From postmaster at ebi.ac.uk Tue May 4 23:14:31 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Wed, 5 May 2004 04:14:31 +0100 (BST) Subject: Warning: E-mail containing attachment(s) blocked Message-ID: <200405050314.i453EVW02604@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: james at ebi.ac.uk Subject: Re: Developement Date: Wed May 5 04:14:31 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: (document09_james.zip) -- MailScanner Email Virus Scanner www.mailscanner.info From henrikki.almusa at helsinki.fi Mon May 10 06:08:32 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 10 May 2004 13:08:32 +0300 Subject: Sigcleave and report Message-ID: <200405101308.32520.henrikki.almusa@helsinki.fi> Hello, There was a bug in sigcleave. The tail text "No scores over " is left in tail after printing report without any hits. If there is multiple sequences in input file and sequence later have hits, then same text appears in report with hits as well. However it seems that there is no function like "ajReportClearTail" so it's fixed by putting empty AjPString in there after writing a report. Would it be useful functions to clear header and tail? If not then, I'll put this to emboss-submit as is. -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: sigcleave_tail_fix.patch Type: text/x-diff Size: 718 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040510/60afbb1a/attachment.bin From Imogene at fiestabrava.com Tue May 18 12:03:48 2004 From: Imogene at fiestabrava.com (Eugenio Watts) Date: Tue, 18 May 2004 19:03:48 +0300 (CST) Subject: Softwares CDS all software under 15$ and 99$! slut Message-ID: <14050440263761.BI41njWXkua74@workbench6.danny89cocolee.net> >Life begins at forty Sensation!! We opened a NEW site with unbeatable prices and products. 1500 WORLD BEST software with 90% discount - that is a really BEST offer just imagine, you can buy ALL software that you ever need and pay price of just one of it! Office 2003 for 50$ - nice deal right ? ;) retail price is 700$ - great savings, huh? Please spend few moments of yours precious time to check our offer - it is more than worth it! http://constantine.reachsoftware.com/?driveway >Absence makes the heart go wander. >The squeaky wheel gets the grease. >Every dog has his day >Lean liberty is better than fat slavery >A place for everything and everything in its place. >Yesterday is ashes; tomorrow wood Only today does the fire burn brightly >There is a time and a place for everything >March winds and April showers bring forth May flowers >A fair exchange is no robbery. >Shame face ah feel like cent ice. >And say, How have I hated instruction, and my heart despised reproof. >Promises are like babies Easy to make, hard to deliver >Don't cross your bridges before you come to them. >Tis better to get things for free, than to work up a sweat >There is no such thing as a free lunch >It is in vain to cast your net where there is no fish >Everything must have a beginning >Rain, Rain, go away, come back another day >Artificial intelligence is no match for natural stupidity From gwilliam at hgmp.mrc.ac.uk Thu May 20 11:38:15 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 20 May 2004 16:38:15 +0100 Subject: Sigcleave and report References: <200405101308.32520.henrikki.almusa@helsinki.fi> Message-ID: <40ACD0E7.A510907D@hgmp.mrc.ac.uk> It looks as if the same problem affects restrict: The text in the tail of the report is not cleared. For example the second sequence in the list has no hits, but the fragments from the first sequence are reported again. Gary % restrict @list -enz acci -site 4 stdout -frag Finds restriction enzyme cleavage sites ######################################## # Program: restrict # Rundate: Thu May 20 16:34:01 2004 # Report_format: table # Report_file: stdout ######################################## #======================================= # # Sequence: AY582533 from: 1 to: 3846 # HitCount: 2 # # Minimum cuts per enzyme: 1 # Maximum cuts per enzyme: 2000000000 # Minimum length of recognition site: 4 # Blunt ends allowed # Sticky ends allowed # DNA is linear # Ambiguities allowed # #======================================= Start End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev 1773 1778 AccI GTMKAC 1774 1776 . . 