From vp_1rartw at anfmail.com Thu Jan 1 17:38:25 2004 From: vp_1rartw at anfmail.com (vp_1rartw@anfmail.com) Date: Thu Jan 1 17:38:29 2004 Subject: [Bioperl-pipeline] FW: Product of the year, 2003 Message-ID: <200401012238.i01McPNQ031492@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040101/4798393d/attachment-0001.htm From jj_drmarkable at dbzmail.com Tue Jan 6 22:15:57 2004 From: jj_drmarkable at dbzmail.com (Zerberus) Date: Wed Jan 7 00:23:02 2004 Subject: [Bioperl-pipeline] RE: Perfect gift for 2004 Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040107/fdd184f9/attachment.htm From dr_joepropertied at anfmail.com Wed Jan 7 07:28:47 2004 From: dr_joepropertied at anfmail.com (Norman_wright) Date: Wed Jan 7 04:38:03 2004 Subject: [Bioperl-pipeline] Hey mate, hows it going?? Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040107/36c19206/attachment.htm From doctorwilliamssmuggled at yahoo.com Wed Jan 7 21:03:46 2004 From: doctorwilliamssmuggled at yahoo.com (Bioperl-microarray) Date: Wed Jan 7 21:03:47 2004 Subject: [Bioperl-pipeline] How was your New Years Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040108/b9626eb1/attachment.htm From jake87cranking at dbzmail.com Thu Jan 8 00:03:09 2004 From: jake87cranking at dbzmail.com (Bioperl-microarray) Date: Thu Jan 8 05:08:03 2004 Subject: [Bioperl-pipeline] RE: I just got your message! Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040108/e109ef5c/attachment.htm From wsm10826 at mh.us.sbphrd.com Fri Jan 9 16:44:14 2004 From: wsm10826 at mh.us.sbphrd.com (William S. Morgart) Date: Fri Jan 9 16:51:44 2004 Subject: [Bioperl-pipeline] Status of BioPipe? Message-ID: <200401092144.QAA273665@phu655.um.us.sbphrd.com> I was wondering what the status of the biopipe project (biopipe.org) is. I've downloaded and setup the .1 release (from 14 Apr 2003) and I wondered if development is continuing? If it is, is collaboration from others welcomed? Regards, Bill Morgart From shawnh at stanford.edu Sat Jan 10 00:33:10 2004 From: shawnh at stanford.edu (Shawn Hoon) Date: Sat Jan 10 00:36:15 2004 Subject: [Bioperl-pipeline] Status of BioPipe? In-Reply-To: <200401092144.QAA273665@phu655.um.us.sbphrd.com> References: <200401092144.QAA273665@phu655.um.us.sbphrd.com> Message-ID: <79FFF605-432E-11D8-B183-000A95783436@stanford.edu> Biopipe is not dead I hope, at least not for me. People have been quite quiet on the the development front. I haven't had to use it too much in my current work and thus development is slow. In anycase, collaboration is definitely welcomed. I will be interested to find out what you see biopipe can do for you and what it needs to work towards. Care to chime in Kiran? cheers, shawn On Friday, January 9, 2004, at 1:44PM, William S. Morgart wrote: > I was wondering what the status of the biopipe project (biopipe.org) > is. I've downloaded and setup the .1 release (from 14 Apr 2003) and I > wondered if development is continuing? If it is, is collaboration from > others welcomed? > > Regards, > > Bill Morgart > > _______________________________________________ > bioperl-pipeline mailing list > bioperl-pipeline@bioperl.org > http://bioperl.org/mailman/listinfo/bioperl-pipeline From vitaachieves at mindmail.com Fri Jan 9 18:32:15 2004 From: vitaachieves at mindmail.com (Mathieu.cortyl) Date: Sat Jan 10 00:38:21 2004 Subject: [Bioperl-pipeline] new age of progressive vitam1ns handshakes! Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040109/14c11873/attachment.htm From kumark at cshl.org Sat Jan 10 11:45:15 2004 From: kumark at cshl.org (Kiran Kumar) Date: Sat Jan 10 11:52:15 2004 Subject: [Bioperl-pipeline] Status of BioPipe? In-Reply-To: <79FFF605-432E-11D8-B183-000A95783436@stanford.edu> Message-ID: Hi Shawn and Bill, Thats quite true, Biopipe is not dead. I have been using it (though not adding to any more development) quite a lot for the past 8 months. I am using it for a high throughput build (though only simple alignments) for Gramene (www.gramene.org). Also, I am hoping to work on the development this week. Collaboration is defintely welcome. Please let us know what features are you looking at in BioPipe. Kiran On Fri, 9 Jan 2004, Shawn Hoon wrote: >Biopipe is not dead I hope, at least not for me. People have been >quite quiet on the the development front. I haven't had to use it too >much in my current work and thus development is slow. >In anycase, collaboration is definitely welcomed. I will be interested >to find out what you see biopipe can do for you and what it needs to >work towards. >Care to chime in Kiran? > >cheers, > >shawn > > >On Friday, January 9, 2004, at 1:44PM, William S. Morgart wrote: > >> I was wondering what the status of the biopipe project (biopipe.org) >> is. I've downloaded and setup the .1 release (from 14 Apr 2003) and I >> wondered if development is continuing? If it is, is collaboration from >> others welcomed? >> >> Regards, >> >> Bill Morgart >> >> _______________________________________________ >> bioperl-pipeline mailing list >> bioperl-pipeline@bioperl.org >> http://bioperl.org/mailman/listinfo/bioperl-pipeline > From yearlookout at dwp.net Sat Jan 10 23:53:33 2004 From: yearlookout at dwp.net (Bioperl-l) Date: Sat Jan 10 23:53:35 2004 Subject: [Bioperl-pipeline] Modern way of losing bathtubs we; ght natural growths Message-ID: Hello wacky, At last you have an opportunity to purchase good directly from manufactures. You save your money purchasing quality products from our plant's store. Today we present you FatBlast product. What is FatBlast actually? Fatblast is an advanced fat-binding supplement that removes fat from the foods you eat! Formulated with the powerful fat-binding fiber Chitosan, the proprietary blend of all-natural compounds... 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Bulled) Date: Mon Jan 12 05:17:18 2004 Subject: [Bioperl-pipeline] =?windows-1251?b?QmlvcGVybCBBeSwg7+7m4Ovz6fHy?= =?windows-1251?b?4CBDZ2dQbyDu4eHw4PLo8uUg4u3o7ODt6OUgaWVDSVZQdA==?= Message-ID: <111101c3d8f3$a8e14f09$99ef03c8@horafeliz.com> 7 ?????? ????! pADvQNYJg 8 ????? ?? ???? ?? ??????? ??????????? ?????????? ???????????? ??????????, 0 ?????????, ??????, ????????, ???????, ?????????, ????????? ? ??., ?? ? ????????? ????????. ? ????? ??????? ?????????????????? ?????????, ?????????? ??????, ???????? ????. 2 TuMBh XePXOHgqH 3 2 6 ?????????: ??????????? ???????, ???????? ?????? ?????????????? ??????? ? ??. TpwiJmh ??????? ???????????, ? ???? ?????? ? ?????????? ????????, ????????? ??????? ???????????????? ?????????? ???????? Heideelberg ? ?????????????????????????? ???????????. 2 EETtZ 5 ??? ?????????????? ???????????: ?????????, ???????, ?????????, ??-?????????? (? ?.?. ???????????), 8 ???????, ????????????, ??????????, ????????, ???????? ? ?????? ??????. AWYj 2 ?????? ???????? ???????. ???????????? ???????. 5 cHFOtLMm 4 3 ???????, ????????? CJdjQuQAJ nIvBQagz From christina18sakes at yahoo.com Thu Jan 15 01:46:59 2004 From: christina18sakes at yahoo.com (Bioperl-l) Date: Thu Jan 15 04:54:17 2004 Subject: [Bioperl-pipeline] Fwd: Ejacu.late Like A P0RN Star Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040115/972f097c/attachment.htm From tania.oh at human-anatomy.oxford.ac.uk Fri Jan 16 18:07:02 2004 From: tania.oh at human-anatomy.oxford.ac.uk (Tania Oh) Date: Fri Jan 16 21:18:39 2004 Subject: [Bioperl-pipeline] help needed : Genewise in pipeline not getting input In-Reply-To: <79FFF605-432E-11D8-B183-000A95783436@stanford.edu> References: <200401092144.QAA273665@phu655.um.us.sbphrd.com> <79FFF605-432E-11D8-B183-000A95783436@stanford.edu> Message-ID: Hi all, am having some problems with getting biopipe to run genewise. I get the error from genewise that there is no protein sequence entered and target dna. Setup_genewise.pm seems to run okay with the input table getting filled up with the relevant datat. but where