From david at leehom.net Fri Oct 1 07:48:16 2004 From: david at leehom.net (asjeet) Date: Fri Oct 1 08:05:09 2004 Subject: [BioPython] =?windows-1251?b?0uX17W/rb+Po6CAyMeNvIOLl6mEgMTE6?= =?windows-1251?q?58=3A57?= Message-ID: <200410011204.i91C4fKr021574@portal.open-bio.org> ? ???????? 2000 ???? ? ?????? ???? ??????? ????????????? ????????????? ???????????? ? ???????? " ???????? ?????", ??? ???????? ??????? ???? ???????????? ????????? ??????????? ???????, ?????????? ? ????????? ??????. ???????????? ???????????? ??? ???????? ??????????? XXI ????. ?? ??????????: ??????? ?????????????????? ?????
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?? ??????? ???????? ???????????????. ????? ?????? ????! ???????? ????????? !! ??????? ??????????? ?? ????? ????????: http://www.pokupki.net From vason at eurotelecom.ru Fri Oct 1 11:19:20 2004 From: vason at eurotelecom.ru (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Fri Oct 1 11:22:01 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dogz/Py5fjl8fLi6P8g7+4g?= =?windows-1251?b?xeLw7u/lLg==?= Message-ID: <181095228.20041001152420@> ?????. ??? ????????? ???! ???????-?????? (5?/4? ? ???????) - ?? 160 ???? ?? ???????? ?????????? ? ????? "???????" 4*, ?/? ????????, 2-?? ?????????,?????????, ??????????. ????????????? ????????????: ????, ????, ????????? ? ??????. ???????.??? ????????? ???. ?????? (4?/3? ? ???????) - ?? 180 ???? ?? ???????? ?????????? ? ????? "????????? ??????" 2*, ?/?, ???????? ?????????,?????????, ??????????. ????????????? ????????????: ????, ???. ????????? ?????. ?????. ????????????? ???. 9 ???? / 8 ????? ????????? ?? 305 ????. ?????????? ? ????? Pansion Akat Krystal 3* ? ????????? ????????: ?\? ?????? ??????-?????- ?????? (????), ???????-??????? ?? ?/? ???????, ?????????? ? ?????, ??????? - ??????? (???????? ????), ????????????? ????????? (7 ?????????),????? ?????, ????? ?????, ??????????? ?????????. ?????. ?????. ????????????? ???. 8 ???? / 7 ????? ????????? ?? 305 ????. ?????????? ? ????? Pansion Akat Krystal 3* ? ????????? ????????: ?/? ??????-?????- ?????? , ???????-???????, ?????????? ? ?????, ??????? - ??????? (???????? ????), ????????????? ?????????, ??????????? ?????????. ??????. ????????? ????????????? ???. ?????? ???????? ? ?????. (?? 5 ????) - 520 ???? ?? ???????? ?????????? ? ????? 3*, ???????????, ?????????, ?????????,?????????? ????????????? ????????????: ???? ???????, ??????????????? ?????????. ???????. ????? - ?? 370 ???? ?? ???????? ????? 3*,???????, ???????????. ???????. ????????????? ???. ???????? ??????? ??? - ?? 369 ???? ?? ???????? ????? 2*, ???????????, ??????????, ?????????, ???????? ????????? ????????????? ????????????: ????, ???. ?????????. ?????????. ???????????? ???. ?????-????-?????? - 905 ????, ???./???? : (095) 7-888-769 ??????? ??? ??????????? ?????: 8-926-230-68-68 8-903-263-18-86 ?????????? ????????? "??????? ? ??????!" ?. "?????????????", ??. ?????????, ?. 12, ???. 6 ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From jasper at seznam.cz Fri Oct 1 13:19:40 2004 From: jasper at seznam.cz (eliot) Date: Fri Oct 1 13:26:23 2004 Subject: [BioPython] =?windows-1251?b?ze7i4P8g6u7r6+Xq9uj/?= Message-ID: <200410011726.i91HQBKr024995@portal.open-bio.org> ???????????? ??????? ??????????? ????? ? ????? ??????? ???? ??? ?? www.elitpresent.ru From dmrg at 020.co.uk Sat Oct 2 19:50:03 2004 From: dmrg at 020.co.uk (dmrg@020.co.uk) Date: Sat Oct 2 20:45:47 2004 Subject: [BioPython] CDs - so billig wie noch nie... Message-ID: Seid Ihr auf der Suche nach guten, günstigen, gebrauchten und auch ungebrauchten CD´s? Dann habt Ihr hier die richtige Adresse gefunden. Das Angebot umfaßt derzeit über 3000 CD´s aus den Richtungen Pop, Rock, Independent, Metal, Deutschrock, Schlager, Techno, Black, und ein wenig Klassik ist ebenfalls vorhanden http://www.jr-cds.de/?id=11553 From tzl-cker at elturista.com Sun Oct 3 18:23:13 2004 From: tzl-cker at elturista.com (jeanine) Date: Sun Oct 3 18:39:36 2004 Subject: [BioPython] =?windows-1251?b?INP+8iDoIPLl7+tvIOIgwmH45ewg5G/s?= =?windows-1251?q?=E5_22=3A33=3A23?= Message-ID: <200410032239.i93MdQKr022129@portal.open-bio.org> ? ???????? 2000 ???? ? ?????? ???? ??????? ????????????? ????????????? ???????????? ? ???????? " ???????? ?????", ??? ???????? ??????? ???? ???????????? ?????????? ???????, ?????????? ? ????????? ??????. ???????????? ???????????? ??? ???????? ??????????? 21?? ????. ?? ??????????: ????? ??????????? ??????????????
?????????????? ??????? ????? ?????????????? ???? ??????
?????????????? ?????????? ??? ??????? ??? ???????
?? ????? ?????? ???????????????. ????? ?????? ????! ?????????? ???????? !!! ??????? ??????????? ?? ????? ?????: http://pokupki.net From nauman.maqbool at agresearch.co.nz Sun Oct 3 21:44:33 2004 From: nauman.maqbool at agresearch.co.nz (Maqbool, Nauman) Date: Sun Oct 3 21:43:56 2004 Subject: [BioPython] running primer3 with multiple sequences Message-ID: Hi I am trying to run eprimer3 using biopython and am not sure how to input multiple options. E.g. if I am reading in a fasta file with hundreds of sequences with different primer design parameters for each sequence, do I have to hard code the parameters individually for each sequence? In the example below: from Bio.Emboss.Applications import Primer3Commandline from Bio.Emboss.Primer import Primer3Parser from Bio.Application import generic_run def get_primers(fasta_record, start, end): open("in.pr3", "w").write(str(fasta_record) + "\n") primer_cl = Primer3Commandline() primer_cl.set_parameter("-sequence", "in.pr3") primer_cl.set_parameter("-outfile", "out.pr3") primer_cl.set_parameter("-productsizerange", "350,500") primer_cl.set_parameter("-target", "%s,%s" % (start, end)) result, r, e = generic_run(primer_cl) parser = Primer3Parser() return parser.parse(open("out.pr3")) def main(fasta_file, output_file): output_handle = open(output_file, "w") output_handle.write("name,forward_primer,reverse_primer\n") parser = Fasta.RecordParser() iterator = Fasta.Iterator(open(fasta_file), parser) while 1: cur_record = iterator.next() if not(cur_record): break primer_record = get_primers(cur_record, 100, 250) if len(primer_record.primers) > 0: primer = primer_record.primers[0] output_handle.write("%s,%s,%s\n" % ( cur_record.title, primer.forward_seq, primer.reverse_seq)) else: print "No primers found for %s" % cur_record.title the start and end positions, i.e. the target area, to be included in the product, remains the same (100 to 250 in this case), how do I change these if I have a different target area for different sequences? Also, how do I use biopython if I give the sequences and parameters in the format below, rather than using a fasta file? PRIMER_SEQUENCE_ID=test_seq1 SEQUENCE=atgatgatgtnnnnnnnnntgatgatgatgcaccatagatgatcacacaccattaaacatcat catcttgatgatgatgcaccatagatgatcacacaccattaaacatcatcatcttaaacatcatcatcttga tgatgatgcaccatagatgatcacacaccataaacatcatcatctgatgatgatgcaccatagatgatcaca caccattaaacatcatcatcttaaacatcatcatcttgatgatgatgcaccatagatgatcacacaccatta aacatcatcatcttaaacatcatcatcttgatgatgatgcaccatagatgatcacacacca INCLUDED_REGION=150,329 PRIMER_OPT_SIZE=19 PRIMER_MIN_SIZE=17 PRIMER_MAX_SIZE=22 PRIMER_PRODUCT_SIZE_RANGE=64-629 PRIMER_EXPLAIN_FLAG=1 = Thanks a lot Nauman ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. 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If you have received this message in error, please notify the sender immediately. ======================================================================= From sekhar at t-online.de Tue Oct 5 22:52:48 2004 From: sekhar at t-online.de (elvin) Date: Tue Oct 5 22:58:00 2004 Subject: [BioPython] =?windows-1251?b?ze7i4P8g6u7r6+Xq9uj/?