANK FOR AFRICA(UBA), Branch Manager, located at Victoria Island , Lagos, Republic Of Nigeria also currently with the bank up to date. The intended business is thus; We had a customer, a foriegner from your country, resident in Nigeria. He runs and maintained a Corporate Account in my branchand had the sum of US$27,623.400(TWENTY SEVEN MILLION SIX HUNDRED AND TWENTY THREE THOUSAND, FOUR HUNDRED UNITED STATES DOLLAR ONLY NO CENTS) as his lastbalance before he died as a result of auto crash. The customer died two years ago and uptil today non of his relative has come to claim his money from the UBA hence the deceased Customer, MR. G.OSBORN died along with whom he filled in the bank's form as his NEXT OF KIN while opening his account with us. Having noticed this, I in collabration with two other top officials of the bank covered up the account all this while. Now we want you as our foreign partner since you are from the same country with the deceased customer to be fronted as his Next Of Kin and forward an APPLICATION LETTER OF CLAIM FOR INHERITANCE of theabove amount. We will use our position to delete and insert your name as the beneficiary of the NEXT OF KIN to his file in the bank for a smooth claims into youraccount for our disbursements. Your response is only what we are waiting for to commence the action as we have animously agreed to give you 25% of the total sum at the end of this transaction into your possession while 70% would be for I and my colleagues and the remaining 5% would be for any form of expenses that may be incurred during the course of this transaction in the both side. Your indication of interest and your urgent reply is being awaited. Please reply me through my private email address:(mr_buba88gana@yahoo.com) Best regards, MR BUBA GANA. From skelley at sciences.sdsu.edu Tue Nov 25 17:14:32 2003 From: skelley at sciences.sdsu.edu (Scott Kelley) Date: Tue Nov 25 17:13:43 2003 Subject: [BioPython] Martel installation In-Reply-To: <200310221521.h9MFL3db020367@portal.open-bio.org> Message-ID: <5.1.1.5.2.20031125141229.022588b8@sciences.sdsu.edu> Can anyone out there tell me where to install Martel? We need it for Clustalw. We tried installing it in site-packages and within Bio but no go. It does not seem to be included in Biopython for Python 2.3. Thanks! -Scott SCOTT T. KELLEY, Ph.D. Assistant Professor Department of Biology E-mail: skelley@sciences.sdsu.edu San Diego State University Phone : 619-594-5371 5500 Campanile Drive Fax : 619-594-5676 San Diego, CA 92182-4614 U.S.A. From chapmanb at uga.edu Tue Nov 25 17:17:13 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Tue Nov 25 17:28:32 2003 Subject: [BioPython] Martel installation In-Reply-To: <5.1.1.5.2.20031125141229.022588b8@sciences.sdsu.edu> References: <200310221521.h9MFL3db020367@portal.open-bio.org> <5.1.1.5.2.20031125141229.022588b8@sciences.sdsu.edu> Message-ID: <20031125221713.GD80145@evostick.agtec.uga.edu> Hi Scott; Hope everything is going well with you. > Can anyone out there tell me where to install Martel? We need it for > Clustalw. We tried installing it in site-packages and within Bio but no go. > It does not seem to be included in Biopython for Python 2.3. Are you using the source distribution or the windows installer? I know it is in the source distribution but I'm not positive about the installer, as I didn't make it this time (and also don't have a windows computer on hand). Either way, it is included in the source distribution so you can get it there. If it's on windows you can just unzip the source and move the Martel directory into site-packages (the same level as Bio, not inside Bio). You should be able to do a import Martel from the python prompt after doing this. If this doesn't work, can you provide some more information about what you mean by "no go" so I can try and provide better help? Brad From chapmanb at uga.edu Tue Nov 25 18:16:22 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Tue Nov 25 18:27:41 2003 Subject: [BioPython] Bio.PDB article in Bioinformatics In-Reply-To: <200311251426.58578.thamelry@vub.ac.be> References: <200311251426.58578.thamelry@vub.ac.be> Message-ID: <20031125231622.GE80145@evostick.agtec.uga.edu> Hi Thomas; > An application note describing Bio.PDB (the Biopython PDB parser and related > code dealing with crystal structures) just appeared in Bioinformatics. For > reference and abstract see below. Great! Congrats on the publication and thanks for doing this -- it's always great to get Biopython mentioned more in the literature. I added a link to it from the Biopython documentation page for permanent reference and all the fame and glory that entails. Now-if-I-could-only-put-that-paper-in-my-thesis-ly yr's, Brad From gspraggon at gnf.org Tue Nov 25 20:08:37 2003 From: gspraggon at gnf.org (Glen Spraggon) Date: Tue Nov 25 20:15:12 2003 Subject: [BioPython] Connecting to Genbank Message-ID: <833E32F61B9F8746878F2A1865BECE6002DC2C@EXCHCLUSTER01.lj.gnf.org> Hi, I have just resurrected an old script ( about six months old) that queries Genbank for sequence information using the gi number. The scrips