2018 2023 AccI GTMKAC 2019 2021 . . #--------------------------------------- # # Fragment lengths: # 1827 # 1774 # 245 # #--------------------------------------- #======================================= # # Sequence: AY582532 from: 1 to: 4635 # HitCount: 0 # # Minimum cuts per enzyme: 1 # Maximum cuts per enzyme: 2000000000 # Minimum length of recognition site: 4 # Blunt ends allowed # Sticky ends allowed # DNA is linear # Ambiguities allowed # #======================================= Start End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev #--------------------------------------- # # Fragment lengths: # 1827 # 1774 # 245 # #--------------------------------------- Henrikki Almusa wrote: > > Hello, > > There was a bug in sigcleave. The tail text "No scores over " is left in tail > after printing report without any hits. If there is multiple sequences in > input file and sequence later have hits, then same text appears in report > with hits as well. > > However it seems that there is no function like "ajReportClearTail" so it's > fixed by putting empty AjPString in there after writing a report. Would it be > useful functions to clear header and tail? If not then, I'll put this to > emboss-submit as is. > > -- > Henrikki Almusa > > ------------------------------------------------------------------------ > Name: sigcleave_tail_fix.patch > sigcleave_tail_fix.patch Type: text/x-diff > Encoding: 7bit -- Gary Williams MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494522 Fax: +44 1223 494512 E-mail: gwilliam at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From henrikki.almusa at helsinki.fi Fri May 21 04:01:44 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 21 May 2004 11:01:44 +0300 Subject: Add ajReportClearTail and header to ajax/ajreport.c [Re: Sigcleave and report] In-Reply-To: <40ACD0E7.A510907D@hgmp.mrc.ac.uk> References: <200405101308.32520.henrikki.almusa@helsinki.fi> <40ACD0E7.A510907D@hgmp.mrc.ac.uk> Message-ID: <200405211101.44012.henrikki.almusa@helsinki.fi> On Thursday 20 May 2004 18:38, Gary Williams, Tel 01223 494522 wrote: > It looks as if the same problem affects restrict: > The text in the tail of the report is not cleared. > For example the second sequence in the list has no hits, but the > fragments from the first sequence are reported again. Well heres two patches (against 2.8.0). First adds the ajReportClearHeader and ajReportClearTail to "ajax/ajreport.c". Second patch makes use of these in sigcleave and restrict. Tested with sigcleave and it seemed to work ok. I'm not sure how much use is the header clearing, but being systematic is better. Comments. I'm pretty sure I didn't put the earlier patch into emboss-submit. And since this is imho better way, I'll put this into emboss-submit if ok. Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: report_clear_ht.patch Type: text/x-diff Size: 1472 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040521/5ce75903/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: restrict_sigcleave.patch Type: text/x-diff Size: 1197 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040521/5ce75903/attachment-0001.bin From return at workmiracle.com Wed May 26 08:38:05 2004 From: return at workmiracle.com (Elisabeth Brown) Date: Wed, 26 May 2004 20:38:05 +0800 Subject: transgenic.cats.st Message-ID: <200405261247.i4QClVOx015808@localhost.localdomain> An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040526/6f2edb23/attachment.html From virusfound at adv.ru Fri May 28 11:24:30 2004 From: virusfound at adv.ru (DrWeb-DAEMON) Date: 28 May 2004 15:24:30 -0000 Subject: Undelivered mail: notice! Message-ID: <20040528152430.28756.qmail@go.adv.ru> Dear User, The message with following attributes has not been delivered. because contains an infected object. Sender = emboss-dev at embnet.org Recipients = gvozdev at img.ras.ru Subject = notice! 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Sincerely, WOM Support Department From postmaster at ebi.ac.uk Wed May 5 03:14:31 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Wed, 5 May 2004 04:14:31 +0100 (BST) Subject: Warning: E-mail containing attachment(s) blocked Message-ID: <200405050314.i453EVW02604@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: james at ebi.ac.uk Subject: Re: Developement Date: Wed May 5 04:14:31 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: (document09_james.zip) -- MailScanner Email Virus Scanner www.mailscanner.info From henrikki.almusa at helsinki.fi Mon May 10 10:08:32 