= Message-ID: <200410060257.i962voKr021930@portal.open-bio.org> ????? ????????? ??????????? ????? ?? ????? www.elitpresent.ru From jamuraa at static24-72-91-222.regina.accesscomm.ca Wed Oct 6 13:00:38 2004 From: jamuraa at static24-72-91-222.regina.accesscomm.ca (jamuraa@static24-72-91-222.regina.accesscomm.ca) Date: Wed Oct 6 12:55:57 2004 Subject: [BioPython] new pharma In-Reply-To: References: Message-ID: <2JGIBL9EL1HDJI7D@static24-72-91-222.regina.accesscomm.ca> Propecia, Viagra, Cialis, Vioxx, Cialis, Lipitor and more! http://tzett.beatypeople.biz/ From kmb28 at calle.in-berlin.de Wed Oct 6 19:34:35 2004 From: kmb28 at calle.in-berlin.de (kmb28@calle.in-berlin.de) Date: Wed Oct 6 22:12:38 2004 Subject: [BioPython] New pharma shop In-Reply-To: References: Message-ID: Xenical, Glucophage, Zyban, Zyban, Ambien, Viagra and more! http://pcomq.beatypeople.biz/ From karin.lagesen at medisin.uio.no Fri Oct 8 09:21:15 2004 From: karin.lagesen at medisin.uio.no (Karin Lagesen) Date: Fri Oct 8 09:20:34 2004 Subject: [BioPython] genbank annotation Message-ID: <20041008132115.GB29370@uracil.uio.no> Hi! I have two genbank genome files, one of the old kind where each region is noted twize, and one where they are unique. What I would like to extract from this is the feature information, in this sort of format: Type start stop direction name In the first case, where almost all regions are noted twize, I'd like to have only one of them included in the list. You have a genbank parser thing in biopython which I'd like to use, however, I cannot figure out how to use it to do this. The files: The first: source 1..2944528 /organism="Listeria monocytogenes" /mol_type="genomic DNA" /strain="EGD-e" /db_xref="taxon:1639" gene 305..1673 /gene="dnaA" RBS 305..310 CDS 318..1673 /codon_start=1 /transl_table=11 /product="Chromosomal replication initiation protein DnaA" /protein_id="CAC98216.1" /db_xref="GI:16409360" /db_xref="GOA:Q8YAW2" /db_xref="UniProt/Swiss-Prot:Q8YAW2" /translation="MQSIEDIWQETLQIVKKNMSKPSYDTWMKSTTAHSLEGNTFIIS APNNFVRDWLEKSYTQFIANILQEITGRLFDVRFIDGEQEENFEYTVIKPNPALDEDG IEIGKHMLNPRYVFDTFVIGSGNRFAHAASLAVAEAPAKAYNPLFIYGGVGLGKTHLM HAVGHYVQQHKDNAKVMYLSSEKFTNEFISSIRDNKTEEFRTKYRNVDVLLIDDIQFL AGKEGTQEEFFHTFNTLYDEQKQIIISSDRPPKEIPTLEDRLRSRFEWGLITDITPPD LETRIAILRKKAKADGLDIPNEVMLYIANQIDSNIRELEGALIRVVAYSSLVNKDITA GLAAEALKDIIPSSKSQVITISGIQEAVGEYFHVRLEDFKAKKRTKSIAFPRQIAMYL SRELTDASLPKIGDEFGGRDHTTVIHAHEKISQLLKTDQVLKNDLAEIEKNLRKAQNM F" gene 1856..3062 /gene="dnaN" RBS 1856..1860 CDS 1867..3012 /codon_start=1 /transl_table=11 /product="DNA polymerase III, beta chain" /protein_id="CAC98217.1" /db_xref="GI:16409361" /db_xref="GOA:Q8YAW1" /db_xref="UniProt/TrEMBL:Q8YAW1" /translation="MKFVIERDRLVQAVNEVTRAISARTTIPILTGIKIVVNDEGVTL TGSDSDISIEAFIPLIENDEVIVEVESFGGIVLQSKYFGDIVRRLPEENVEIEVTSNY QTNISSGQASFTLNGLDPMEYPKLPEVTDGKTIKIPINVLKNIVRQTVFAVSAIEVRP VLTGVNWIIKENKLSAVATDSHRLALREIPLETDIDEEYNIVIPGKSLSELNKLLDDA SESIEMTLANNQILFKLKDLLFYSRLLEGSYPDTSRLIPTDTKSELVINSKAFLQAID RASLLARENRNNVIKLMTLENGQVEVSSNSPEVGNVSENVFSQSFTGEEIKISFNGKY MMDALRAFEGDDIQISFSGTMRPFVLRPKDAANPNEILQLITPVRTY" The second: source 1..4214630 /strain=168 /organism="Bacillus subtilis subsp. subtilis str. 168" /mol_type="genomic DNA" /db_xref="taxon:224308" CDS 410..1750 /function="initiation of chromosome replication (DNA synthesis)" /gene="dnaA" /protein_id="CAB11777.1" /locus_tag="BSU00010" /transl_table=11 /translation="MENILDLWNQALAQIEKKLSKPSFETWMKSTKAHSLQGDTLTIT APNEFARDWLESRYLHLIADTIYELTGEELSIKFVIPQNQDVEDFMPKPQVKKAVKED TSDFPQNMLNPKYTFDTFVIGSGNRFAHAASLAVAEAPAKAYNPLFIYGGVGLGKTHL MHAIGHYVIDHNPSAKVVYLSSEKFTNEFINSIRDNKAVDFRNRYRNVDVLLIDDIQF LAGKEQTQEEFFHTFNTLHEESKQIVISSDRPPKEIPTLEDRLRSRFEWGLITDITPP DLETRIAILRKKAKAEGLDIPNEVMLYIANQIDSNIRELEGALIRVVAYSSLINKDIN ADLAAEALKDIIPSSKPKVITIKEIQRVVGQQFNIKLEDFKAKKRTKSVAFPRQIAMY LSREMTDSSLPKIGEEFGGRDHTTVIHAHEKISKLLADDEQLQQHVKEIKEQLK" /db_xref="GOA:P05648" /db_xref="SUBTILIS:BG10065" /db_xref="SWISS-PROT:P05648" /note="alternate gene name: dnaH, dnaJ, dnaK" CDS 1939..3075 /locus_tag="BSU00020" /transl_table=11 /translation="MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDDGVSF TGSDSDISIESFIPKEEGDKEIVTIEQPGSIVLQARFFSEIVKKLPMATVEIEVQNQY LTIIRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNLIRQTVFAVSTSETRP ILTGVNWKVEQSELLCTATDSHRLALRKAKLDIPEDRSYNVVIPGKSLTELSKILDDN QELVDIVITETQVLFKAKNVLFFSRLLDGNYPDTTSLIPQDSKTEIIVNTKEFLQAID RASLLAREGRNNVVKLSAKPAESIEISSNSPEIGKVVEAIVADQIEGEELNISFSPKY MLDALKVLEGAEIRVSFTGAMRPFLIRTPNDETIVQLILPVRTY" /product="DNA polymerase III (beta subunit)" /function="DNA synthesis" /gene="dnaN" /EC_number="2.7.7.7" /protein_id="CAB11778.1" /db_xref="GOA:P05649" /db_xref="SUBTILIS:BG10066" /db_xref="SWISS-PROT:P05649" /note="alternate gene name: dnaG, dnaK" Karin -- Karin Lagesen, PhD student karin.lagesen@medisin.uio.no http://www.cmbn.no/rognes/ From sbassi at asalup.org Fri Oct 8 13:49:46 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Fri Oct 8 13:49:20 2004 Subject: [BioPython] Bioinformatics mailing list Message-ID: <4166D33A.9070704@asalup.org> GenesDigitales presents 2 new bioinformatics mailing list. Bioinfo is the name of a new mailing list hosted at DNALinux.com. This will be a place to ask for help and give a helping hand regarding bioinformatics. Topics included are: sequence analisis, software, aligment, primer design, microarrays, and much more. If you work with bioinformatics tools you are invited to join Bioinfo mailing list. The other list is called BioinfoES has the same aims as above but it is for Spanish speaking people. English-only bioinformatics mailing list: Bionfo (http://dnalinux.com/mailman/listinfo/bioinfo_dnalinux.com) Spanish bioinformatics mailing list: BioinfoES (http://dnalinux.com/mailman/listinfo/bioinfoes_dnalinux.com) -- 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 jules at ujsa.com Sat Oct 9 08:28:39 2004 From: jules at ujsa.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Sat Oct 9 08:38:49 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dog2MXLys7D0MDUyN8hISHU?= =?windows-1251?b?8/Lh7uvq6CEhISDS4Ozv7u/l9+Dy/CEhISDS6PHt5e3o5SEhIQ==?= Message-ID: <192521766.20041009123339@> ???????????!!!????????!!! ???????????!!! ????????!!! ?????????? ?????!!! 1. ???????? (????????, ?????, ??????, ?????, ???????...). ??????????? ?????? 6?6 M&R "Chameleon" (???, ??????????????????: 3+0, 960 ??????? ??????? ? ?????). ???????? ? ?????????? ????? 1 ???? 2 ????? 3 ????? 4 ????? 50 ??. 5,7 6,24 6,86 7,48 100 ??. 5,59 5,85 6,16 6,55 300 ??. 5,12 5,34 5,53 5,76 500 ??. 5,00 5,16 5,32 5,51 3000 ??. 4,74 4,84 4,50 4,65 5000 ??. 4,53 4,63 4,77 4,88 (???? ??????? ? ???????? ???????? ?? ??????? ???????? ???????.) 2. ??????????, ??????, ???????, ??????, ??????, ???? (?????? ???????? ? ???, ????????, ????? - ??????, ??????? ?/?...) ?????????????? ?????? Winnon, ??????? ????????? 30?30 ??. ???? ???????????????? ???? ????????? ????????? ??????????? ? ? ???????? ?????: ???????????. Winnon - 121. ????????? ?? ?????, ?????????, ???????, ??????, ??????????, ????, ???????, ????. ????, ????????????????. ????????. ???????? ??????? (??????, ???????, ????), ?????, ???????. ?? ???????? ?? ????, ???/????: ???????? ?????, ????????, ????????, ????????, ???????????, ?????????, ???. ?????? ?? ??????, ????????: ?????, ????????, ???????... ????????????? ?????????????, ???????, ?????????????, ????? -????, ?????? ?????, ????? ??? ?????? ?? ?????. ??????? ????? ???????????? ????????- ?????????? ????????? ?? ?????????. ?????????? ?????. ?????????? ??????, ???????, ?????? ???????????. ???????????? ?????????? ????????,?????????????? ???????, ??????????,???????? ??????? ????????? ???????????. ??????? ????? ?????? ?? ????????: (095) 7-888-769 (095) 101-3527 (????????.) 8 (926)523-42-41 (?????????????) ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From kingb at caltech.edu Mon Oct 11 19:04:53 2004 From: kingb at caltech.edu (Brandon King) Date: Mon Oct 11 19:04:15 2004 Subject: [BioPython] Is BioPython thread safe? Message-ID: <416B1195.9050106@caltech.edu> Hi All, I'm trying to use BioPython within a thread of my main program and I end up getting this error. Is BioPython intended to be thread safe? TraceBack: from Bio.Blast import NCBIStandalone File "/usr/lib/python2.3/site-packages/Bio/__init__.py", line 106, in ? _load_registries() File "/usr/lib/python2.3/site-packages/Bio/__init__.py", line 98, in _load_registries module = __import__("Bio.config.