gets the gi information by calling Gi_list=Genbank.search_for("gi|number") Then sequence information is extracted from Gi_list. The problem is that although this used to work it now it doesn't. It doesn't throw an exception either just keeps going. Has something changed with Genbank. Cheers Glen From Peter.Bienstman at UGent.be Wed Nov 26 02:23:44 2003 From: Peter.Bienstman at UGent.be (Peter Bienstman) Date: Wed Nov 26 02:30:14 2003 Subject: [BioPython] Connecting to Genbank In-Reply-To: <833E32F61B9F8746878F2A1865BECE6002DC2C@EXCHCLUSTER01.lj.gnf.org> References: <833E32F61B9F8746878F2A1865BECE6002DC2C@EXCHCLUSTER01.lj.gnf.org> Message-ID: <200311260823.44896.Peter.Bienstman@UGent.be> On Wednesday 26 November 2003 02:08, Glen Spraggon wrote: > Hi, > I have just resurrected an old script ( about six months old) that > queries Genbank for sequence information using the gi number. The scrips > gets the gi information by calling > > Gi_list=Genbank.search_for("gi|number") > > Then sequence information is extracted from Gi_list. The problem is that > although this used to work it now it doesn't. It doesn't throw an > exception either just keeps going. Has something changed with Genbank. Could you send us the accession number where the problem occurs? Otherwise it's hard to track down what happens ;-) Cheers, Peter -- ------------------------------------------------ Peter Bienstman Ghent University, Dep. of Information Technology Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium tel: +32 9 264 34 45, fax: +32 9 264 35 93 WWW: http://photonics.intec.UGent.be email: Peter.Bienstman@UGent.be ------------------------------------------------ From mdehoon at ims.u-tokyo.ac.jp Wed Nov 26 08:39:16 2003 From: mdehoon at ims.u-tokyo.ac.jp (Michiel Jan Laurens de Hoon) Date: Wed Nov 26 08:42:31 2003 Subject: [BioPython] Martel installation In-Reply-To: <20031125221713.GD80145@evostick.agtec.uga.edu> References: <200310221521.h9MFL3db020367@portal.open-bio.org> <5.1.1.5.2.20031125141229.022588b8@sciences.sdsu.edu> <20031125221713.GD80145@evostick.agtec.uga.edu> Message-ID: <3FC4AD04.1050005@ims.u-tokyo.ac.jp> For some reason, the Martel files were indeed missing from the Windows installers of Biopython. I have made new Windows installers that now contain Martel. They are available at http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/biopython-1.23.win32-py2.2.exe http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/biopython-1.23.win32-py2.3.exe (I'll remove these links once the installers are available from the Biopython website, I haven't figured out yet how to do that). --Michiel. Brad Chapman wrote: > Hi Scott; > Hope everything is going well with you. > > >>Can anyone out there tell me where to install Martel? We need it for >>Clustalw. We tried installing it in site-packages and within Bio but no go. >>It does not seem to be included in Biopython for Python 2.3. > > > Are you using the source distribution or the windows installer? I > know it is in the source distribution but I'm not positive about the > installer, as I didn't make it this time (and also don't have a > windows computer on hand). > > Either way, it is included in the source distribution so you can get > it there. If it's on windows you can just unzip the source and move > the Martel directory into site-packages (the same level as Bio, > not inside Bio). You should be able to do a import Martel from the > python prompt after doing this. > > If this doesn't work, can you provide some more information about > what you mean by "no go" so I can try and provide better help? > > Brad > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From gspraggon at gnf.org Wed Nov 26 10:39:51 2003 From: gspraggon at gnf.org (Glen Spraggon) Date: Wed Nov 26 10:46:24 2003 Subject: [BioPython] Connecting to Genbank Message-ID: <833E32F61B9F8746878F2A1865BECE609F5F72@EXCHCLUSTER01.lj.gnf.org> Hi Again, No gi number that I have tried works there appears to be no connection you can try gi|15834378 but the same sort of call works with BioPerl. Cheers Glen -----Original Message----- From: Peter Bienstman [mailto:Peter.Bienstman@UGent.be] Sent: Tuesday, November 25, 2003 11:24 PM To: Glen Spraggon; biopython@biopython.org Subject: Re: [BioPython] Connecting to Genbank On Wednesday 26 November 2003 02:08, Glen Spraggon wrote: > Hi, > I have just resurrected an old script ( about six months old) > that queries Genbank for sequence information using the gi number. The > scrips gets the gi information by calling > > Gi_list=Genbank.search_for("gi|number") > > Then sequence information is extracted from Gi_list. The problem is > that although this used to work it now it doesn't. It doesn't throw an > exception either just keeps going. Has something changed with Genbank. Could you send us the accession number where the problem occurs? Otherwise it's hard to track down what happens ;-) Cheers, Peter -- ------------------------------------------------ Peter Bienstman Ghent University, Dep. of Information Technology Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium tel: +32 9 264 34 