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 10 May 2004 13:08:32 +0300 Subject: Sigcleave and report Message-ID: <200405101308.32520.henrikki.almusa@helsinki.fi> Hello, There was a bug in sigcleave. The tail text "No scores over " is left in tail after printing report without any hits. If there is multiple sequences in input file and sequence later have hits, then same text appears in report with hits as well. However it seems that there is no function like "ajReportClearTail" so it's fixed by putting empty AjPString in there after writing a report. Would it be useful functions to clear header and tail? If not then, I'll put this to emboss-submit as is. -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: sigcleave_tail_fix.patch Type: text/x-diff Size: 718 bytes Desc: not available URL: From Imogene at fiestabrava.com Tue May 18 16:03:48 2004 From: Imogene at fiestabrava.com (Eugenio Watts) Date: Tue, 18 May 2004 19:03:48 +0300 (CST) Subject: Softwares CDS all software under 15$ and 99$! slut Message-ID: <14050440263761.BI41njWXkua74@workbench6.danny89cocolee.net> >Life begins at forty Sensation!! We opened a NEW site with unbeatable prices and products. 1500 WORLD BEST software with 90% discount - that is a really BEST offer just imagine, you can buy ALL software that you ever need and pay price of just one of it! Office 2003 for 50$ - nice deal right ? ;) retail price is 700$ - great savings, huh? Please spend few moments of yours precious time to check our offer - it is more than worth it! http://constantine.reachsoftware.com/?driveway >Absence makes the heart go wander. >The squeaky wheel gets the grease. >Every dog has his day >Lean liberty is better than fat slavery >A place for everything and everything in its place. >Yesterday is ashes; tomorrow wood Only today does the fire burn brightly >There is a time and a place for everything >March winds and April showers bring forth May flowers >A fair exchange is no robbery. >Shame face ah feel like cent ice. >And say, How have I hated instruction, and my heart despised reproof. >Promises are like babies Easy to make, hard to deliver >Don't cross your bridges before you come to them. >Tis better to get things for free, than to work up a sweat >There is no such thing as a free lunch >It is in vain to cast your net where there is no fish >Everything must have a beginning >Rain, Rain, go away, come back another day >Artificial intelligence is no match for natural stupidity From gwilliam at hgmp.mrc.ac.uk Thu May 20 15:38:15 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Thu, 20 May 2004 16:38:15 +0100 Subject: Sigcleave and report References: <200405101308.32520.henrikki.almusa@helsinki.fi> Message-ID: <40ACD0E7.A510907D@hgmp.mrc.ac.uk> It looks as if the same problem affects restrict: The text in the tail of the report is not cleared. For example the second sequence in the list has no hits, but the fragments from the first sequence are reported again. Gary % restrict @list -enz acci -site 4 stdout -frag Finds restriction enzyme cleavage sites ######################################## # Program: restrict # Rundate: Thu May 20 16:34:01 2004 # Report_format: table # Report_file: stdout ######################################## #======================================= # # Sequence: AY582533 from: 1 to: 3846 # HitCount: 2 # # Minimum cuts per enzyme: 1 # Maximum cuts per enzyme: 2000000000 # Minimum length of recognition site: 4 # Blunt ends allowed # Sticky ends allowed # DNA is linear # Ambiguities allowed # #======================================= Start End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev 1773 1778 AccI GTMKAC 1774 1776 . . 2018 2023 AccI GTMKAC 2019 2021 . . #--------------------------------------- # # Fragment lengths: # 1827 # 1774 # 245 # #--------------------------------------- #======================================= # # Sequence: AY582532 from: 1 to: 4635 # HitCount: 0 # # Minimum cuts per enzyme: 1 # Maximum cuts per enzyme: 2000000000 # Minimum length of recognition site: 4 # Blunt ends allowed # Sticky ends allowed # DNA is linear # Ambiguities allowed # #======================================= Start End Enzyme_name Restriction_site 5prime 3prime 5primerev 3primerev #--------------------------------------- # # Fragment lengths: # 1827 # 1774 # 245 # #--------------------------------------- Henrikki Almusa wrote: > > Hello, > > There was a bug in sigcleave. The