%s" % module, {}, {}, ["Bio","config"]) File "/usr/lib/python2.3/site-packages/Bio/config/FormatRegistry.py", line 26, in ? import _support File "/usr/lib/python2.3/site-packages/Bio/config/_support.py", line 26, in ? from Bio.MultiProc.copen import copen_fn File "/usr/lib/python2.3/site-packages/Bio/MultiProc/copen.py", line 322, in ? signal.signal(signal.SIGTERM, _handle_sigterm) ValueError: signal only works in main thread -Brandon King From curienri at yahoo.com Tue Oct 12 06:52:41 2004 From: curienri at yahoo.com (enrico curiotto) Date: Tue Oct 12 06:52:02 2004 Subject: [BioPython] regular expression and filtering dna strings Message-ID: <20041012105241.19684.qmail@web40712.mail.yahoo.com> Hello everybody, I have the following problem: A have a series of strings, some of them are DNA strings (so they contain only ACGT), other not. How can I filter out not DNA strings? Maybe this can be properly done quickly with regular expression in python, without using biopython. Does anyone know how to do that with regular expression ? Thank you very much, Enrico. _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From lpritc at scri.sari.ac.uk Tue Oct 12 07:58:25 2004 From: lpritc at scri.sari.ac.uk (Leighton Pritchard) Date: Tue Oct 12 07:57:56 2004 Subject: [BioPython] regular expression and filtering dna strings In-Reply-To: <20041012105241.19684.qmail@web40712.mail.yahoo.com> References: <20041012105241.19684.qmail@web40712.mail.yahoo.com> Message-ID: <416BC6E1.1080809@scri.sari.ac.uk> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Enrico, If your DNA strings never contain anything other than ACGT, then a result other than 'None' for re.search('[^ACGT]', your_string) will be diagnostic for non-DNA sequences. A None result will not, however, be diagnostic for DNA... Python 2.3.2 (#1, Dec 12 2003, 11:27:04) [GCC 3.3.2 20031022 (Red Hat Linux 3.3.2-1)] on linux2 Type "help", "copyright", "credits" or "license" for more information. |>> import re |>> a = 'ACGTGTACGT' |>> b = 'ACAGFTAGAT' |>> re.search('[^ACGT]', a) |>> print re.search('[^ACGT]', a) None |>> print re.search('[^ACGT]', b) <_sre.SRE_Match object at 0xbf511368> HTH, enrico curiotto wrote: | Hello everybody, | I have the following problem: | A have a series of strings, some of them are DNA strings (so they | contain only ACGT), other not. | How can I filter out not DNA strings? | Maybe this can be properly done quickly with regular expression | in python, without using biopython. | Does anyone know how to do that with regular expression ? | Thank you very much, | Enrico. | | | | | | _______________________________ | Do you Yahoo!? | Declare Yourself - Register online to vote today! | http://vote.yahoo.com | _______________________________________________ | BioPython mailing list - BioPython@biopython.org | http://biopython.org/mailman/listinfo/biopython | | - -- Dr Leighton Pritchard AMRSC D104, PPI, Scottish Crop Research Institute Invergowrie, Dundee, DD2 5DA, Scotland, UK E: lpritc@scri.sari.ac.uk W: http://bioinf.scri.sari.ac.uk/lp/index.shtml T: +44 (0)1382 562731 ext.2405 F: +44 (0)1382 568578 PGP key FEFC205C: GPG key E58BA41B: http://www.keyserver.net -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.3 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFBa8bhL1gZ+OWLpBsRAneTAJ9TFvjonzps8zDaCxZxbQe+iyNFygCfcjzO PxYU8Q+zAFZkVl62lakWd24= =5tI1 -----END PGP SIGNATURE----- From guo198010 at tom.com Tue Oct 12 11:09:46 2004 From: guo198010 at tom.com (guo198010@tom.com) Date: Tue Oct 12 11:09:01 2004 Subject: [BioPython] Software for Search-Engine, Mail, DNS, and more Message-ID: <004301c4b06d$827c13f0$0201a8c0@allfaxxh> Software for Search-Engine, Mail, DNS, and more http://cn.1618.net http://hk.1618.net http://tw.1618.net http://us.1618.net ftp://1618NET:E171BB2D873546689C770BCBE415B3F6@ftp.1618.net SORRY: this message is created by robot! From lancer at ujsa.com Wed Oct 13 04:28:37 2004 From: lancer at ujsa.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Wed Oct 13 04:42:34 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dogz/Py5fjl8fLi6P8g7+4g?= =?windows-1251?b?xeLw7u/lLg==?= Message-ID: <177094092.20041013083337@> ?????. ??? ????????? ???! ???????-?????? (5?/4? ? ???????) - ?? 160 ???? ?? ???????? ?????????? ? ????? "???????" 4*, ?/? ????????, 2-?? ?????????,?????????, ??????????. ????????????? ????????????: ????, ????, ????????? ? ??????. ???????.??? ????????? ???. ?????? (4?/3? ? ???????) - ?? 180 ???? ?? ???????? ?????????? ? ????? "????????? ??????" 2*, ?/?, ???????? ?????????,?????????, ??????????. ????????????? ????????????: ????, ???. ????????? ?????. ?????. ????????????? ???. 9 ???? / 8 ????? ????????? ?? 305 ????. ?????????? ? ????? Pansion Akat Krystal 3* ? ????????? ????????: ?\? ?????? ??????-?????- ?????? (????), ???????-??????? ?? ?/? ???????, ?????????? ? ?????, ??????? - ??????? (???????? ????), ????????????? ????????? (7 ?????????),????? ?????, ????? ?????, ??????????? ?????????. ?????. ?????. ????????????? ???. 8 ???? / 7 ????? ????????? ?? 305 ????. ?????????? ? ????? Pansion Akat Krystal 3* ? ????????? ????????: ?/? ??????-?????- ?????? , ???????-???????, ?????????? ? ?????, ??????? - ??????? (???????? ????), ????????????? ?????????, ??????????? ?????????. ??????. ????????? ????????????? ???. ?????? ???????? ? ?????. (?? 5 ????) - 520 ???? ?? ???????? ?????????? ? ????? 3*, ???????????, ?????????, ?????????,?????????? ????????????? ????????????: ???? ???????, ??????????????? ?????????. ???????. ????? - ?? 370 ???? ?? ???????? ????? 3*,???????, ???????????. ???????. ????????????? ???. ???????? ??????? ??? - ?? 369 ???? ?? ???????? ????? 2*, ???????????, ??????????, ?????????, ???????? ????????? ????????????? ????????????: ????, ???. ?????????. ?????????. ???????????? ???. ?????-????-?????? - 905 ????, ???./???? : (095) 7-888-769 ??????? ??? ??????????? ?????: 8-926-230-68-68 8-903-263-18-86 ?????????? ????????? "??????? ? ??????!" ?. "?????????????", ??. ?????????, ?. 12, ???. 6 ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From noreply at bestlabdeals.com Thu Oct 14 12:45:00 2004 From: noreply at bestlabdeals.com (Best Lab Deals) Date: Thu Oct 14 09:57:04 2004 Subject: [BioPython] buying lab equipment can be fun Message-ID: <200410141645.i9EGj00W010661@earth.planetharvest.com> Best Lab Deals is the one source for researchers, industrial professionals, scientists, physicians, educators and hobbyists to find more than 40,000 products at prices up to 70% below retail. Precision calibration - repair service Best Lab Deals 919-661-8030 Subscribe to our special offers list and also receive our free online newsletter, with problem-solving ideas, trends and other critical information. This message is to verify that you wish to have your email address added to our newsletter distribution list. You MUST click here to have your email address added to our list. http://bestlabdeals.com/lists/confirm.php?uid=ce7555ec8230bd0153fa1d3de37961c2 This is to ensure that someone does not add your address to our list without your prior knowledge or consent. Unless you respond to this email, your address is not added to our mailing list! Thanks, Customer Service From sbassi at asalup.org Thu Oct 14 12:17:57 2004 From: sbassi at asalup.org (Sebastian Bassi) Date: Thu Oct 14 12:14:12 2004 Subject: [BioPython] Transplanting Biopython to a live file system Message-ID: <33373.200.5.115.171.1097770677.webmail@panel.powered-hosting.com> Hello all, I did copy Bio, mx and Numeric from a working linux installation to another (under Site-Packages). Then I tried to "import Bio" from the new system and I got there is no module named Bio. I know this not a kosher way to install Biopython, but I have to do it this way to make it available on DNALinux that it is a liveCD (a working linux system from CD, like Knoppix). Do you may know what went wrong? I think I solved something like this 2 month ago when I transplanted Biopython to the AMD64 (because it didnt compile on AMD64, so I transplanted) and it worked. But this time, it doesnt :( From basu at pharm.sunysb.edu Thu Oct 14 15:03:44 2004 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Thu Oct 14 15:05:58 2004 Subject: [BioPython] flatfile index using OBDA registry system and biopython Message-ID: <416ECD90.9040304@pharm.sunysb.edu> Hi, I have just started using biopython and wants to use OBDA registry system to index the swissprot flat files. My goal is to access and make indexed file using different language. I already searched through the biopython docs but couldn't really figure out how to call the registry system from biopython. I have already setup a a seqdatabase.ini file, now to use that from biopython. Any idea, help will be highly appreciated. Thanks in advance, Siddhartha From =?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?= Sat Oct 16 00:37:17 2004 From: =?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?= (=?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?=) Date: Sat Oct 16 00:40:31 2004 Subject: [BioPython] =?iso-2022-jp?b?GyRCIXZMJD41QnohdT41Qno5LTlwIiMbKEI=?= =?iso-2022-jp?b?GyRCIzMyLzFfISIjNTIvMV9FeSROPH1GfjxUQjM9UCEmPlo1ciRHGyhC?= =?iso-2022-jp?b?GyRCPVBNaCRrIiNHLzZiJE8bKEI4GyRCQGlLfDFfQ3k2YiRHSVQbKEI=?= =?iso-2022-jp?b?GyRCTVciIzdKNSQyc0l8Mys7TyROO34kMyQ9JUElYyVzJTkhISEhGyhC?= =?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?= =?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?