45, fax: +32 9 264 35 93 WWW: http://photonics.intec.UGent.be email: Peter.Bienstman@UGent.be ------------------------------------------------ From Peter.Bienstman at UGent.be Wed Nov 26 11:06:33 2003 From: Peter.Bienstman at UGent.be (Peter Bienstman) Date: Wed Nov 26 11:12:59 2003 Subject: [BioPython] Connecting to Genbank In-Reply-To: <833E32F61B9F8746878F2A1865BECE609F5F72@EXCHCLUSTER01.lj.gnf.org> References: <833E32F61B9F8746878F2A1865BECE609F5F72@EXCHCLUSTER01.lj.gnf.org> Message-ID: <200311261706.33438.Peter.Bienstman@UGent.be> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Ah, so it's not a parsing problem then. I'm not familiar with the network access code to GenBank, so perhaps somebody else can help you here. Brad? Peter On Wednesday 26 November 2003 16:39, Glen Spraggon wrote: > Hi Again, > No gi number that I have tried works there appears to be no > connection you can try gi|15834378 but the same sort of call works with > BioPerl. > > Cheers > > Glen > > -----Original Message----- > From: Peter Bienstman [mailto:Peter.Bienstman@UGent.be] > Sent: Tuesday, November 25, 2003 11:24 PM > To: Glen Spraggon; biopython@biopython.org > Subject: Re: [BioPython] Connecting to Genbank > > On Wednesday 26 November 2003 02:08, Glen Spraggon wrote: > > Hi, > > I have just resurrected an old script ( about six months old) > > that queries Genbank for sequence information using the gi number. The > > > > scrips gets the gi information by calling > > > > Gi_list=Genbank.search_for("gi|number") > > > > Then sequence information is extracted from Gi_list. The problem is > > that although this used to work it now it doesn't. It doesn't throw an > > > > exception either just keeps going. Has something changed with Genbank. > > Could you send us the accession number where the problem occurs? > Otherwise > it's hard to track down what happens ;-) > > Cheers, > > Peter - -- - ------------------------------------------------ Peter Bienstman Ghent University, Dep. of Information Technology Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium tel: +32 9 264 34 45, fax: +32 9 264 35 93 WWW: http://photonics.intec.UGent.be email: Peter.Bienstman@UGent.be - ------------------------------------------------ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.3 (GNU/Linux) iD8DBQE/xM+J4dgPAIjyquoRApSUAKDZCWgzqfNe8yrifJiTOpTDcKx4uACbBTIx 9L2qhFVW5r1lXphK1DIzv0s= =aXGy -----END PGP SIGNATURE----- From gspraggon at gnf.org Wed Nov 26 11:15:56 2003 From: gspraggon at gnf.org (Glen Spraggon) Date: Wed Nov 26 11:22:27 2003 Subject: [BioPython] Connecting to Genbank Message-ID: <833E32F61B9F8746878F2A1865BECE609F5F74@EXCHCLUSTER01.lj.gnf.org> Hi Again, Thanks, I have found a work around for it to get the information I need but it does seem that the GenBank.search_for function is not working for gi numbers - it does work for text searches in the script however. Cheers Glen -----Original Message----- From: Peter Bienstman [mailto:Peter.Bienstman@UGent.be] Sent: Wednesday, November 26, 2003 8:07 AM To: Glen Spraggon; biopython@biopython.org Subject: Re: [BioPython] Connecting to Genbank -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Ah, so it's not a parsing problem then. I'm not familiar with the network access code to GenBank, so perhaps somebody else can help you here. Brad? Peter On Wednesday 26 November 2003 16:39, Glen Spraggon wrote: > Hi Again, > No gi number that I have tried works there appears to be no > connection you can try gi|15834378 but the same sort of call works > with BioPerl. > > Cheers > > Glen > > -----Original Message----- > From: Peter Bienstman [mailto:Peter.Bienstman@UGent.be] > Sent: Tuesday, November 25, 2003 11:24 PM > To: Glen Spraggon; biopython@biopython.org > Subject: Re: [BioPython] Connecting to Genbank > > On Wednesday 26 November 2003 02:08, Glen Spraggon wrote: > > Hi, > > I have just resurrected an old script ( about six months old) > > that queries Genbank for sequence information using the gi number. > > The > > > > scrips gets the gi information by calling > > > > Gi_list=Genbank.search_for("gi|number") > > > > Then sequence information is extracted from Gi_list. The problem is > > that although this used to work it now it doesn't. It doesn't throw > > an > > > > exception either just keeps going. Has something changed with > > Genbank. > > Could you send us the accession number where the problem occurs? > Otherwise it's hard to track down what happens ;-) > > Cheers, > > Peter - -- - ------------------------------------------------ Peter Bienstman Ghent University, Dep. of Information Technology Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium tel: +32 9 264 34 45, fax: +32 9 264 35 93 WWW: http://photonics.intec.UGent.be email: Peter.Bienstman@UGent.be - ------------------------------------------------ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.3 (GNU/Linux) iD8DBQE/xM+J4dgPAIjyquoRApSUAKDZCWgzqfNe8yrifJiTOpTDcKx4uACbBTIx 9L2qhFVW5r1lXphK1DIzv0s= =aXGy -----END PGP SIGNATURE----- From chapmanb at uga.edu Wed Nov 26 13:46:33 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Wed