tail text "No scores over " is left in tail > after printing report without any hits. If there is multiple sequences in > input file and sequence later have hits, then same text appears in report > with hits as well. > > However it seems that there is no function like "ajReportClearTail" so it's > fixed by putting empty AjPString in there after writing a report. Would it be > useful functions to clear header and tail? If not then, I'll put this to > emboss-submit as is. > > -- > Henrikki Almusa > > ------------------------------------------------------------------------ > Name: sigcleave_tail_fix.patch > sigcleave_tail_fix.patch Type: text/x-diff > Encoding: 7bit -- Gary Williams MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494522 Fax: +44 1223 494512 E-mail: gwilliam at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From henrikki.almusa at helsinki.fi Fri May 21 08:01:44 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 21 May 2004 11:01:44 +0300 Subject: Add ajReportClearTail and header to ajax/ajreport.c [Re: Sigcleave and report] In-Reply-To: <40ACD0E7.A510907D@hgmp.mrc.ac.uk> References: <200405101308.32520.henrikki.almusa@helsinki.fi> <40ACD0E7.A510907D@hgmp.mrc.ac.uk> Message-ID: <200405211101.44012.henrikki.almusa@helsinki.fi> On Thursday 20 May 2004 18:38, Gary Williams, Tel 01223 494522 wrote: > It looks as if the same problem affects restrict: > The text in the tail of the report is not cleared. > For example the second sequence in the list has no hits, but the > fragments from the first sequence are reported again. Well heres two patches (against 2.8.0). First adds the ajReportClearHeader and ajReportClearTail to "ajax/ajreport.c". Second patch makes use of these in sigcleave and restrict. Tested with sigcleave and it seemed to work ok. I'm not sure how much use is the header clearing, but being systematic is better. Comments. I'm pretty sure I didn't put the earlier patch into emboss-submit. And since this is imho better way, I'll put this into emboss-submit if ok. Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: report_clear_ht.patch Type: text/x-diff Size: 1472 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: restrict_sigcleave.patch Type: text/x-diff Size: 1197 bytes Desc: not available URL: From return at workmiracle.com Wed May 26 12:38:05 2004 From: return at workmiracle.com (Elisabeth Brown) Date: Wed, 26 May 2004 20:38:05 +0800 Subject: transgenic.cats.st Message-ID: <200405261247.i4QClVOx015808@localhost.localdomain> An HTML attachment was scrubbed... URL: From virusfound at adv.ru Fri May 28 15:24:30 2004 From: virusfound at adv.ru (DrWeb-DAEMON) Date: 28 May 2004 15:24:30 -0000 Subject: Undelivered mail: notice! Message-ID: <20040528152430.28756.qmail@go.adv.ru> Dear User, The message with following attributes has not been delivered. because contains an infected object. Sender = emboss-dev at embnet.org Recipients = gvozdev at img.ras.ru Subject = notice! Message-ID = [unknown-id] Antivirus filter report: --- Dr.Web report --- ======== drweb.tmp_GyTo5x - archive MAIL [text:plain] - Ok visa.doc.pif packed by PETITE visa.doc.pif infected with Win32.HLLM.Netsky.based ======== known virus is found : 1 evaluation key used : 1 --- Dr.Web report --- The original message was stored in archive record named: drweb.infected_T0riil After 3 days message will be deleted from archive. In order to receive the original message, please send request to , referring to the archive record name given above. --- Antivirus service provided by Dr.Web(R) Daemon for Unix (http://www.drweb.ru, http://www.dials.ru/english) -------------- next part -------------- ????????? ??????????? emboss-dev at embnet.org, ?????????, ???????????? ???? ?? ??????(??) gvozdev at img.ras.ru ???????????? ? ?? ???? ??????????. --- Dr.Web report --- ======== drweb.tmp_GyTo5x - archive MAIL [text:plain] - Ok visa.doc.pif packed by PETITE visa.doc.pif infected with Win32.HLLM.Netsky.based ======== known virus is found : 1 evaluation key used : 1 --- Dr.Web report --- ???? ????????? ????????? ? ????????? ??? ??????: drweb.infected_T0riil ????? 3 ??? ????????? ????? ???????. ??? ?? ???????? ??? ????????? ?????????? ? ?????????????? ?? ?????? , ?????? ???, ??? ??????? ???? ????????? ????????? ? ?????????. --- ???????????? ?????? ???????? ???????? Dr.Web(R) Daemon for Unix (?????????? ? 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