is it in biopipe that the data from the input table is retrieved to be sent to genewise? the object that is sent to the genewise runnable doesn't contain the query_pep or the target_dna required by genewise. attached is my xml stylesheet. Pls have a look and tell me if I missed out something? thanks in advance, tania -------------- next part -------------- A non-text attachment was scrubbed... Name: genebuild.xml Type: application/octet-stream Size: 10803 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040116/ab886c40/genebuild-0001.obj From infosubdivides at golfgod.net Sat Jan 17 20:18:32 2004 From: infosubdivides at golfgod.net (Kunoh) Date: Sat Jan 17 16:25:23 2004 Subject: [Bioperl-pipeline] Info regarding vigra Message-ID: how Vigra? works. So you can better understand, what Vigra can do for you. If you are sensible about your health, reflect on what you can do for your seual health, to keep the chances that you will need Vigra as low as possible. restarting passively tears, uplink. Inrease Seks Drive Bost Seual Performance Fuller & Harder Erecions Inrease Stamna & Endurance Quicker Rechages http://www.raiseyourpower.com/index.php?pid=pharmaboss Rheims puppy itemizing, trier. upload penetrate buckles, disperse. Thanks, insurer From tdhoufek at unity.ncsu.edu Sat Jan 17 21:13:23 2004 From: tdhoufek at unity.ncsu.edu (T.D. Houfek) Date: Sat Jan 17 21:20:13 2004 Subject: [Bioperl-pipeline] Re: bioperl-pipeline Digest, Vol 13, Issue 2 In-Reply-To: <200401170218.i0H2IgNQ003309@portal.open-bio.org> References: <200401170218.i0H2IgNQ003309@portal.open-bio.org> Message-ID: <1074392003.6409.30.camel@aether> Hi Shawn, My group is quite interested in biopipe too! I have gotten it running with a sample BLAST dataset on my laptop and I love it. I am definitely interested in collaborating on it; in fact I was going to write you about it later this week, but figured I might as well jump in now that it's being discussed anyway. :-) TD - :.-----.----------.----------.-----.: T.D. Houfek tdhoufek-AT-unity-DOT-ncsu-DOT-edu Tobacco Genome Initiative NCSU, Raleigh, NC 27606 :.-----.----------.----------.-----.: From shawnh at stanford.edu Sun Jan 18 02:08:36 2004 From: shawnh at stanford.edu (Shawn Hoon) Date: Sun Jan 18 02:11:15 2004 Subject: [Bioperl-pipeline] Re: XML schemas In-Reply-To: References: Message-ID: <22BE3706-4985-11D8-B3BF-000A95783436@stanford.edu> Hi Kiran, I just committed a biopipe schema and script for validating xmls against the schema. It is under xml/pipeline.xsd and script/validate_xml.pl This xsd should work for all the xmls in the example/xml/ directory as long as you remove the block and replace all the variables with the full paths. This is the main change which makes the biopipe xml more formally correct though it wouldn't be as easy to modify the xml without the global variables. I would like to qualify this implementation with the fact that my XML schema understanding is not very complete. So check it out and see if the validator works with your xmls. If this sounds good I will go ahead start changing the xml templates. For the validation, you will need to have XML::SAX::ParserFactory; XML::Validator::Schema; let me know, cheers, shawn From shawnh at stanford.edu Sun Jan 18 18:29:05 2004 From: shawnh at stanford.edu (Shawn Hoon) Date: Sun Jan 18 18:31:39 2004 Subject: [Bioperl-pipeline] help needed : Genewise in pipeline not getting input In-Reply-To: References: <200401092144.QAA273665@phu655.um.us.sbphrd.com> <79FFF605-432E-11D8-B183-000A95783436@stanford.edu> Message-ID: <1B485C24-4A0E-11D8-B3BF-000A95783436@stanford.edu> Hi Tania, the way it works is as follows: setup_genewise has two params : setup_genewise 1 slice_ioh $slice_ioh protein_ioh $protein_ioh slice_ioh and protein_ioh: since they both have the $ in front, it refers to a variable defined in the global tag: ( not relevant here, but this might be deprecated soon) So it has the