Nov 26 13:57:49 2003 Subject: [BioPython] Connecting to Genbank In-Reply-To: <833E32F61B9F8746878F2A1865BECE609F5F74@EXCHCLUSTER01.lj.gnf.org> References: <833E32F61B9F8746878F2A1865BECE609F5F74@EXCHCLUSTER01.lj.gnf.org> Message-ID: <20031126184633.GF80145@evostick.agtec.uga.edu> Hi Glen, Peter; Glen: > > > I have just resurrected an old script ( about six months old) > > > that queries Genbank for sequence information using the gi number. > > > The scrips gets the gi information by calling > > > > > > Gi_list=Genbank.search_for("gi|number") > > > > > > Then sequence information is extracted from Gi_list. The problem is > > > that although this used to work it now it doesn't. It doesn't throw > > > an exception either just keeps going. Has something changed with > > > Genbank. Peter: > > Could you send us the accession number where the problem occurs? Glen: > > No gi number that I have tried works there appears to be no > > connection you can try gi|15834378 but the same sort of call works > > with BioPerl. The problem with the supplied GI number is that it is a protein sequence and by default search_for uses the nucleotide database. If you use the protein database things should work fine: >>> from Bio import GenBank >>> gi_list = GenBank.search_for("gi|15834378", database = "protein") >>> gi_list ['15834378'] If you use a nucleotide sequence (ala gi|38446359) the default works fine: >>> gi_list = GenBank.search_for("gi|38446359") >>> gi_list ['38446359'] So probably the best solution is to explicitly supply a database for your searches. Hopefully this helps! Brad From chapmanb at uga.edu Wed Nov 26 14:01:41 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Wed Nov 26 14:12:57 2003 Subject: [BioPython] Martel installation In-Reply-To: <3FC4AD04.1050005@ims.u-tokyo.ac.jp> References: <200310221521.h9MFL3db020367@portal.open-bio.org> <5.1.1.5.2.20031125141229.022588b8@sciences.sdsu.edu> <20031125221713.GD80145@evostick.agtec.uga.edu> <3FC4AD04.1050005@ims.u-tokyo.ac.jp> Message-ID: <20031126190141.GG80145@evostick.agtec.uga.edu> Hi Michiel; > For some reason, the Martel files were indeed missing from the Windows > installers of Biopython. I have made new Windows installers that now > contain Martel. They are available at > > http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/biopython-1.23.win32-py2.2.exe > http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/biopython-1.23.win32-py2.3.exe Thanks! I put them up on the biopython website. > (I'll remove these links once the installers are available from the > Biopython website, I haven't figured out yet how to do that). Basically, you just put them in /home/websites/biopython.org/files on the biopython.org computer. Do you have an account there? If not and you want to maintain them I can add you (I also don't mind just copying them over from your machine -- your choice). Modifying the website is a little tricker but not much. I wrote up some documentation about the website here: http://www.biopython.org/docs/developer/website_technical.html If you want to get more into it (and you are definitely welcome to :-). Speaking of the website -- Jeff, it looks like you didn't check in the latest version of the download page when you made the last release (the copy in CVS still has the 1.22 page). Would you mind checking that in when you get a chance? Sweet. Thanks again Michiel for maintaining the Windows installers. Brad From jeffrey.chang at duke.edu Wed Nov 26 14:12:10 2003 From: jeffrey.chang at duke.edu (Jeffrey Chang) Date: Wed Nov 26 14:18:37 2003 Subject: [BioPython] Martel installation In-Reply-To: <20031126190141.GG80145@evostick.agtec.uga.edu> References: <200310221521.h9MFL3db020367@portal.open-bio.org> <5.1.1.5.2.20031125141229.022588b8@sciences.sdsu.edu> <20031125221713.GD80145@evostick.agtec.uga.edu> <3FC4AD04.1050005@ims.u-tokyo.ac.jp> <20031126190141.GG80145@evostick.agtec.uga.edu> Message-ID: <6F120071-2044-11D8-85D2-000A956845CE@duke.edu> On Nov 26, 2003, at 2:01 PM, Brad Chapman wrote: > Speaking of the website -- Jeff, it looks like you didn't check in > the latest version of the download page when you made the last > release (the copy in CVS still has the 1.22 page). Would you mind > checking that in when you get a chance? Sweet. Oops, sorry about that. Good catch! I've checked it in now. Jeff From mikekolo at tiscali.co.uk Wed Nov 26 18:18:28 2003 From: mikekolo at tiscali.co.uk (mikekolo@tiscali.co.uk) Date: Wed Nov 26 18:25:39 2003 Subject: [BioPython] Good day Message-ID: <200311262325.hAQNPag0005096@portal.open-bio.org> Chief Paul musa Federal Ministry Of Works & Housing Federal seretariat, Lagos-Nigeria. Dear Sir, BUSINESS PROPOSAL: TRANSFER OF US$22.5 M (TWENTY TWO MILLION, FIVE HUNDRED THOUSAND UNITED STATES DOLLARS) & BUSINESS INVESTMENTS PARTNERSHIP. First, I must solicit your strictest confidence in this transaction, this is by virtue of it's nature as being utterly confidential andtop secret as you were introduced to me in confidence through the effortof an associate of mine who is in the foreign trade division of mycountry's consulate in the