= Message-ID: <24149111.1097901437368.JavaMail.nobody@hosyou-r01.mine.nu> biopython@biopython.org$BMM(B $B!!(B $B!!!!7P:QJ88K!!%a%k%^%,C4EvLpBt(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $Bl9g$O$=$N;]$r(B http://gogoway.pimpdomain.com/melmaga/teishi.html$B$^$G(B $B%a!<%k%^%,%8%s9-9p?=$79~$_$O!"$=$N;]$r(Bhttp://gogoway.pimpdomain.com/doc/honmousikomi.htm$B$^$G(B $B%a!<%k%^%,%8%s9XFI$N?=$79~$N>l9g$O!"$=$N;]$r(Bhttp://gogoway.pimpdomain.com/melmaga/$B$^$G(B $B!!!!(B--$B#6@iK|1_$G4jK>$OC#@.!!(B----$B!!J}K!$O$"$j$^$9!*!!(B------$B!!#6@iK|1_0J2e$NCK=w$J$i=PMh$k![(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B:#$NG:$_$O!&!&!@iK|1_$G2r7h=PMh$k!*L\E*$K$b;HMQ=PMh$k!*@83h8~>e=PMh$k(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B>-Mh$NIT0B$O!&!&!@iK|1_Cy6b$G0B?4=PMh$k!*0B?48~>e$N:`NA$O;q6b$G=PMh$k!*(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B=PMh$k$NJ}K!$OM-$j$^$9!#(B $B"!(,!N#P#R!O(,(,7J5$$O5^2sI|3+;O$7$^$7$?(,"#(B $B#22/1_!"(B $B#32/1_!"(B $B#52/#9@iK|1_<}F~Z5rM-<}F~%S%8%M%9!U7P1DeCK=w?=$79~$_=PMh$^$9!#(B $B!!!!!!I{6H!&7s6H!&EZF|7P1D2K3hMQ7P1D$NJ}!9$KBg9%I>!*(B $B!!!!!!!!(B $B!!!!!!!!#3#8G/$N\$7$/$O(B http://gogoway.pimpdomain.com$B!!(B $B!!!!!!!!!!!!2?;v$bO@$h$j>Z5r!&1=$h$j>Z5r!&>u67>Z5r$h$jJ*E*>Z5r!&:[H=41$HF1$8J*E*>Z5r$N$_$G;v$K$h$j%@%&%s%m!<%I$7$F;HMQ$7$F$$$^$9!#%a!<%k%"%I%l%9!&(B $B!!%5!<%P!!!O2hA|$N$_$r6&M-$7;HMQ$7$F$$$^$9!#(B *-----$B#P#R(B------------------------------------------------------------------------------------------------* $B!!!!!!!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B $B9%$-$J;~4V$K%5%$%I%S%8%M%9(B! $B$7$+$b!V40A4:_Bp!W"v(B $B!!(B $B$@$C$Fe$2$?$s$@$b$s(B! $BM%$7$5$,(B $B$$!A$C$Q$$(B o(^$B"&(B^)o$B=i$a$F$NI{<}F~$OMb7n$K$b$i$($?$o(B(*^-$B!,(B)v $B!z(B:*:$B!y(B http://www.powz.ne.nu $B!y(B:*:$B!z(B *-----$B#P#R(B------------------------------------------------------------------------------------------------* $B#87n%W%l%*!<%W%sFCJL1o8NJg=8$N30;q7O%M%C%H%o!<%/4k6H$N0lHL8xJgOH(B $B!!!!!!!!!!(B $B!!(B http://askmebiz.net/click/2/ad5.cgi $B!z!y(B $B!2#P#R!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!y!z!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!2!y!z(B $B!!(B $B1?L?$rJQ$($k%o%s%/%j%C%/$bM-$j$^$9!#!!FCJL5.IP@J!!;D$j$o$:$+(B *-------------------------------------------------------* $B!z(Bo(^$B"`(B^o) $BKhF|$,%a%C%A%c3Z$7$$$s$G$9$%$%!7W;;5!!"9bB.%3%$%s%+%&%s%?!l!W!"!VBgGW:V!W$,$"$J$?$N7HBS$GM7$Y$^$9!*(B $B!!!!!!!!!!!J(BBREW$B!"(BVodafone$BBP1~!K(B $B#1%"%W%j!o#1#5#7!A$G$9$N$G!"$*;E;v$N9g4V$N$A$g$C$H$7$?B)H4$-$K(B $B!!$*5$7Z$K@'Hs$4MxMQ2<$5$$"v(B http://www.metro-japan.com/mobile/index.html $B!z(B--$B!~(B-$B!N(BPR]-$B!z(B--$B"!(B--$B!z(B--$B!~(B--$B!z!z(B-$B!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B-$B!~(B--$B!z(B--$B"!(B--$B!z=i$a$F$NI{<}F~$OMb7n(B--$B!~(B-$B!z(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B $B!!(B $B9%$-$J;~4V$K%5%$%I%S%8%M%9(B! $B$7$+$b!V40A4:_Bp!W"v$@$C$Fe$2$?$s$@$b$s(B! $BM%$7$5$,(B $B$$!A$C$Q$$(B o $B!!!!!!!!!!!!!!!!!!!!!!!!!!!z(B:*:$B!y(B http://www.powz.ne.nu $B!y(B:*:$B!z(B $B!!!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B $B!y(B:*:$B!z!z(B:*:$B!y(B *:$B!z(B $B!!!!!}!!K\F|$bEj9F!*$"$j$,$H$&$4$6$$$^$7$?"v!}%a%k%^%,H/9TpJspJs$K4X$7$FH/9T5$/$@$5$$!#7G:\5-;v$K4X$9$k$*Ld$$9g$o$;$OD>@\Ej9Fl9g$O5$/$@$5$$!#(B $B!!!!!!!!!!!!$^$?9-9pFbMF$K$h$C$F$O!!7G:\$r95$($5$;$F$$$?$@$/>l9g$b$4$6$$$^$9!#(B $B!!!!!!!!!!!!9-9p$r?=$79~$s$G$$$?$@$$$?J}$K$O!"%a!<%k%^%,%8%s$rG[?.$5$;$F$$$?$@$-$^$9!#(B $B!!!!!!!!!!!!$4N;>5$N>e!!$*?=$79~$_$/$@$5$$!#(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(Bhttp://gogoway.pimpdomain.com/doc/honmousikomi.htm ---------------------------------------------------------- $B!!!!!!!!!!!!!!!!!!!!!!(B $B%a!<%k%^%,%8%s!!9-9pC4EvLpBt!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!!!!!!!!!!!(B ------------------------------------------- 10$B7n(B16$BF|(B5$B;~H/I=(B $B8E20(B $B@2$l(B $B@2$l(B $B?73c(B $B@2$l$N$A;~!9F^$j(B $B@2$l(B $B6bBt(B $B@2$l(B $B@2$l(B $BBg:e(B $B@2$l(B $B@2$l(B $B2,;3(B $B@2$l(B $B@2$l(B $B9-Eg(B $B@2$l(B $B@2$l(B $B9b>>(B $B@2$l(B $B@2$l(B $BJ!2,(B $B@2$l(B $B@2$l(B $B When I attempt to build biopython using setup.py I get syntax errors that don't make any sense. My python distribution appears to be working normally for all other applications and scripts. I'm wondering if anybody else has encountered this and resolved it? # ./setup.py build ./setup.py: line 21: Distutils based setup script for Biopython. [help and version info snipped] : No such file or directory ./setup.py: line 26: syntax error near unexpected token `(' ./setup.py: line 26: `if sys.version_info[:2] < (2, 2):' ----------------- There is a very long delay between the "no such file or directory" error and the syntax error message. I'm using redhat enterprise 3 (Red Hat Enterprise Linux WS release 3 (Taroon Update 3)) with the following kernel: Linux blahblah.ucalgary.ca 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 EDT 2004 i686 i686 i386 GNU/Linux and this python version: Python 2.2.3 (#1, Aug 8 2003, 08:44:02) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-13)] on linux2 Type "help", "copyright", "credits" or "license" for more information. From idoerg at burnham.org Wed Oct 20 18:40:12 2004 From: idoerg at burnham.org (Iddo) Date: Wed Oct 20 18:39:04 2004 Subject: [BioPython] Installation problems In-Reply-To: <4176E409.2000504@ucalgary.ca> References: <4176E409.2000504@ucalgary.ca> Message-ID: <4176E94C.9080003@burnham.org> Try: python setup.py build Make sure you have 2.2 at least. 2.3 is better. Cheers, Iddo Walter Ash wrote: > When I attempt to build biopython using setup.py I get syntax errors > that don't make any sense. My python distribution appears to be > working normally for all other applications and scripts. I'm > wondering if anybody else has encountered this and resolved it? > > # ./setup.py build > ./setup.py: line 21: Distutils based setup script for Biopython. > > [help and version info snipped] > > : No such file or directory > ./setup.py: line 26: syntax error near unexpected token `(' > ./setup.py: line 26: `if sys.version_info[:2] < (2, 2):' > > ----------------- > > There is a very long delay between the "no such file or directory" > error and the syntax error message. I'm using redhat enterprise 3 > (Red Hat Enterprise Linux WS release 3 (Taroon Update 3)) with the > following kernel: > > Linux blahblah.ucalgary.ca 2.4.21-20.ELsmp #1 SMP Wed Aug 18 20:46:40 > EDT 2004 i686 i686 i386 GNU/Linux > > and this python version: > > Python 2.2.3 (#1, Aug 8 2003, 08:44:02) > [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-13)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 North Torrey Pines Road La Jolla, CA 92037 USA T: (858) 646 3100 x3516 F: (858) 713 9930 http://ffas.ljcrf.edu/~iddo From hawaii2005 at vreme.yubc.net Thu Oct 21 16:30:09 2004 From: hawaii2005 at vreme.yubc.net (IPSI-2005) Date: Thu Oct 21 16:29:02 2004 Subject: [BioPython] Reminder, IPSI conferences, Hawaii and Amalfi (Italy), vip/bb Message-ID: <200410212030.i9LKU9Ao021634@vreme.yubc.net> Dear potential speaker: On behalf of the organizing committee, I would like to extend a cordial invitation for you to attend one or both of the upcoming IPSI BgD Multidisciplinary (M.), Interdisciplinary (I.), and Transdisciplinary (T.) conferences (the M.I.T. research approach). Please note, all those who attended an IPSI conference once, always like to come back! If you have not attended an IPSI conference so far, please check with those who did (you can find their names on our web). The first will be in Hawaii: IPSI-2005 HAWAII Big Island Hawaii (arrival: 6 January 2005 / departure: 9 January 2005) Deadlines: 20 October 2004 (abstract, only 100 words) / 20 November 2004 (full paper) The second will be in Amalfi, Italy: IPSI-2005 AMALFI Amalfi, Italy (arrival: 17 February 2005 / departure: 20 February 2005.) Deadlines: 30 October 2004 (abstract) / 10 December 2004 (full papers) All IPSI BgD conferences are non-profit. They bring together the elite of the world of science; so far, we have had seven Nobel Laureates speaking at the opening ceremonies). The conferences always take place in some of the most attractive locations in the world. These conferences are in line with the newest recommendations of the US National Science Foundation and from the European Union to stress multidisciplinary, interdisciplinary, and transdisciplinary research. The speakers and activities at the conferences truly support this type of scientific interaction. Topics of interest include, but