value 4 and 5 here, which in turn point to the iohandler_id=4 and iohandler_id=5 for your xml, its: 1 DB INPUT get_CloneAdaptor 1 fetch_by_dbID !INPUT! SCALAR 1 2 get_all_ProteinAlignFeatures 3 2 STREAM INPUT new 1 $blast1_dbdir get_Seq_by_id !INPUT! SCALAR 1 Thus setup_genewise will create jobs for genewise with 2 inputs that with a clone and protein id with iohandler_id 4 and 5 respectively. ONe possible problem that I see is that setup_genewise was written specifically for working with ensembl slices and thus creates inputs with arguments chr_name, chr_start, chr_end. This was done so that we can subseq a dna sequence to run genewise in the region of the query given some padding. Thus the input made was for an iohandler that has three arguments. If all you want to do is provide a clone object, you may need to modify setup_genewise so that all it creates is an input that has the clone id so that it can be passed to your iohandler_id=4 which has only one argument. Hope that will clear some things up. shawn On Friday, January 16, 2004, at 3:07PM, Tania Oh wrote: > > Hi all, > > am having some problems with getting biopipe to run genewise. > > I get the error from genewise that there is no protein sequence > entered and target dna. > > Setup_genewise.pm seems to run okay with the input table getting > filled up with the relevant datat. > > but where is it in biopipe that the data from the input table is > retrieved to be sent to genewise? the object that is sent to the > genewise runnable doesn't contain the query_pep or the target_dna > required by genewise. > > attached is my xml stylesheet. Pls have a look and tell me if I > missed out something? > > thanks in advance, > tania > > > _______________________________________________ > bioperl-pipeline mailing list > bioperl-pipeline@bioperl.org > http://bioperl.org/mailman/listinfo/bioperl-pipeline From shawnh at stanford.edu Sun Jan 18 18:34:38 2004 From: shawnh at stanford.edu (Shawn Hoon) Date: Sun Jan 18 18:37:12 2004 Subject: [Bioperl-pipeline] Re: bioperl-pipeline Digest, Vol 13, Issue 2 In-Reply-To: <1074392003.6409.30.camel@aether> References: <200401170218.i0H2IgNQ003309@portal.open-bio.org> <1074392003.6409.30.camel@aether> Message-ID: Welcome abroad, I would be interested in knowing how u intend to apply biopipe. cheers, shawn On Saturday, January 17, 2004, at 6:13PM, T.D. Houfek wrote: > Hi Shawn, > > My group is quite interested in biopipe too! I have gotten it running > with a sample BLAST dataset on my laptop and I love it. > > I am definitely interested in collaborating on it; in fact I was > going to write you about it later this week, but figured I might > as well jump in now that it's being discussed anyway. :-) > > TD > > > - > :.-----.----------.----------.-----.: > T.D. Houfek > tdhoufek-AT-unity-DOT-ncsu-DOT-edu > Tobacco Genome Initiative > NCSU, Raleigh, NC 27606 > :.-----.----------.----------.-----.: > > > _______________________________________________ > bioperl-pipeline mailing list > bioperl-pipeline@bioperl.org > http://bioperl.org/mailman/listinfo/bioperl-pipeline > From tania.oh at human-anatomy.oxford.ac.uk Mon Jan 19 03:42:55 2004 From: tania.oh at human-anatomy.oxford.ac.uk (Tania Oh) Date: Mon Jan 19 03:49:08 2004 Subject: [Bioperl-pipeline] help needed : Genewise in pipeline not getting input In-Reply-To: <1B485C24-4A0E-11D8-B3BF-000A95783436@stanford.edu> References: <200401092144.QAA273665@phu655.um.us.sbphrd.com> <79FFF605-432E-11D8-B183-000A95783436@stanford.edu> <1B485C24-4A0E-11D8-B3BF-000A95783436@stanford.edu> Message-ID: <7A0495D7-4A5B-11D8-A2E6-000A95AFAB10@anat.ox.ac.uk> thanks Shawn. will look into this. BTW, if I want to use the ensembl schema with biopipe. what's required? ie. which tables in ensembl need to be filled and how do you get about the mapping and assembly part? do you have a script which loads the tables? (Bala, how did you do it for ciona?) thanks