Unitedkingdoom.What I am about to devulge to you in this letter is top secret and if it offends or does not meet with your business ethics, I crave your indulgence. I am the chairman of the Contract Review Panel (CRP) set up by the present civilian Government of Nigeria to review contracts awarded by the past military administration. In the course of our work at the CRP, we discovered this fund which resulted from gross over invoicing and re-valuation of contracts by top government officials of the last administration. The companies that executed the contracts have been duly paid and the contracts commissioned leaving the sum of US$22.5 Million floating in the escrow account of the Central Bank of Nigeria ready for payment. I have therefore been mandated as a matter of trust by my colleagues in the committee to look for an overseas partner to whom we could transfer the sum of US$22.5M legally su-bcontracting the entitlement to you/your company. This is bearing in mind that our civil service code of conduct forbids us from owning foreign company or running foreign account while in government service hence the need for an oversea partner. We have agreed that the funds will be shared thus after it has been paid into your account: (1) 30% of the money will go to you for acting as the beneficiary of the fund. (2) 10% has been set aside as an abstract projection for reimbursment to both parties for incidental expences that may be incurred in the course of the transaction. (3) 60% to us the government officials (with which we wish to commence an importation business in conjunction with you in your country). All logistics are in place and all modalities worked out for the smooth conclusion of the transaction within ten to fourteen days of commencement after receipt of the following information: Your full name/company name, address, company's details & ctivities,telephone & fax numbers.These information will enable us make the applications and lodge claims to the concerned ministries & agencies in favour of you/your company and it is pertinent to state here that this transaction is entirely based on trust as the solar bank draft or certified cheque drawable in any of the Central Bank of Nigeria correspondent bankers in America, Asia and Europe is going to be made in your name. Also the confidentiality of of this transaction cannot be over-emphasized as it is only known between you and us. Please acknowledge the receipt of this Email and indicate your interest as we have limited time for this transaction. I await your prompt and positive response to this business proposal. Yours Faithfully, Chief Paul musa From sbassi at asalup.org Thu Nov 27 07:27:39 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Thu Nov 27 07:29:39 2003 Subject: [BioPython] search for overlapping count Message-ID: <3FC5EDBB.6010400@asalup.org> Hi, I'm about to finish the DNA melt function. But I need a function to count overlapping ocurrences of a string. string.count doesn't count overlapping ocurrences. For string.count, aagtctaaagctac has 2 "aa", but in fact there is 3 "aa". -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From sbassi at asalup.org Thu Nov 27 12:52:39 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Thu Nov 27 13:38:19 2003 Subject: [BioPython] New function ready (dna melting temperature) Message-ID: <3FC639E7.6040606@asalup.org> Hello, As I promised before (back to Nov-4), I wrote a function to get the DNA melting temperature. Since I don't have CVS access, I'll post it here. It would be trivial to make a version for RNA, with a optional parameter that if checked would mean is RNA. What do you think? import string import math def Tm_dan(s,dnac=50,saltc=50): """Returns DNA mt using nearest neighbor thermodynamics. dnac is DNA concentration [nM] and saltc is salt concentration [mM] Works as EMBOSS dan, taken from (Breslauer et al. Proc. Natl. Acad. Sci. USA 83, 3746-3750 and Baldino et al. Methods in Enzymol. 168, 761-777). Overcount function thanks to Greg Singer , rest by Sebastian Bassi """ def overcount(st,p): """Returns how many p are on st, works even for overlapping""" ocu=0 x=0 while 1: try: i=st.index(p,x) except ValueError: break ocu=ocu+1 x=i+1 return ocu sup=string.upper(s) r = 1.98717 LogDNA = r * math.log(c/4e9) vh=0 vs=0 vh=(overcount(sup,"AA"))*7.9+(overcount(sup,"TT"))*7.9+(overcount(sup,"AT"))*7.2+(overcount(sup,"TA"))*7.2+(overcount(sup,"CA"))*8.5+(overcount(sup,"TG"))*8.5+(overcount(sup,"GT"))*8.4+(overcount(sup,"AC"))*8.4 vh=vh+(overcount(sup,"CT"))*7.8+(overcount(sup,"AG"))*7.8+(overcount(sup,"GA"))*8.2+(overcount(sup,"TC"))*8.2 vh=vh+(overcount(sup,"CG"))*10.6+(overcount(sup,"GC"))*9.8+(overcount(sup,"GG"))*8+(overcount(sup,"CC"))*8 vs=(overcount(sup,"AA"))*22.2+(overcount(sup,"TT"))*22.2+(overcount(sup,"AT"))*20.4+(overcount(sup,"TA"))*21.3 vs=vs+(overcount(sup,"CA"))*22.7+(overcount(sup,"TG"))*22.7+(overcount(sup,"GT"))*22.4+(overcount(sup,"AC"))*22.4 vs=vs+(overcount(sup,"CT"))*21.0+(overcount(sup,"AG"))*21.0+(overcount(sup,"GA"))*22.2+(overcount(sup,"TC"))*22.2 