are not limited to: * Internet * Computer Science and Engineering * Management and Business Administration * Education * e-Medicine * Electrical Engineering * Bioengineering * Environmental Protection * e-Economy. * Social Impacts of e-World If you would like more information on either conference, please reply to this e-mail message (one can also find more information on the web). If you plan to submit an abstract and paper, please let us know immediately for planning purposes. Sincerely Yours, Prof. V. Milutinovic Chairman IPSI BgD Conferences * * * CONTROLLING OUR E-MAILS TO YOU * * * If you would like to continue to be informed about future IPSI BgD conferences, please reply to this e-mail message with a subject line of SUBSCRIBE. If you would like to be removed from our mailing list, please reply to this e-mail message with a subject line of REMOVE. From kingb at caltech.edu Thu Oct 21 17:42:58 2004 From: kingb at caltech.edu (Brandon King) Date: Thu Oct 21 17:41:47 2004 Subject: [BioPython] Is BioPython thread safe? In-Reply-To: <416B1195.9050106@caltech.edu> References: <416B1195.9050106@caltech.edu> Message-ID: <41782D62.2030507@caltech.edu> Hello All, Did I not give enough information about the problem? Any one have any suggestions or ideas? -Brandon King Brandon King wrote: > Hi All, > I'm trying to use BioPython within a thread of my main program and > I end up getting this error. Is BioPython intended to be thread safe? > > TraceBack: > > from Bio.Blast import NCBIStandalone > File "/usr/lib/python2.3/site-packages/Bio/__init__.py", line 106, in ? > _load_registries() > File "/usr/lib/python2.3/site-packages/Bio/__init__.py", line 98, in > _load_registries > module = __import__("Bio.config.%s" % module, {}, {}, > ["Bio","config"]) > File "/usr/lib/python2.3/site-packages/Bio/config/FormatRegistry.py", > line 26, in ? > import _support > File "/usr/lib/python2.3/site-packages/Bio/config/_support.py", line > 26, in ? > from Bio.MultiProc.copen import copen_fn > File "/usr/lib/python2.3/site-packages/Bio/MultiProc/copen.py", line > 322, in ? signal.signal(signal.SIGTERM, _handle_sigterm) > ValueError: signal only works in main thread > > -Brandon King > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > From cariaso at yahoo.com Thu Oct 21 18:24:41 2004 From: cariaso at yahoo.com (Mike Cariaso) Date: Thu Oct 21 18:23:30 2004 Subject: [BioPython] Is BioPython thread safe? In-Reply-To: <41782D62.2030507@caltech.edu> Message-ID: <20041021222441.73821.qmail@web52705.mail.yahoo.com> I only use biopython occasionally, but have been through similar issues with perl, and will share what I can. I think the lack of responses indicates that no one can say authoritatively, since there are so many developers. Presumably some parts of biopython are threadsafe, but that may be more a matter of luck than of design. Doing threadsafe signals is considerably more complex than non-threadsafe. If you don't see a lot of code gymnastics and comments about threads, any library using signals for is very unlikely to be threadsafe. if you need biopython and threads, you'll probably have to wrap all biopython code behind a single semaphore, and prevent concurrent access. Depending on what you're doing this may serialize all your code, or only a portion. Manually inspect the most crucial biopython components and see if you can use multiple semaphors, perhaps one for pieces which use signals, and another for components which read/write class variables. Gradually keep decreasing the granularity of the semaphors. Also look for places where signals are used only as timeouts, and replace these with another thread. Its probably going to be real painful. --- Brandon King wrote: > Hello All, > Did I not give enough information about the > problem? Any one have > any suggestions or ideas? > > -Brandon King > > Brandon King wrote: > > > Hi All, > > I'm trying to use BioPython within a thread of > my main program and > > I end up getting this error. Is BioPython intended > to be thread safe? > > > > TraceBack: > > > > from Bio.Blast import NCBIStandalone > > File > "/usr/lib/python2.3/site-packages/Bio/__init__.py", > line 106, in ? > > _load_registries() > > File > "/usr/lib/python2.3/site-packages/Bio/__init__.py", > line 98, in > > _load_registries > > module = __import__("Bio.config.%s" % module, > {}, {}, > > ["Bio","config"]) > > File > "/usr/lib/python2.3/site-packages/Bio/config/FormatRegistry.py", > > > line 26, in ? > > import _support > > File > "/usr/lib/python2.3/site-packages/Bio/config/_support.py", > line > > 26, in ? > > from Bio.MultiProc.copen import copen_fn > > File > "/usr/lib/python2.3/site-packages/Bio/MultiProc/copen.py", > line > > 322, in ? signal.signal(signal.SIGTERM, > _handle_sigterm) > > ValueError: signal only works in main thread > > > > -Brandon King > > > > _______________________________________________ > > BioPython mailing list - BioPython@biopython.org > > http://biopython.org/mailman/listinfo/biopython > > > > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > ===== Mike Cariaso From filippo.geraci at iit.cnr.it Fri Oct 22 08:30:35 2004 From: filippo.geraci at iit.cnr.it (Geraci Filippo) Date: Fri Oct 22 08:29:30 2004 Subject: [BioPython] similarity and string alignments Message-ID: <4178FD6B.6020906@iit.cnr.it> Hey, I'm working in DNA fragment assembly. Using BioPython I've not found a librery implementing similarity and string alignments. I wrote a C library to provide local,global and semiglobal similarity and build each possible string alignment and I wrote the extension for python. I'd like to know if these functions already exist and I lose my time or otherwise how to contribute to biopython project regards Filippo From nhussein at gmail.com Fri Oct 22 12:29:24 2004 From: nhussein at gmail.com (Nur Hussein) Date: Fri Oct 22 12:28:15 2004 Subject: [BioPython] Biopython and Bioperl features compared Message-ID: <1c97f00004102209293fa82d07@mail.gmail.com> Hello, I am new to this mailing list, so I'm sorry if this question has been asked before. Is there a website or document which compares the features of BioPerl and BioPython? If my reckoning is correct, they both offer similar features, but some features in BioPerl are lacking in Biopython (and vice versa). I have tried searching the mailing list archives and the FAQ's but this issue has not been addressed directly, as far as I could discover. Thank you. -= Nur Hussein =- From idoerg at burnham.org Fri Oct 22 12:29:37 2004 From: idoerg at burnham.org (Iddo) Date: Fri Oct 22 12:28:30 2004 Subject: [BioPython] similarity and string alignments In-Reply-To: <4178FD6B.6020906@iit.cnr.it> References: <4178FD6B.6020906@iit.cnr.it> Message-ID: <41793571.3060601@burnham.org> Hi Geraci, Local & global alignments are implemented in Bio.pairwise2, you might want to check that. If you have any additional funcitonality to add, which you can wrap in Python, that would be great, of course!! Cheers, Iddo Geraci Filippo wrote: > Hey, > I'm working in DNA fragment assembly. Using BioPython I've not found a > librery implementing similarity and string alignments. > > I wrote a C library to provide local,global and semiglobal similarity > and build each possible string alignment and I wrote the extension for > python. > > I'd like to know if these functions already exist and I lose my time > or otherwise how to contribute to biopython project > > regards > > Filippo > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > > -- 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) 713 9930 http://ffas.ljcrf.edu/~iddo From benny at ujsa.com Sat Oct 23 23:40:30 2004 From: benny at ujsa.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Sat Oct 23 23:45:53 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4Dogxebl5O3l4u3o6ugg5Ov/?= =?windows-1251?b?IMLg8SEhIQ==?= Message-ID: <134241125.20041024034530@> ???????????, ?????????????, ?????????, ???. ?????, ?????????!!! ???????? ?????! ???? ????? ???? ???? ?? ??????! ?????! ????????? ??? ????? ??????, (???? ????? ?????? ???????? ??????????? ?????????? ? ????), ?? ?????????: (095) 101-35-27 ??? 7-888-769!!! ???? ???????????? ????????? ??? ???????? ? ????????? ? ?????????? ????????!!! ?????????? 14,5 ? 20,6 ??, ???????????? / ??????????????, ??????? ?? ??????? ? ????????? ???????: 100 ??. - 4,62 ???? ?? ??./ 4,78 ???? ?? ??. 500 ??. - 4,22 ???? ?? ??./ 4,38 ???? ?? ??. 1000 ??. - 4.02 ???? ?? ??./ 4,18 ???? ?? ??. ?????????? 14,5 ? 