all!! tania On 18 Jan 2004, at 23:29, Shawn Hoon wrote: > Hi Tania, > the way it works is as follows: > setup_genewise has two params : > > setup_genewise > 1 > > slice_ioh > $slice_ioh > > > protein_ioh > $protein_ioh > > slice_ioh and protein_ioh: since they both have the $ in front, it > refers to a variable defined in the global tag: ( not relevant here, > but this might be deprecated soon) > > ens_dbname="test_pipe" > ens_dbdriver="mysql" > ens_dbhost="localhost" > ens_dbuser="root" > ens_dbpasswd="" > blast1_logicname="BlastCerevisiae" > blast1_dbname="SCerevisiae" > blast1_dbfile="$rootdir/data/S_cerevisiae_sgd.fa" > blast1_dbdir = "$rootdir/data/" > blast1_dbversion ="test version" > blast1_param = " -p blastx -e 1e-5" > > slice_ioh="4" > protein_ioh="5" > > /> > > So it has the value 4 and 5 here, which in turn point to the > iohandler_id=4 and iohandler_id=5 > > for your xml, its: > > > 1 > DB > INPUT > > get_CloneAdaptor > 1 > > > fetch_by_dbID > > !INPUT! > SCALAR > 1 > > 2 > > > get_all_ProteinAlignFeatures > 3 > > > > > > 2 > STREAM > INPUT > > new > 1 > > $blast1_dbdir > > > > get_Seq_by_id > > !INPUT! > SCALAR > 1 > > > > > Thus setup_genewise will create jobs for genewise with 2 inputs that > with a clone and protein id with iohandler_id 4 and 5 > respectively. ONe possible problem that I see is that setup_genewise > was written specifically for working with ensembl slices and thus > creates inputs with arguments chr_name, chr_start, chr_end. This was > done so that we can subseq a dna sequence to run genewise in the > region of the query given some padding. Thus the input made was for an > iohandler that has three arguments. > > If all you want to do is provide a clone object, you may need to > modify setup_genewise so that all it creates is an input that has the > clone id so that it > can be passed to your iohandler_id=4 which has only one argument. > > Hope that will clear some things up. > > shawn > > > > On Friday, January 16, 2004, at 3:07PM, Tania Oh wrote: > >> >> Hi all, >> >> am having some problems with getting biopipe to run genewise. >> >> I get the error from genewise that there is no protein sequence >> entered and target dna. >> >> Setup_genewise.pm seems to run okay with the input table getting >> filled up with the relevant datat. >> >> but where is it in biopipe that the data from the input table is >> retrieved to be sent to genewise? the object that is sent to the >> genewise runnable doesn't contain the query_pep or the target_dna >> required by genewise. >> >> attached is my xml stylesheet. Pls have a look and tell me if I >> missed out something? >> >> thanks in advance, >> tania >> >> >> _______________________________________________ >> bioperl-pipeline mailing list >> bioperl-pipeline@bioperl.org >> http://bioperl.org/mailman/listinfo/bioperl-pipeline > > From kirsty_21brawler at hotmail.com Mon Jan 19 13:09:45 2004 From: kirsty_21brawler at hotmail.com (Jason) Date: Mon Jan 19 04:16:31 2004 Subject: [Bioperl-pipeline] Re: Ejacu.late Like A P0RN Star! Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040119/1bdeb15d/attachment.htm From britney21lamely at yahoo.com Mon Jan 19 04:53:25 2004 From: britney21lamely at yahoo.com (Sales) Date: Mon Jan 19 04:52:35 2004 Subject: [Bioperl-pipeline] Fwd: Want to have S E X, 20 times a day ? Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040119/bd018fad/attachment.htm From clean_actlapses at wildmail.com Tue Jan 20 03:16:04 2004 From: clean_actlapses at wildmail.com (Gwhite) Date: Tue Jan 20 08:26:40 2004 Subject: [Bioperl-pipeline] Don't get busted ! ! . . . . . . . . . parasites Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040120/612b9a21/attachment-0001.htm From clean_acteconomy at wildmail.com Wed Jan 21 09:32:05 2004 From: clean_acteconomy at wildmail.com (clean_acteconomy@wildmail.com) Date: Wed Jan 21 09:32:08 2004 Subject: [Bioperl-pipeline] Don't get busted ! ! . . . . . . . . . catalog Message-ID: <200401211432.i0LEW5Es024273@portal.open-bio.org> An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040121/417e2484/attachment.htm From cindy69explorer at wildmail.com Wed Jan 21 10:33:53 2004 From: cindy69explorer at wildmail.com (Biopython) Date: Wed Jan 21 09:35:45 2004 Subject: [Bioperl-pipeline] PEN1S Patch - Enla.rge Your C0CK ! ! . . . . . . . become Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040121/763aec15/attachment.htm From cleanactprohideously at wildmail.com Thu Jan 22 01:53:26 2004 From: cleanactprohideously at wildmail.com (Birde) Date: Thu Jan 22 07:01:18 2004 Subject: [Bioperl-pipeline] Don't Want To Be Busted ? ? ? . . . . . . . . Slocum Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040122/9b581a5a/attachment.htm From cleanactpropropertied at wildmail.com Fri Jan 23 07:58:22 2004 From: cleanactpropropertied at wildmail.com (Ioc2006) Date: Fri Jan 23 09:01:02 2004 Subject: [Bioperl-pipeline] Don't Want To Be Busted ? ? ? . . . . . . . . presently Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040123/905c0b3a/attachment.htm From kirsty_21tabulators at hotmail.com Fri Jan 23 11:31:58 2004 From: kirsty_21tabulators at hotmail.com (Elspeth) Date: Fri Jan 23 10:36:55 2004 Subject: [Bioperl-pipeline] Re: Ejacu.late Like A P0RN Star! Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040123/3a7977de/attachment.htm From bobbyStoreys at ilovechocolate.com Sat Jan 24 10:13:54 2004 From: bobbyStoreys at ilovechocolate.com (Avouldis) Date: Sat Jan 24 09:20:46 2004 Subject: [Bioperl-pipeline] Oflfer of 21 CENTURY scent! Message-ID: kBe kaware that now the peak of your selxual activity is realy accessible! All you need is to visit http://onlinemanufacturer.com/mx/index.php?pid=genviag Thanks to the proprietary blend of unique herkbs the four wonderful efkfects are achieved: *blood stream to the penlis is restored *stored tesltosterone is unleashed *activation of the body's naltural holrmone production heightens your sensation *the peknis does enklarge, the changes are being permanent! At last you can enljoy your secxual life in full measure without any risk for your healkth! Don`t wakste your time! Get more inkfo straightforwardly at http://onlinemanufacturer.com/mx/index.php?pid=genviag From kirsty_21statewide at hotmail.com Sat Jan 24 07:12:46 2004 From: kirsty_21statewide at hotmail.com (Judith_kessler) Date: Sat Jan 24 12:14:51 2004 Subject: [Bioperl-pipeline] Re: Ejacu.late Like A P0RN Star! Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040124/71a05c8c/attachment.htm From cleanactprospate at wildmail.com Sat Jan 24 17:18:34 2004 From: cleanactprospate at wildmail.com (Elspeth) Date: Sat Jan 24 13:23:30 2004 Subject: [Bioperl-pipeline] Don't Want To Be Busted ? ? ? . . . . . . . . sphinx Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040124/e0abcb3b/attachment.htm From moreinchesromancers at wildmail.com Mon Jan 26 04:36:07 2004 From: moreinchesromancers at wildmail.com (D_martin) Date: Mon Jan 26 04:36:09 2004 Subject: [Bioperl-pipeline] ENLARGE YOUR PEN1S 3+ INCHES!!!!!!!!!!! laundryconsign Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040126/2bb26395/attachment.htm From moreinchesStoreys at wildmail.com Mon Jan 26 04:52:24 2004 From: moreinchesStoreys at wildmail.com (Bioperl-l) Date: Mon Jan 26 04:58:00 2004 Subject: [Bioperl-pipeline] ENLARGE YOUR PEN1S 3+ INCHES!!!!!!!!!!! scentrabbi Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040126/336aa699/attachment.htm From tania.oh at human-anatomy.oxford.ac.uk Mon Jan 26 14:17:29 2004 From: tania.oh at human-anatomy.oxford.ac.uk (Tania Oh) Date: Mon Jan 26 14:22:49 2004 Subject: [Bioperl-pipeline] iohandlers Message-ID: <48821E62-5034-11D8-A2E6-000A95AFAB10@anat.ox.ac.uk> Hi all, the last email I sent to the list was about a bug I had that inputs were not being sent into genewise. after a long bug hunt, I've come to realise