vs=vs+(overcount(sup,"CG"))*27.2+(overcount(sup,"GC"))*24.4+(overcount(sup,"GG"))*19.9+(overcount(sup,"CC"))*19.9 entropy = -10.8 - vs entropy = entropy + ((len(s)-1) * (math.log10(saltconc/1000.0))*0.368) dTm = ((-vh*1000) / (entropy+LogDNA)) - 273.15 print vh,vs,entropy return dTm -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info -------------- next part -------------- A non-text attachment was scrubbed... Name: primertm3fun.zip Type: application/x-zip-compressed Size: 911 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20031127/72f38c8a/primertm3fun.bin From bakareabubaka at sify.com Thu Nov 27 14:17:12 2003 From: bakareabubaka at sify.com (MRS. MARIAM ABACHA (WIDOW).) Date: Thu Nov 27 14:24:49 2003 Subject: [BioPython] reply immediately, Message-ID: <200311271924.hARJO1g0011470@portal.open-bio.org> DEAR SIR, IT IS WITH HEART FULL OF HOPE THAT I WRITE TO SEEK YOUR HELP IN THE CONTEXT BELOW. I AM MRS, MARIAM ABACHA (WIDOW) THE WIFE OF FORMER HEAD OF STATE OF NIGERIA, GENERAL SANI ABACHA WHO'S SUDDEN DEATH OCCURRED ON THE 8TH OF JUNE, 1998. AS A RESULT OF CARDIAC ARREST WHILE STILL IN GOVERNMENT.I GOT YOUR EMAIL CONTACT FROM ONE OF THE MY FAMILY FRIEND A DIRECTOR, WITH THE NIGERIA CHEMBERS OF COMMERCE AND INDUSTRY. I HAVE NO DOUBT ABOUT YOUR CAPACITY AND GOODWILL TO ASSIST ME IN RECEIVING INTO YOUR PERSONAL BANK ACCOUNT (FOR SAFETY) THE SUM OF US$32,800,000.00 (THIRTY TWO MILLION, EIGTH HUNDRED THOUSAND US DOLLAS) WILLED AND DEPOSITED IN MY LATE HUSBAND'S FAVOUR THIS MONEY IS CURRENTLY DEPOSITED WITH A SECURITY COMPANY IN TWO TRUNK BOXES AS BELONGINGS AWAITING COLLECTION. AS IT IS LEGALLY REQUIRED, THE ADMINISTRATION OF MY LATE HUSBAND'S PROPERTIES IS UNDER THE AUTHORITY OF THE FAMILY'S LAWYER SINCE THE DEMISE OF MY HUSBAND, THE PRESENT REGIME (GOVERNMENT) HAS BEEN PROBING MY LATE HUSBAND'S WEALTH. PRESENTLY, SOME CASH ASSETS WITHIN AND OUTSIDE NIGERIA HAVE BEEN FROZEN AND SEIZED.FORTUNATELY, OUR FAMILY LAWYER HAD SECRETLY PROTECTED THE PERSONAL WILL OF MY LATE HUSBAND FROM THE NOTICE OF THE GOVERNMENT MEANWHILE, I AND EVERY MEMBER OF MY FAMILY ARE BEING MONITORED AND ALSO DENIAD ACCESS TO FINANCIAL DEALING WITHIN AND OUTSIDE NIGERIA.HENCE, I WAS ADVICE BY MY PERSONAL ASSISTANCE TO EMPLOYE THE ASSISTANCE OF A NEUTRAL INDIVIDUAL OUTSIDE NIGERIA AND WITH THE LEGAL BACKING OF MY FAMILY LAWYER TO POSE AS THE BENEFICIARY OF THE WILLED MONEY AND THEREFORE CLAIM THE CONSIGNMENT FROM THE SECURITY COMPANY FOR BENEFIT OF US ALL. THE GOVERNMENT HAD EARLIER PLACED FOREIGN EMBARGO ON ALL OUR FAMILY MEMBERS, SEIZED ALL KNOWN LOCAL AND INTERNATIONAL OUTFITS OF OUR BUSINESS EMPIRE. THE SITUATION HAS BEEN SO TERRIBLE THAT WE ARE VIRTUALLY LIVING ON THE ASSISTANCE OF OUR WELL WISHERS. IN VIEW OF THIS PLIGHT THEREFORE, I EXPECT YOU TO BE TRUST WORTHY AND KIND ENOUGH TO RESPOND TO MY MAIL TO SAVE MY FAMILY AND I FROM A HOPELESS FUTURE. I HEREBY AGREE TO CONPENSATE YOUR SINCERE AND CANDID EFFORT IN THIS REGARD WITH 20% OF THE FUND WHEN FINALLY RECEIVED IN YOUR PERSONAL BANK ACCOUNT.MY LAWYER WILL MAKE EVERY ARRENGMENTS TO EFFECT COMPLETE DISLODGMENT OF THIS MONEY WITHIN A WEEK OF THE RECEIPT OF YOUR RESPONSE THROUGH E-MAIL.PLEASE, ALL CONTACT ON PHONE MUST BE THROUGH OUR FAMILY LAWYER- OR MY PERSONAL ASSISTANCE WHILE YOU COMMUNICATE WITH ME ON EMAIL AS I AND MY FAMILY MEMBER IS BEEN HEAVELY MONITORED BY THE GOVERNMENT. I WILL ALSO FORWARD THE EMAIL AND PHONE NUMBER OF MY FAMILY AFTER YOUR RESPONSE. I LOOK FORWARD TO YOUR QUICK RESPONSE. MAY ALLAH BLESS YOU. BEST WISHES, MRS. MARIAM ABACHA (WIDOW). mariam_abachaa2003@yahoo.com NB: PLEASE I WILL WANT YOU TO GO THROUGH THE FOLLOWING WEBSITE INOTHER TO CONFIRM MORE ON THE ISSUES OF THE ABACHA AND THE FEDERAL GOVERNMENT SEIZURE AND FROZON ON THE ABACHA'S WEALTH. http://news.bbc.co.uk/1/hi/world/africa/877113.stm http://news.bbc.co.uk/1/hi/world/africa/909972.stm http://www.marcosbillions.com/marcos/Dictators%20Abacha.htm From idoerg at burnham.org Thu Nov 27 14:21:11 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu Nov 27 14:28:26 2003 Subject: [BioPython] Spam Filtering? Message-ID: <3FC64EA7.1010809@burnham.org> Should we put a spam filter on our lists? Or start non-member moderation? ./I -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From sbassi at asalup.org Thu Nov 27 15:37:21 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Thu Nov 27 16:48:37 2003 Subject: [BioPython] Tm with RNA support Message-ID: <3FC66081.7040306@asalup.org> Here is the version with RNA support (by default is DNA), to enable the RNA tm, use rna=1 as argument. import string import math def Tm_dan(s,dnac=50,saltc=50,rna=0): """Returns DNA/RNA tm using nearest neighbor thermodynamics. dnac is DNA/RNA concentration [nM] and saltc is salt concentration [mM] rna=0 is for DNA (default), for RNA, rna should be <>0. Works as EMBOSS dan, taken from (Breslauer et al. Proc. Natl. Acad. Sci. USA 83, 3746-3750 and Baldino et al. Methods in Enzymol. 