20,6 ??, ????????????, ??????? ?? ???? ? ????????? ???????: 100 ??. - 22,85 ???? ?? ??. 500 ??. - 22,45 ???? ?? ??. 1000 ??. - 22,25 ???? ?? ??. ?????????? 8,7 ? 15,5 ??, ????????????, ??????? ?? ??????? ? ????????? ???????: 100 ??. - 5,19 ???? ?? ??. 500 ??. - 4,65 ???? ?? ??. 1000 ??. - 4,45 ???? ?? ??. ???????????? 8,7 ? 15,5 ??, ??????? ?? ??????? ? ????????? ???????: 100 ??. - 4,5 ???? ?? ??. 500 ??. - 4,1 ???? ?? ??. 1000 ??. - 3,9 ???? ?? ??. ???????? ??????????, 32,5 ? 10,5 ??, ??????? ?? ??????? / ???? ? ????????? ???????: 100 ??. - 5,55 ???? ?? ??./ 32,1 ???? ?? ??. 500 - 5,15 ???? ?? ??./ 31,75 ???? ?? ??. 1000 - 4,95 ???? ?? ??./ 31,55 ???? ?? ??. ?????????? ????? 8,7 ? 15,5 ??, ???. ?? ??????? ? ????????? ???????: 100 ??. - 4,28 ???? ?? ??. 500 ??. - 3,88 ???? ?? ??. 1000 - 3,68 ???? ?? ??. ??????? ??????-????? ? ?????????? ???????? - ??????????, ???????, ?????????? ?????, ? ????????? ?? ?????? ????????, ??? ?????? 100 ??., ?????? ?? 83,52 ???? ?? ?????. ????????? ????????? ???????????? ???????????? ????????. ? ??????? ???? ????????? ???????????? ??????, ??????, ??????. ??????????? ???? ?? ?????????! ????????, ???????????, ???????????, ????????????, ?????????? ?????! ????????? ???????? ????????? ? ?????? ????????. ????????? ???????????? ?????: - ?????? ?? 25 ??.??. - 80 ????; - ?????? ?? 25 ??.?? - 110 ????. ??????????? ????????? ?????? ?? ???????? ?????????? 50 ????. ??? ??????? ??????? ????????? ????!!! ????????? ?????????? - ??????! ???? ?????? - ??????, ??????? ? ??. ????? ??????? ???????? ?????????. ???? ???????????, ???????????, ????????????, ???????????! ????? ??????? ??????? ????????? - ??????, ?????, ?????, ??????. ????? ??????? ????????? ?? ??????? - ?????, ???????, ?????, ???????, ?????-?????, ??????, ?????? ? ????? ?????? ??????. ? ??? ????? ????????????????. ???.: (095) 101-35-27, 7-888-769 ???? ?????????? ? ????? ?????? ?????? ?????????!!! ???????!!! ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From saccenti at cerm.unifi.it Mon Oct 25 11:36:18 2004 From: saccenti at cerm.unifi.it (Edoardo Saccenti) Date: Mon Oct 25 11:34:59 2004 Subject: [BioPython] score alignments Message-ID: <200410251736.18375.saccenti@cerm.unifi.it> Dear All, I'm wondering if given an alignment it is possible to get an "alignment score" just like when you run ClustalW via web. Is it possibile using Bio.Align or other methods? Greetings Edoardo -- "Raffiniert ist der Herr Gott, aber boshaft ist Er nicht." --- Dr. Edoardo Saccenti FiorGen Farmacogenomic Foundation CERM Nuclear Magnetic Resonace Research Center Scientific Pole - University of Florence Via Luigi Sacconi n? 6 50019 Sesto Fiorentino (FI) tel: +39 055 4574193 fax: +39 055 4574271 saccenti@cerm.unifi.it www.cerm.unifi.it From kingb at caltech.edu Mon Oct 25 14:38:46 2004 From: kingb at caltech.edu (Brandon King) Date: Mon Oct 25 14:37:29 2004 Subject: [BioPython] Is BioPython thread safe? In-Reply-To: <20041021222441.73821.qmail@web52705.mail.yahoo.com> References: <20041021222441.73821.qmail@web52705.mail.yahoo.com> Message-ID: <417D4836.6030208@caltech.edu> Hi Mike, Thanks for the response... I really appreciate it. I'll look into the semaphor solution or just make an external command line program which I can call from another python program. Thanks again! -Brandon King Mike Cariaso wrote: >I only use biopython occasionally, but have been >through similar issues with perl, and will share what >I can. > >I think the lack of responses indicates that no one >can say authoritatively, since there are so many >developers. Presumably some parts of biopython are >threadsafe, but that may be more a matter of luck than >of design. > >Doing threadsafe signals is considerably more complex >than non-threadsafe. If you don't see a lot of code >gymnastics and comments about threads, any library >using signals for is very unlikely to be threadsafe. > >if you need biopython and threads, you'll probably >have to wrap all biopython code behind a single >semaphore, and prevent concurrent access. Depending on >what you're doing this may serialize all your code, or >only a portion. Manually inspect the most crucial >biopython components and see if you can use multiple >semaphors, perhaps one for pieces which use signals, >and another for components which read/write class >variables. Gradually keep decreasing the granularity >of the semaphors. Also look for places where signals >are used only as timeouts, and replace these with >another thread. > >Its probably going to be real painful. > > > >--- Brandon King wrote: > > > >>Hello All, >> Did I not give enough information about the >>problem? Any one have >>any suggestions or ideas? >> >>-Brandon King >> >>Brandon King wrote: >> >> >> >>>Hi All, >>> I'm trying to use BioPython within a thread of >>> >>> >>my main program and >> >> >>>I end up getting this error. Is BioPython intended >>> >>> >>to be thread safe? >> >> >>>TraceBack: >>> >>> from Bio.Blast import NCBIStandalone >>> File >>> >>> >>"/usr/lib/python2.3/site-packages/Bio/__init__.py", >>line 106, in ? >> >> >>> _load_registries() >>> File >>> >>> >>"/usr/lib/python2.3/site-packages/Bio/__init__.py", >>line 98, in >> >> >>>_load_registries >>> module = __import__("Bio.config.%s" % module, >>> >>> >>{}, {}, >> >> >>>["Bio","config"]) >>> File >>> >>> >"/usr/lib/python2.3/site-packages/Bio/config/FormatRegistry.py", > > >>>line 26, in ? >>> import _support >>> File >>> >>> >"/usr/lib/python2.3/site-packages/Bio/config/_support.py", > > >>line >> >> >>>26, in ? >>> from Bio.MultiProc.copen import copen_fn >>> File >>> >>> >"/usr/lib/python2.3/site-packages/Bio/MultiProc/copen.py", > > >>line >> >> >>>322, in ? signal.signal(signal.SIGTERM, >>> >>> >>_handle_sigterm) >> >> >>>ValueError: signal only works in main thread >>> >>>-Brandon King >>> >>>_______________________________________________ >>>BioPython mailing list - BioPython@biopython.org >>>http://biopython.org/mailman/listinfo/biopython >>> >>> >>> >>> >>_______________________________________________ >>BioPython mailing list - BioPython@biopython.org >>http://biopython.org/mailman/listinfo/biopython >> >> >> > > >===== >Mike Cariaso > > > > From Richard.Christen at unice.fr Fri Oct 22 09:47:42 2004 From: Richard.Christen at unice.fr (christen) Date: Mon Oct 25 15:20:43 2004 Subject: [BioPython] retrieve genbank record Message-ID: <41790F7E.7020705@unice.fr> Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: christen.vcf Type: text/x-vcard Size: 323 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biopython/attachments/20041022/0e3ad5c9/christen.vcf From saccenti at cerm.unifi.it Tue Oct 26 05:42:30 2004 From: saccenti at cerm.unifi.it (Edoardo Saccenti) Date: Tue Oct 26 05:41:17 2004 Subject: [BioPython] nj files form alignments Message-ID: <200410261142.30245.saccenti@cerm.unifi.it> Is it possible to create phylogenitc tree using Clustalw for Bio?? I need to get the nj file from the alignement of two sequences! thanks -- "Raffiniert ist der Herr Gott, aber boshaft ist Er nicht." --- Dr. Edoardo Saccenti FiorGen Farmacogenomic Foundation CERM Nuclear Magnetic Resonace Research Center Scientific Pole - University of Florence Via Luigi Sacconi n? 6 50019 Sesto Fiorentino (FI) tel: +39 055 4574193 fax: +39 055 4574271 saccenti@cerm.unifi.it www.cerm.unifi.it From kael at sonic.net Tue Oct 26 18:56:08 2004 From: kael at sonic.net (Kael Fischer) Date: Tue Oct 26 18:54:47 2004 Subject: [BioPython] BLAST in a python generator In-Reply-To: <417D4836.6030208@caltech.edu> References: <20041021222441.73821.qmail@web52705.mail.yahoo.com> <417D4836.6030208@caltech.edu> Message-ID: <6.1.1.1.2.20041026150248.01ff8ec0@pop.sonic.net> Regarding threads and Biopython. I've been experimenting with keeping BLAST running in a separate thread using a python generator. Then calling the .next() method of the generator when I want to run the next query. The query is held in a stringIO buffer that the generator can read. The Idea is that the overhead of reading the database needn't be repeated as that is part of the generator's state. This is the first time I've written a generator. Unfortunately I don't seem to be able to get _all_ of the output of the BLAST record. Most of the time my select loops return only part of the result. The code below is one of several schemes I've tried. For those interested in the idea, here is some of the code: (no Biopython in this snippet) def BLASTpipe(inBuf, blastDB = genomeDB): """Generator for a BLAST process. inBuf is a StringIO buffer