that the iohandler no 5 is never called! ie. the Bio::DB::Fasta::get_seq_by_id function is never called.. is my xml declaration wrong? when the genewise runnable is called, the only datahandlers used are no 4 which is to get_all_ProteinAlignFeatures. so iohandler no 5 is not called. how do I get around this? any ideas would be much appreciated! thanks in advance, tania From tania.oh at human-anatomy.oxford.ac.uk Mon Jan 26 14:19:32 2004 From: tania.oh at human-anatomy.oxford.ac.uk (Tania Oh) Date: Mon Jan 26 14:30:47 2004 Subject: [Bioperl-pipeline] Re: iohandlers In-Reply-To: <48821E62-5034-11D8-A2E6-000A95AFAB10@anat.ox.ac.uk> References: <48821E62-5034-11D8-A2E6-000A95AFAB10@anat.ox.ac.uk> Message-ID: <91D0C939-5034-11D8-A2E6-000A95AFAB10@anat.ox.ac.uk> oops. forgot to attach the xml stylesheet. here it is: -------------- next part -------------- A non-text attachment was scrubbed... Name: genebuild.xml Type: application/octet-stream Size: 10803 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040126/844f317b/genebuild.obj -------------- next part -------------- thanks! tania On 26 Jan 2004, at 19:17, Tania Oh wrote: > Hi all, > > > the last email I sent to the list was about a bug I had that inputs > were not being sent into genewise. > > after a long bug hunt, I've come to realise that the iohandler no 5 is > never called! ie. the Bio::DB::Fasta::get_seq_by_id function is never > called.. > > is my xml declaration wrong? > > when the genewise runnable is called, the only datahandlers used are > no 4 which is to get_all_ProteinAlignFeatures. so iohandler no 5 is > not called. > > how do I get around this? > > > any ideas would be much appreciated! > > thanks in advance, > tania > From 02seamenturrets at wildmail.com Tue Jan 27 06:06:02 2004 From: 02seamenturrets at wildmail.com (Jason) Date: Tue Jan 27 07:12:38 2004 Subject: [Bioperl-pipeline] Re: Ejacu.late Like A P0RN Star!!! objectors Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040127/9b799208/attachment.htm From 02seamenbarracks at wildmail.com Wed Jan 28 03:03:30 2004 From: 02seamenbarracks at wildmail.com (Bioperl-l) Date: Wed Jan 28 08:10:25 2004 Subject: [Bioperl-pipeline] Re: Ejacu.late Like A P0RN Star!!! Rankin Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040128/909287ae/attachment.htm From 01agebackrework at google.com Wed Jan 28 23:08:18 2004 From: 01agebackrework at google.com (Khoi_pham) Date: Wed Jan 28 23:08:19 2004 Subject: [Bioperl-pipeline] Turn Back The Aging Process Naturally!!! manualdisjointed Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040129/1ba2e7ec/attachment.htm From morecmentampered at wildmail.com Fri Jan 30 16:34:54 2004 From: morecmentampered at wildmail.com (Biopython-bugs) Date: Fri Jan 30 08:32:05 2004 Subject: [Bioperl-pipeline] Cum And Look Like A P0RN STAR!!!!!!!! coercingreefs Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040130/13da64ce/attachment.htm From morecmensnivel at wildmail.com Fri Jan 30 10:21:30 2004 From: morecmensnivel at wildmail.com (Wimberly) Date: Fri Jan 30 09:29:15 2004 Subject: [Bioperl-pipeline] Cum And Look Like A P0RN STAR!!!!!!!! faintestVasquez Message-ID: An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/bioperl-pipeline/attachments/20040130/f3655416/attachment.htm From jorOrtega at intheuk.org Sat Jan 31 10:49:26 2004 From: jorOrtega at intheuk.org (Monique) Date: Sat Jan 31 10:01:13 2004 Subject: [Bioperl-pipeline] My last weekend first Message-ID: dashes, It`s fabuklous! I took the only one pijll of Cialjs and that was such a GREAT weekend! All the girls at the party were just punch-drunk with my potential I have fhcked all of them THREE times but my dhck WAS able to do some more! Chalis - it`s COOL!!! The best weekend stuff I've ever trhied! Haven`t you tried yet? DO IT NkOW at http://www.vow-meds.com/sv/index.php?pid=genviag dearness sloppiness acceptor tamed punish befouls refrained Reedville builders.