168, 761-777). Overcount function thanks to Greg Singer , rest by Sebastian Bassi """ def overcount(st,p): """Returns how many p are on st, works even for overlapping""" ocu=0 x=0 while 1: try: i=st.index(p,x) except ValueError: break ocu=ocu+1 x=i+1 return ocu sup=string.upper(s) r = 1.98717 LogDNA = r * math.log(c/4e9) vh=0 vs=0 if rna==0: vh=(overcount(sup,"AA"))*7.9+(overcount(sup,"TT"))*7.9+(overcount(sup,"AT"))*7.2+(overcount(sup,"TA"))*7.2+(overcount(sup,"CA"))*8.5+(overcount(sup,"TG"))*8.5+(overcount(sup,"GT"))*8.4+(overcount(sup,"AC"))*8.4 vh=vh+(overcount(sup,"CT"))*7.8+(overcount(sup,"AG"))*7.8+(overcount(sup,"GA"))*8.2+(overcount(sup,"TC"))*8.2 vh=vh+(overcount(sup,"CG"))*10.6+(overcount(sup,"GC"))*9.8+(overcount(sup,"GG"))*8+(overcount(sup,"CC"))*8 vs=(overcount(sup,"AA"))*22.2+(overcount(sup,"TT"))*22.2+(overcount(sup,"AT"))*20.4+(overcount(sup,"TA"))*21.3 vs=vs+(overcount(sup,"CA"))*22.7+(overcount(sup,"TG"))*22.7+(overcount(sup,"GT"))*22.4+(overcount(sup,"AC"))*22.4 vs=vs+(overcount(sup,"CT"))*21.0+(overcount(sup,"AG"))*21.0+(overcount(sup,"GA"))*22.2+(overcount(sup,"TC"))*22.2 vs=vs+(overcount(sup,"CG"))*27.2+(overcount(sup,"GC"))*24.4+(overcount(sup,"GG"))*19.9+(overcount(sup,"CC"))*19.9 else: vh=(overcount(sup,"AA"))*6.6+(overcount(sup,"TT"))*6.6+(overcount(sup,"AT"))*5.7+(overcount(sup,"TA"))*8.1+(overcount(sup,"CA"))*10.5+(overcount(sup,"TG"))*10.5+(overcount(sup,"GT"))*10.2+(overcount(sup,"AC"))*10.2 vh=vh+(overcount(sup,"CT"))*7.6+(overcount(sup,"AG"))*7.6+(overcount(sup,"GA"))*13.3+(overcount(sup,"TC"))*13.3 vh=vh+(overcount(sup,"CG"))*8.0+(overcount(sup,"GC"))*14.2+(overcount(sup,"GG"))*12.2+(overcount(sup,"CC"))*12.2 vs=(overcount(sup,"AA"))*18.4+(overcount(sup,"TT"))*18.4+(overcount(sup,"AT"))*15.5+(overcount(sup,"TA"))*16.9 vs=vs+(overcount(sup,"CA"))*27.8+(overcount(sup,"TG"))*27.8+(overcount(sup,"GT"))*26.2+(overcount(sup,"AC"))*26.2 vs=vs+(overcount(sup,"CT"))*19.2+(overcount(sup,"AG"))*19.2+(overcount(sup,"GA"))*35.5+(overcount(sup,"TC"))*35.5 vs=vs+(overcount(sup,"CG"))*19.4+(overcount(sup,"GC"))*34.9+(overcount(sup,"GG"))*29.7+(overcount(sup,"CC"))*29.7 entropy = -10.8 - vs entropy = entropy + ((len(s)-1) * (math.log10(saltconc/1000.0))*0.368) dTm = ((-vh*1000) / (entropy+LogDNA)) - 273.15 print vh,vs,entropy return dTm -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info -------------- next part -------------- A non-text attachment was scrubbed... Name: tm.zip Type: application/x-zip-compressed Size: 1131 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20031127/43a0f1c1/tm.bin From isiomawilly2000 at netscape.net Thu Nov 27 23:08:16 2003 From: isiomawilly2000 at netscape.net (Dr Isioma Williams) Date: Thu Nov 27 23:14:51 2003 Subject: [BioPython] HELLO Message-ID: <200311280414.hAS4Ecg0013641@portal.open-bio.org> from the desk of : DR ISIOMA WILLIAMS DIRECT TEL: 234-1-776 2501 (24HRS) TEL: 234-1-804 4824 FAX: 234-1-759 2574 EMAIL: isiomaw@yahoo.com.au STRICTLY CONFIDENTIAL WE ARE MEMBERS OF A SPECIAL COMMITTEE ON PROJECT IMPLEMENTATION OF THE NIGERIAN NATIONAL PETROLEUM CORPORATION (NNPC). THIS COMMITTEE IS PRINCIPALLY CONCERNED WITH CONTRACT AWARDS AND APPROVAL. WITH OUR POSITIONS, WE HAVE SUCCESSFULLY SECURED FOR OURSELVES THE SUM OF SIXTEEN MILLION, FIVE HUNDRED THOUSAND UNITED STATES DOLLARS (US$16.5M). MY COLLEAGUES AND I DURING THE COURSE OF OUR OFFICIAL ASSIGNMENT AWARDED SERIES OF CONTRACTS TO FOREIGN FIRMS ON AGREED 5% COMMISSION OR PROFIT ON THEIR CONTRACT SUM. HOWEVER THE 5% COMMISSION WHICH AMOUNTED TO US$16.5M AFTER AUDIT REPORT IS LEFT UNCLAIMED IN THE FLOATING ACCOUNT OF MY COMPANY [NNPC]. THIS CONTRACT IN QUESTION WERE FOR THE SUPPLY OF PETRO CHEMICAL EQUIPMENT AND COMPUTERS TO MY COMPANY THE NIGERIAN NATIONAL PETROLEUM CORPORATION [NNPC] IN 1999. THE CONTRACTORS HAVE EXECUTED THEIR PROJECT AS SPECIFIED IN THE CONTRACT AGREEMENT AND WERE PAID ACCORDINGLY. RECENTLY, THE NEW CIVILIAN GOVERNMENT STARTED PAYING OFF ALL THE INDEBTED FOREIGN CONTRACTORS TO MY COMPANY THAT EXECUTED CONTRACTS AS FAR BACK AS 1990 2002 IN ORDER TO LAUNDER A GOOD IMAGE OF THEIR GOVERNMENT BEFORE THE UNITED NATION. CONSEQUENT TO THIS DEVELOPMENT, WE CONSIDER THIS A GREAT OPPORTUNITY FOR US TO CARRYOUT THE TRANSFER OF THESE FUNDS TO A SAFE ACCOUNT OVERSEAS WHICH WE BELIEVE YOU WILL BE IN A POSITION TO HELP US IN TRANSFERRING THESE FUNDS [US$16.5M] INTO YOUR NOMINATED ACCOUNT. IT HAS BEEN AGREED THAT THE OWNER OF THE ACCOUNT WILL BE COMPENSATED WITH 20% OF THE REMITTED FUNDS, WHILE WE KEEP 70%, AND 10% WILL BE SET ASIDE TO OFFSET EXPENSES AND PAY THE NECESSARY TAXES. ALL MODALITIES OF THIS TRANSACTION HAVE BEEN WORKED OUT AND ONCE STARTED WILL NOT TAKE MORE THAN 10 WORKING DAYS, WITH YOUR FULL SUPPORT. THIS TRANSACTION IS 100% RISK FREE.IF THIS PROPOSAL SATISFIES YOU, PLEASE REACH US ONLY BY FAX OR PHONE, FOR MORE INFORMATION. IT MIGHT BE DIFFICULT TO GET THROUGH TO ME, BECAUSE OF POOR TELECOMMUNICATION SYSTEM HERE. PLEASE KEEP TRYING, YOU WILL DEFINITELY GET THROUGH. PLEASE TREAT AS URGENT AND VERY CONFIDENTIAL. YOURS FAITHFULLY, DR ISIOMA WILLIAMS NB: FOR CONFIDENTIAL REASONS AND DUE TO THE POOR COMMUNICATION SYSTEM IN MY COUNTRY, MOST OFTEN FOREIGN CALLS COULD BE DIVERTED TO THE WRONG PERSON. SO, FOR YOU TO BE VERY SURE YOU ARE RIGHTLY SPEAKING WITH ME, IT IS VERY IMPORTANT THAT WHEN YOU CALL AND ASK