that contains one or more query sequences. .next() processes the query(s) in inBuf. inBuf is consumed and a tuple of the output and error strings is returned. """ # Format DB, if necessary if not os.access(blastDB + '.nhr' ,os.R_OK) \ or not os.access(blastDB + '.nin' ,os.R_OK) \ or not os.access(blastDB + '.nsq' ,os.R_OK): # db is not formatted tmpDbFile = NamedTemporaryFile() userDbFile = file(blastDB,'r') tmpDbFile.write(userDbFile.read()) userDbFile.close() tmpDbFile.flush() blastDB = tmpDbFile.name # format db os.system('%s -pF -l /dev/null -i%s' % (formatdb_exe, blastDB)) blast_in, blast_out, blast_err = os.popen3(blast_exe + \ ' -p blastn -d %s ' % (blastDB), 't',1) while True: outString = '' errString = '' inBuf.seek(0) inQuery = inBuf.read() blast_in.write(inQuery) inBuf.seek(0) inBuf.truncate() readyReaders, undef, undef = select([blast_out,blast_err],[],[],0.5) while readyReaders != []: if blast_out in readyReaders: outString = blast_out.read(1) while blast_out in select([blast_out],[],[],0.5) [0]: outString += blast_out.read(1) if blast_err in readyReaders: errString = blast_err.read(1) while blast_err in select([blast_err],[],[],0.5) [0]: errString += blast_err.read(1) readyReaders, undef, undef = select([blast_out],[],[],0.5) yield outString, errString # end Comments? Kael -- Kael Fischer, Ph.D. DeRisi Lab, University of California San Francisco Desk: 415-514-4320 kael@derisilab.ucsf.edu From e.picardi at unical.it Tue Oct 26 06:51:47 2004 From: e.picardi at unical.it (Ernesto) Date: Tue Oct 26 22:25:22 2004 Subject: [BioPython] equation Message-ID: <016501c4bb49$ccbb4c10$572561a0@Travelmate> Hi all, I would normalize a DNA substitution matrix to have the sum of off diagonal entries equal 1. How can I estimate parameters to this scope in Python? For example in the most complicated case I should solve the following equation: 2a(Fac)+2b(Fag)+2c(Fcg)+2d(Fta)+2e(Fct)+2f(Fgt) = 1 where Fac Fag Fcg Fta Fct Fgt are known. I would detect a b c d e. Thanks a lot Ernesto From nomy2020 at yahoo.com Wed Oct 27 01:23:05 2004 From: nomy2020 at yahoo.com (Bzy Bee) Date: Wed Oct 27 01:21:43 2004 Subject: [BioPython] Comparing short sequences against a large fasta file In-Reply-To: <200410251537.i9PFajKt017627@portal.open-bio.org> Message-ID: <20041027052305.62771.qmail@web51803.mail.yahoo.com> Hi I have made some advancement in writing up a script for searching short sequences against a fasta format file 9with protein coding genes). Basically the program takes an input file and the length of the sequence to be searched (say 10mer or so) from the command line, and then takes the first 10mer of the first sequence in the file and searches the entire file for that 10mer, then moves one base forward and searches the next 10 mer and so on. I have used python dictionaries to keep the sequence names and the locations of oligos (a call to keys (sequence names) prints out the values (location of oligo) of the keys). The problem I am facing is that the program works fine on a smaller version of file if the length of the sequence to be searched i 10 mer, but fails on the entire file 9with 3000 or so sequences). It does work on larger file too but I have to reduce the length of the seqeunce to only 5 bases. I think it is either the issue of memory allocation or may be the maximum length of dictionary. I would have thought that the memory to the dictionary is dynamically allocated. your suggestions will be very much appreciated. here's the code: ============================= from string import * import os, sys, string from Bio.SeqIO import SeqIO, Seq, Dictionaries, FASTA from Bio import Fasta def findOlig(dna, prim): loc = [] count = 0 site = dna.find(prim) while site != -1: loc.append(site) site = dna.find(prim, site + 1) count += 1 return loc #prim, count # print 'primer sequence: ', prim, 'no of times present:', count, 'oligo site:', loc #to get the reverse of a given sequence def revSeq(dna): myseq = list(dna) myseq.reverse() return join(myseq, '') #to get the reverse complement of a sequence def revComp(dna): comp = dna.translate(maketrans("AGCTagct", "TCGAtcga")) lcomp = list(comp) lcomp.reverse() return join(lcomp, '') def gcContent(dna): '''This method finds gc percent of a given sequence ''' length = len(dna) count_gc = count(dna, 'g') + count(dna, 'G') + count(dna, 'c') + count(dna, 'C') gc = float(count_gc)/length *100 return gc def main(): """ Reads sequences from a file in fasta format, calculates the GC content of the sequences in the file. Finds sliding nmers (reads nmers from the stndin and compares them with the sequences in the file. """ infile = sys.argv[1] nmer = atoi(sys.argv[2]) handle = open(infile) it = FASTA.FastaReader(handle) seqs = [] for seq in it: seqs.append(seq) handle.close() # Calculates GC contents of the sequences in the file c = 0 seq_gc = 0.0 for seq in seqs: seq_gc = seq_gc + (gcContent(seq.seq.tostring())) c = c+1 total_gc = (seq_gc)/c # print total_gc num_seqs = 0 for seq in seqs: #find the nmers starting from first sequence in the file for i in range(len(seq.seq.tostring())): prim = seq.seq.tostring()[i:i+nmer] name_seq = '' location = [] prim_p = [] olig_p = 0.0 percent_p = 0.0 s1_dict = {} s2_dict = {} seq_dict = {} # stops when the oligo sequence is smaller than the input nmer if len(prim) < nmer: break # search for the defined oligo in all the sequences in the file one by one for myseq in seqs: f_olig = findOlig(myseq.seq.tostring(),prim) # work only with sequences where the oligo is found if f_olig != []: olig_p+=1 name_seq = myseq.name[0] location = f_olig # stores the names and locations of the seqeunces and oligo being searched # in a dictionary s1_dict = {name_seq:location} seq_dict.update(s1_dict) # calculates the % of sequences with the oligo being searched percent_p = olig_p/len(seqs)*100 # and reports only those oligos present in >=90% of sequences if percent_p >= 90.0: print prim#, ",", i,"GC content:", gcContent(prim) # print "seq name and primer location are: ", seq_dict # print "primer ", i, "present in ", olig_p, "seqeunces" # print "primer ", i, "present in ", percent_p, "percent seqs" # prints out the keys and values of the dictionary s2_dict = seq_dict s_keys = [] s_keys = s2_dict.keys() # print s_keys for j in range(len(s_keys)): id_j = '' try: while s_keys!=-1: id_j = s_keys.pop(0) print id_j, ",", s2_dict[id_j] except IndexError: pass if __name__ == '__main__': main() ============================= Thanks JA __________________________________ Do you Yahoo!? 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As a result of popular demand, the book has been a top "Featured Item" in some top on-line bookstores in some subjects, such as "Personal Practical Guides" in "Nonfiction" and "Reference", "Conduct" in "Health, Mind & Body", "Life skills guides", "Ethics & Moral Philosophy", ... "The book will also be effective for violence prevention for the whole society." said some experts. How to make the world peaceful and better --- You can find the solution in the book. Let's work together to make the world peaceful and better! The author, John Newton, holds a Ph.D. from MIT, and does researches at Harvard. His long-term research on "The personal conduct in the human society of the 21st century" resulted in this book. Before the human beings went into the 21st century, the compassionate, merciful, courageous and farsighted Dr. Newton had issued a number of warning predictions, some of which have already been proved in the new century. The book is introduced by NCWO, headquartered beside Harvard University and MIT, two leading institutes of new knowledge and literature. NCWO is an educational, charitable, non-profit, non-partisan, volunteer-supported, and honorary organization; it endeavors to make the 21st century nicer than ever before. To accomplish its mission, NCWO is proud to introduce this book. The Web site of NCWO has been chosen as one of "Top Non Profit Sites Chosen by Type Non Profit Editors". The book is available in two types of binding: Hardcover (ISBN 0967370574; case bound, Smyth sewn; with dust jacket) and Paperback (ISBN 0967370582; perfect bound). Both editions are unabridged, and are printed on 60 lb, natural, acid-free, excellent and healthful paper. You can get the book from many fine on-line bookstores and traditional bookstores. For your convenience, (if you wish for an Internet link; otherwise you may skip this section) I herewith provide you with a link directly to the book page