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 ????.
?? ??????????:
??????? ?????????????????? ?????
??????????????? ????? (?????????? ????? ??????????? ??????????)
?????????????? ?????????? ??? ??????? ??? ???????
?? ??????? ????????
???????????????. ????? ?????? ????!
???????? ????????? !! ??????? ??????????? ?? ????? ????????:
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. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. 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;yEg(B $B@2$l(B $B@2$l(B
$BFaGF(B $BF^$j;~!9@2$l(B $BF^$j$N$A0l;~1+(B
From wlash at ucalgary.ca Wed Oct 20 18:17:45 2004
From: wlash at ucalgary.ca (Walter Ash)
Date: Wed Oct 20 18:16:36 2004
Subject: [BioPython] Installation problems
Message-ID: <4176E409.2000504@ucalgary.ca>
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!?
Yahoo! Mail Address AutoComplete - You start. We finish.
http://promotions.yahoo.com/new_mail
From Timwq at maxis.net.my Wed Oct 27 08:11:18 2004
From: Timwq at maxis.net.my (Barbara Valery)
Date: Wed Oct 27 08:19:29 2004
Subject: [BioPython] LSSITES NEWS - Lolita PICTURE & MOVIES at 45 Lolita
Sites
In-Reply-To: <3JJ7I1EA774C280L@biopython.org>
References: <3JJ7I1EA774C280L@biopython.org>
Message-ID: <7FL892F4BF946L09@maxis.net.my>
Dear Biopython,
wanna real lolita sites with real pics? Tired of endless top lists, pop-ups and blind links? Tired of all the same lolita pics on the net? Stop wasting your time! You won't find what you want for free. Join the oldest and most reputable lolita pay site on the net listed below! There and only there will you find over 10000 real uncensored pics and hundreds of videos of nude teens and preteens - boys and girls! I've seen hundreds of pay underage girls sites and I've chosen only the best for you. All underage girls and videos of the net are there! Plus these sites are updated weekly with their own lolita photos and videos made by their photographers exclusively for their sites. If you ever considered joining a pay lolita site, choose any site below and you won't regret! Check them out!
LAST UPDATE : October 22, 2004
TOTAL SITES IN PORTAL: 170
Visit us at: http://x-adult.hk.st
Have a nice day ...
Unsubscribe link: in the bottom of the site
Adult Review,
10.22.2004
From men-shen at moebelheinrich.de Wed Oct 27 12:18:27 2004
From: men-shen at moebelheinrich.de (=?Windows-1251?B?YW5uLW1hcmk=?=)
Date: Wed Oct 27 12:34:22 2004
Subject: [BioPython] =?windows-1251?b?z/Du9OXx8eju7eDr/O3g/yDw5err4Ozg?=
=?windows-1251?b?IOIgyO3y5fDt5fLl?=
Message-ID: <200410271634.i9RGYGKr017164@portal.open-bio.org>
???????????????? ??????? ? ???? ????????.
???????? ????? ?????????? ?? ??????????? ???????,
? ????? ????? ??? ?????????????? ?????.
???????? ????????, ????? ?????? ???? (???? 2004).
?????????? ?????? ?????????.
?????????????? ??????.
????????? ?????? ?? ???????? (095) 505-4931
From dr_anthony_batea at pisem.net Fri Oct 29 05:12:33 2004
From: dr_anthony_batea at pisem.net (Dr. Bate)
Date: Fri Oct 29 05:13:05 2004
Subject: [BioPython] To You as a Good Person
Message-ID: <380-220041052991233480@oemcomputer>
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.
You may ask yourself
> How to make people like you and respect you
> How to win friends
> How to let your conduct help your health, work, job, career, success, relationships, spirit, mind, well-being, ...
> How to make your life smoother and happier
> How to do whatever you like without being unpleasant to other people
> How to develop good conduct in your children or students
> How to make the world peaceful and better
You can find all the answers to these questions, and much more, in this great handbook:
" Complete Conduct Principles for the 21st Century " by Dr. John Newton
It is the best educational GIF T idea for children, friends, relatives, classmates, students, parents, teachers, other educators, ..., particularly at this special time.
BENEFITS to each individual reader: Many! -- such as for health, work, job, career, success, self-improvement, education, relationships, spirit, mind, well-being, and much more -- almost all the areas that are important to you in the 21st century. People around you will benefit, too. (Please see the preface of the book for details.)
EVERYONE may find this handbook useful and helpful, regardless of age (from children to oldsters), occupation, rank, status, gender, religious belief, race, nationality, country, or region.
If you are a parent or a teacher, you can learn how to develop good conduct in your children or students from this handbook. Please advise your children or students to read the book. It will result in great benefits for both you and them.
This book is a must for EVERYONE to be better prepared for personal conduct for the rest of the 21st century.
The book's content is obvious from its title. The complete useful conduct principles cover not only what we should do, but also what we should not do -- especially those faults people make often and easily.
This timely, unique, and very important handbook is designed to suit most people, and is self-contained and user-friendly.
The book was also praised as "a compendium of concisely expressed, practical, informative, pertinent, workable advice" by Michael J. Carson, a professional book reviewer.
"Unlike most books of this subject, it is NOT a religious book, nor is a collection of old conduct rules."
This book is significantly different and better than competitive works.
Some of its innovative contents may help solve problems that the Western culture cannot.
The book's merit and importance have been recognized and praised by many experts, elected public officials, and world leaders.
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! $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(B29$BF|(B17$B;~H/I=(B
$B8E20(B $BF^$j(B $B1+(B
$B?73c(B $B@2$l(B $BF^$j$N$A0l;~1+(B
$B6bBt(B $B@2$l$N$A;~!9F^$j(B $BF^$j$N$A0l;~1+(B
$BBg:e(B $BF^$j$N$A0l;~1+(B $BF^$j0l;~1+(B
$B2,;3(B $BF^$j$N$A0l;~1+(B $B1+$N$AF^$j(B
$B9-Eg(B $BF^$j$N$A0l;~1+(B $B1+(B
$B9b>>(B $BF^$j0l;~1+(B $B1+(B
$BJ!2,(B $BF^$j$N$A0l;~1+(B $B1+(B
$B;yEg(B $B1+(B $B1+$N$AF^$j(B
$BFaGF(B $B@2$l(B $B@2$l(B
From biopython-dev-bounces at portal.open-bio.org Sat Oct 30 22:44:27 2004
From: biopython-dev-bounces at portal.open-bio.org (biopython-dev-bounces@portal.open-bio.org)
Date: Sat Oct 30 22:44:31 2004
Subject: [BioPython] Your message to Biopython-dev awaits moderator approval
Message-ID:
Your mail to 'Biopython-dev' with the subject
Re: Thanks :)
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/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