FOR ME, THE MOMENT I PICK UP THE PHONE, YOU SHOULD ASK ME FOR THE "CODE WORD" AND MY ANSWER WOULD BE "SUCCESS" BEFORE WE PROCEED DISCUSSIONS, BUT IF I DO NOT SAY"SUCCESS", THAT MEANS YOU ARE NOT SPEAKING WITH ME JUST DISCONNECT THE LINE AND CALL ME BACK TILL I GIVE YOU THE CODE WORD. From sbassi at asalup.org Fri Nov 28 06:29:35 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Fri Nov 28 06:31:35 2003 Subject: [BioPython] Tm with RNA support In-Reply-To: <3FC711FE.5000107@clondiag.com> References: <3FC66081.7040306@asalup.org> <3FC711FE.5000107@clondiag.com> Message-ID: <3FC7319F.2050402@asalup.org> Peter Slickers wrote: > Hei Sebastian, > its a good idee to add a Tm function to biopython. But the Breslauer > parameter set is dated. I strongly recommend not to use Breslauer > parameters for any new code. SantaLucia has published a superior > parameter set in 1997. The calculation schema is mainly the same, both > are based on nearest neighbor increments (but no increments > for 1-3 or 1-4 neighbors). The SantaLucia parameter set also includes > increments for the end of the duplex. This gives much more consistent > results for long duplexes. Breslauer should not be used for oligos > longer than about 30 to 40 nt. > SantaLucia J Jr,Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1460-5. > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9465037&dopt=Abstract Ok, you're right. That's way I asked before starting. I've just downloaded the paper you quoted and I will work in a new version. -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From dr_edward2003okon at spinfinder.com Fri Nov 28 16:27:54 2003 From: dr_edward2003okon at spinfinder.com (Dr Edward Okon) Date: Fri Nov 28 16:36:27 2003 Subject: [BioPython] Urgent message from Dr Edward Okon Message-ID: <200311282134.hASLXeg0018137@portal.open-bio.org> Sir, REQUEST FOR BUSINESS PARTNERSHIP INTRODUCTION & BIO-DATA I am Dr Edward Okon Chairman Ministerial Contracts Evaluation and Implementation Committee in the Federal Ministry of Aviation. My position is very sensitive. I am married with children and hold degrees in Public Administration and Medical Studies. I am due for retirement any moment from now, after many years in service. REASONS FOR CONTACTING YOU I require urgently, your unreserved assistance in providing me with a safe and reliable bank account with full details viz: Name and Address of Bank, Telephone, Telex and Fax numbers anywhere in the world where I can transfer the sum of $27.5Million United States Dollars only. The purpose of transfer is to take care of my retirement by investing in viable business you might deem fit to advise. NATURE OF BUSINESS AND SOURCE OF FUNDS FOR TRANSFER Since the inception of the present government, series of contracts have been awarded by the Federal Ministry of Aviation based on supplies (AIRPORT NAVIGATIONAL ELECTRONICS), INSTRUMENT LANDING EQUIPMENT (ILE),AND RADAR EQUIPMENT, VOR SYSTEMS MONITORS/ DISTANCE MEASURING EQUIPMENT (DME), SECONDARY SURVEILLANCE RADAR (SSR), INSTALLATION OF ONE UNIT OF INSRUMENT, LANDING SYSTEMS AND RADAR EQUIPMENT at Abuja International Airport) amounting to several millions of US Dollars. The above sum (US$27.5M) has shown in record as surplus some of the over-invoiced contracts carried in the last developmental quarter. Presently, I have arranged for the money to be kept in a coded bank account with the Central Bank of Nigeria, until I am able to source for a reliable Expatriate Partner whom I can present as the beneficiary of the funds. You will take the status of the contractor who executed the contract, and I will arrange the supportive documents for the transfer. MODE OF SHARING 25% will go to you for making available to us a company or personal account number, giving me your unreserved assistance and keeping strictly the rules of this transaction until transfer of the funds is effected. 5% is for any contingencies and all miscellaneous expenses incurred during the course of the transaction, procurement of vital documents, tips and all expenses including phones/ fax bills, hotels bills, taxes and bank charges must be reconciled upon confirmation of the payment by the DEBT MANAGEMENT OFFICE (DMO) OF THE PRESIDENCY 70% will be shared between me and a few colleagues of mine whose help will be highly needed throughout this period in question. OTHER PERTINENT DETAILS Everything about this transaction is real. The money is clean, after putting in so many years in service, it is only normal for me to take good measures to secure my period in retirement. I have put in resources and time to bring this transaction to this level, which means that it represents a lot to me, and hopefully with help from you, in just a matter of weeks, it shall come to mean a lot to you too as we meet in your country to celebrate the closing of the deal. Kindly acknowledge your willingness through my private email:(dr_edward2003okon@pathfinder.gr)t to enable us commence effective process to finalize this matter. Thanking you for anticipated co-operation. Yours sincerely, Dr Edward Okon Chairman of the Committee.