of each edition in eBay's Half.com, a popular on-line dis count mall: for paperback: http://half.com/cat/buy/prod.cgi?cpid=2425993 for hardcover: http://half.com/cat/buy/prod.cgi?cpid=2425992 Please forward this e-mail to people you know -- children, friends, relatives, classmates, students, parents, teachers, other educators, ..., because they can benefit from it, too. This can be a wonderful kindness you provide to them! biopython, best wishes to you! Sincerely yours, Anthony Bate, Ph.D. Cambridge, Massachusetts, USA P.S. Some educational units, ranging from the level of nation or state to individual school or university, have ordered the book as textbook, reference book, gift to students, or as an active action to prevent school violence, to improve education and to benefit students, teachers & parents. To have more people benefit from the book, please consider suggesting to the schools -- your children attend, or you yourself attend, have attended before, teach at, or serve -- that the book be used for fundraising for the schools. The book is an ideal fundraising tool. For example, it may used as a premium or a re-sale product for the fundraising. The successful fundraising will significantly help school education. Better yet, each supporter and his/her family will benefit from the book. Suggesting to the parent-teacher associations (organizations) (PTA/PTO) of the schools is also a good idea. \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ This is intended to be a unique time only message, and I will never share your email address with others. I am sending this message to you as a voluntary charitable task, NOT for commercial profit. Thank you for your kindly consideration. If you still want to request no (accidental) future message from me at the email address where this message was received, please send me a reply email by using your email "Reply" function, or to the return email address of this email displayed in the header information (on the line of "Reply-to:") of this email, with subject line: delete (your email address) //////////////////////////////////////////////////////////////////////////////////////////////////// Box 38 2584, Cambridge, Massachusetts, 02238, United States of America From biopython-dev-bounces at portal.open-bio.org Sat Oct 30 01:29:29 2004 From: biopython-dev-bounces at portal.open-bio.org (biopython-dev-bounces@portal.open-bio.org) Date: Sat Oct 30 01:29:36 2004 Subject: [BioPython] Your message to Biopython-dev awaits moderator approval Message-ID: Your mail to 'Biopython-dev' with the subject Re: Hello Is being held until the list moderator can review it for approval. The reason it is being held: Message has a suspicious header Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://biopython.org/mailman/confirm/biopython-dev/1aedb264dc89acc11eafe693eeb5a3a1a5644a25 From =?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?= Sat Oct 30 04:15:21 2004 From: =?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?= (=?iso-2022-jp?Q?=1B=24B=236=40iK=7C1=5F=24N=3C=7D=1B=28B?=) Date: Sat Oct 30 04:18:37 2004 Subject: [BioPython] =?iso-2022-jp?b?GyRCIXZMJD41QnohdT41Qno5LTlwIiMbKEI=?= =?iso-2022-jp?b?GyRCIzMyLzFfISIjNTIvMV9FeSROPH1GfjxUQjM9UCEmPlo1ciRHGyhC?= =?iso-2022-jp?b?GyRCPVBNaCRrIiNHLzZiJE8bKEI4GyRCQGlLfDFfQ3k2YiRHSVQbKEI=?= =?iso-2022-jp?b?GyRCTVciIzdKNSQyc0l8Mys7TyROO34kMyQ9JUElYyVzJTkhISEhGyhC?= =?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?= =?iso-2022-jp?b?GyRCISEhISEhISEhISEhISEhISEhISEhISEhISEhISEhGyhC?= Message-ID: <13668971.1099124121114.JavaMail.nobody@hosyou-r01.mine.nu> biopython@biopython.org$BMM(B $B!!(B $B!!!!7P:QJ88K!!%a%k%^%,C4EvLpBt(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $Bl9g$O$=$N;]$r(B http://gogoway.pimpdomain.com/melmaga/teishi.html$B$^$G(B $B%a!<%k%^%,%8%s9-9p?=$79~$_$O!"$=$N;]$r(Bhttp://gogoway.pimpdomain.com/doc/honmousikomi.htm$B$^$G(B $B%a!<%k%^%,%8%s9XFI$N?=$79~$N>l9g$O!"$=$N;]$r(Bhttp://gogoway.pimpdomain.com/melmaga/$B$^$G(B $B!!!!(B--$B#6@iK|1_$G4jK>$OC#@.!!(B----$B!!J}K!$O$"$j$^$9!*!!(B------$B!!#6@iK|1_0J2e$NCK=w$J$i=PMh$k![(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B:#$NG:$_$O!&!&!@iK|1_$G2r7h=PMh$k!*L\E*$K$b;HMQ=PMh$k!*@83h8~>e=PMh$k(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B>-Mh$NIT0B$O!&!&!@iK|1_Cy6b$G0B?4=PMh$k!*0B?48~>e$N:`NA$O;q6b$G=PMh$k!*(B $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!(B $B=PMh$k$NJ}K!$OM-$j$^$9!#(B $B"!(,!N#P#R!O(,(,7J5$$O5^2sI|3+;O$7$^$7$?(,"#(B $B#22/1_!"(B $B#32/1_!"(B $B#52/#9@iK|1_<}F~Z5rM-<}F~%S%8%M%9!U7P1DeCK=w?=$79~$_=PMh$^$9!#(B $B!!!!!!I{6H!&7s6H!&EZF|7P1D2K3hMQ7P1D$NJ}!9$KBg9%I>!*(B $B!!!!!!!!(B $B!!!!!!!!#3#8G/$N\$7$/$O(B http://gogoway.pimpdomain.com$B!!(B $B!!!!!!!!!!!!2?;v$bO@$h$j>Z5r!&1=$h$j>Z5r!&>u67>Z5r$h$jJ*E*>Z5r!&:[H=41$HF1$8J*E*>Z5r$N$_$G;v$K$h$j%@%&%s%m!<%I$7$F;HMQ$7$F$$$^$9!#%a!<%k%"%I%l%9!&(B $B!!%5!<%P!!!O2hA|$N$_$r6&M-$7;HMQ$7$F$$$^$9!#(B *-----$B#P#R(B------------------------------------------------------------------------------------------------* $B!!!!!!!Z2H;v$r$7$J$,$i:_Bp%S%8%M%9![(B $B9%$-$J;~4V$K%5%$%I%S%8%M%9(B! 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The reason it is being held: Message has a suspicious header Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://biopython.org/mailman/confirm/biopython-dev/825b3bb40ebde26d860a1e1ccf9efa1b9dbf12c4 From jean-fra at guadalupano.com Sun Oct 31 17:05:59 2004 From: jean-fra at guadalupano.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Sun Oct 31 17:15:35 2004 Subject: [BioPython] =?windows-1251?b?0OXq6+Ds4DogyOfk5evo/yDo5yDq7ubo?= =?windows-1251?b?IO/uIOjt5Oji6OTz4Ov87e7s8yDn4Org5/MhISEg0PP37eD/IPDg4e7y?= =?windows-1251?q?=E0!!!?= Message-ID: <1810251163.20041031221059@> ??????? ??????? ?? ??????????????? ??????!!! ?????? ??????!!! ??????? ?? ????: ?????????????, ?????? 9,5 ? 6,5 ?? - 5 ?.?. ???????, ?????? 16 ? 12 ?? - 11 ?.?. ????? ??? ?????? ??????? ?5 - ?? 20 ?.?. ????? ????, ????? ??? ????? ??????? ?4 - ?? 30 ?.?. ??????? ? ??????????? ??????????? ????????? ( ??????, ???????, ????, ?????, ???????) ???????????? ( ??????, ???????, ????? ?????) ???????? ???????????? ???????? ?? ????? ???????? ?? ????: ?????, ???????, ????????, ?????, ???????????, ?????????, ????????? ???? ? ?????? ? ???????. ??????? ????? ????????? ? ????? ???????????? ??????????. ????? ?????, ???? ???????????????? ???? ????????? ????????? ??????????? ? ??????: ??????????? ?) ???????? (????????, ?????, ??????, ?????, ???????...). ??????????? ?????? 6?6 M&R "Chameleon" (???, ??????????????????: 3+0, 960 ??????? ??????? ? ?????). ?) ??????????, ??????, ???????, ??????, ??????, ???? (?????? ???????? ? ???, ????????, ????? - ??????, ??????? ?/?...) ?????????????? ?????? Winnon, ??????? ????????? 30?30 ??. ???????????. Winnon - 121. ????????? ?? ?????, ?????????, ???????, ??????, ??????????, ????, ???????, ????. ????, ????????????????. ??????? ????? ???????????? ????????- ?????????? ????????? ?? ?????????. ?????????? ?????. ?????????? ??????, ???????, ?????? ???????????. ???????????? ?????????? ????????,?????????????? ???????, ??????????,???????? ??????? ????????? ???????????. ??????? ????? ?????? ?? ????????: ? ??? ????????? ??????? ??? ??????????? ? ?????????? ? ?????????! (095) 7-888-769 (095) 101-3527 (????????.) 8 (926) 523 - 42-41 (?????????????) ?? ????? ??????? ????????? ???????? ???????????????. ??????? ?? ?????????? ?????? ? ?????? ????? ????? ? ????? "??" - ????????? ???????????, ? ????? "????" - ???????: (???????? ??????????? ????, ????????, ??????, ?????? ? ??.) ???? ?? ?? ??????? ???????? ????????? ??????????? ?? ??????????? ?????, ?? ?????? ??????? ???? ????? ?? ????? ???? ??????, ??????? ??? ?????? ? ????? ??????? ???????? ? ???? ??????, ?? ??????: nevajno2000@yahoo.com ?? ?????? ???? ???????, ??? ?? ?? ????? ???? ?????? ??? ???????? ????? ?? ????? ???? ??????. ?????? ???? ???????????? 20 ????? ??????? ??????. From biopython-dev-bounces at portal.open-bio.org Sun Oct 31 20:57:44 2004 From: biopython-dev-bounces at portal.open-bio.org (biopython-dev-bounces@portal.open-bio.org) Date: Sun Oct 31 20:57:50 2004 Subject: [BioPython] Your message to Biopython-dev awaits moderator approval Message-ID: Your mail to 'Biopython-dev' with the subject Re: Is being held until the list moderator can review it for approval. The reason it is being held: Message has a suspicious header Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://biopython.org/mailman/confirm/biopython-dev/fcb52d58cee55ab6b7b5882aceb3ba28125c20f8