From SUPPORT at BACKGROUNDINVESTIGATION.US Tue Jun 1 02:41:27 2004 From: SUPPORT at BACKGROUNDINVESTIGATION.US (SUPPORT at BACKGROUNDINVESTIGATION.US) Date: Mon, 31 May 2004 22:41:27 -0800 Subject: You are being researched Message-ID: ****NOT COMMERCIAL EMAIL**** A user is looking into your background at our website. One of our users has begun the process of meeting people who know you via our website for the purpose of researching your background. This email was automatically sent to you to inform you of this. The user doing the research provided us with your email address. Why did we send you this email? We feel that we have a responsibility to inform research subjects so that they have an opportunity to find out what is being said. To view all of the postings at our website about this email address use this link: http://k.womr.biz/sel.php?a=search&b=5&c=emboss-dev%40embnet.org Why do people use our website? 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To add to Do Not Email List click here: http://2.shyx.biz/lx.php?a=donotemail&b=emboss-dev at embnet.org Best Regards, Support Department From henrikki.almusa at helsinki.fi Mon Jun 14 05:20:41 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 14 Jun 2004 12:20:41 +0300 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg Message-ID: <200406141220.41863.henrikki.almusa@helsinki.fi> Hello, There might be a need for doing sequences with a list of patterns. Now at the moment there is only tfscan and patmatmotifs that uses list of patterns to search in seqeunces. The problem is that tfscan uses only fixed sequences and patmatmotifs uses a directory of files. I propose to modify reg and fuzz pattern searches to read a "fasta format of pattern" file. Example file using dreg might be >pat1 [ac]{2}gg >pat2 [gc]{3}att Pattern could span multiple lines. I would be willing to try out some changes in fuzz group as start. Should the code that reads the pattern file reading be coded somewhere else (eg not in fuzznuc.c)? Any feedback or suggestions etc would be welcome -- Henrikki Almusa From gwilliam at hgmp.mrc.ac.uk Mon Jun 14 05:26:09 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 14 Jun 2004 10:26:09 +0100 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg References: <200406141220.41863.henrikki.almusa@helsinki.fi> Message-ID: <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> Should the file of patterns allow each pattern to have its own allowed number of mismatches? >pat1 ggataata[ac]{2}gg >pat2 gcggcatgtagc[gc]{3}att Gary Henrikki Almusa wrote: > > Hello, > > There might be a need for doing sequences with a list of patterns. Now at the > moment there is only tfscan and patmatmotifs that uses list of patterns to > search in seqeunces. The problem is that tfscan uses only fixed sequences and > patmatmotifs uses a directory of files. > > I propose to modify reg and fuzz pattern searches to read a "fasta format of > pattern" file. Example file using dreg might be > > >pat1 > [ac]{2}gg > >pat2 > [gc]{3}att > > Pattern could span multiple lines. > > I would be willing to try out some changes in fuzz group as start. Should the > code that reads the pattern file reading be coded somewhere else (eg not in > fuzznuc.c)? > > Any feedback or suggestions etc would be welcome > -- > Henrikki Almusa -- 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 gwilliam at hgmp.mrc.ac.uk Wed Jun 16 06:25:18 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 16 Jun 2004 11:25:18 +0100 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg References: <200406141220.41863.henrikki.almusa@helsinki.fi> <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> <200406161305.17606.henrikki.almusa@helsinki.fi> Message-ID: <40D0200E.A52A3D58@hgmp.mrc.ac.uk> Henrikki, Would it be a good idea to overload the pattern qualifier of fuzz(nuc|pro|tran) and [pd]reg so that they understand '@filename' to be a pattern list filename, in the same way as restrict will either read a comma-delimited list of enzyme names or a '@filename' of a list of enzymes? So: fuzznuc could then be run as normal: fuzznuc em:hsfau -patt 'acgacga[gc]' -out test.out or with a pattern list: fuzznuc em:hsfau -patt '@patfile' -out test.out Gary Henrikki Almusa wrote: > > On Monday 14 June 2004 12:26, Gary Williams, Tel 01223 494522 wrote: > > Should the file of patterns allow each pattern to have its own allowed > > number of mismatches? > > > > >pat1 > > > > ggataata[ac]{2}gg > > > > >pat2 > > > > gcggcatgtagc[gc]{3}att > > No reason why not. > > Now the coding itself. Since reading that file is pretty low level stuff, it > should probably be in "ajax/" dir? My obj c abilities are not perhaps that > good. Anyone willing to help on the .c side? > > What might be needed in .h (names can be changed). This mainly is for using > the pattern in program. This is now currently just what I could come up with, > so I can go completely off here :). > > struct AjSPattern { > AjPStr name; > AjPStr opropat; > AjPStr propat; > AjPRegex regexpat; > ajint mismatch; > } AjOPattern; > #define AjPPattern AjOPattern* > > struct AjSPatlist { > AjPList patlist; > ajint type; # 0 regex, 1 prosite > } AjPOPatlist; > #define AjPPatlist AjOPatlist* > > AjBool ajPatlistGetNext (patlist, &pattern); > void ajPatlistRewind (patlist); > ajint ajPatlistGetType (patlist); > > AjPStr ajPatternGetName (pattern); > ajint ajPatternGetType (pattern); > whether propat is not NULL in struct should work > ajint ajPatternGetMismatch (pattern); > AjPStr ajPatternGetPro (pattern); > AjPStr ajPatternGetOrigPro (pattern); > AjPRegex ajPatternGetRegex (pattern); > AjPStr ajPatternGetPattern (pattern); > should return string representation of pattern it has > > Acd would need propably new file type, patlist. It should be defined in the > programs acd file, whether the pattern is regex or prosite. This would allow > the reading (and compiling the patterns) in acd command. > > acdGetPatlist(); > > Comments? > -- > Henrikki Almusa -- 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 Wed Jun 16 06:30:27 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 16 Jun 2004 13:30:27 +0300 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg In-Reply-To: <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> References: <200406141220.41863.henrikki.almusa@helsinki.fi> <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> Message-ID: <200406161330.27542.henrikki.almusa@helsinki.fi> On Monday 14 June 2004 12:26, Gary Williams, Tel 01223 494522 wrote: > Should the file of patterns allow each pattern to have its own allowed > number of mismatches? > > >pat1 > > ggataata[ac]{2}gg > > >pat2 > > gcggcatgtagc[gc]{3}att No reason why not. Now the coding itself. Since reading that file is pretty low level stuff, it should probably be in "ajax/" dir? My obj c abilities are not perhaps that good. Anyone willing to help on the .c side? What might be needed in .h (names can be changed). This mainly is for using the pattern in program. This is now currently just what I could come up with, so I can go completely off here :). struct AjSPattern { AjPStr name; AjPStr opropat; AjPStr propat; AjPRegex regexpat; ajint mismatch; } AjOPattern; #define AjPPattern AjOPattern* struct AjSPatlist { AjPList patlist; ajint type; # 0 regex, 1 prosite } AjPOPatlist; #define AjPPatlist AjOPatlist* AjBool ajPatlistGetNext (patlist, &pattern); void ajPatlistRewind (patlist); ajint ajPatlistGetType (patlist); AjPStr ajPatternGetName (pattern); ajint ajPatternGetType (pattern); whether propat is not NULL in struct should work ajint ajPatternGetMismatch (pattern); AjPStr ajPatternGetPro (pattern); AjPStr ajPatternGetOrigPro (pattern); AjPRegex ajPatternGetRegex (pattern); AjPStr ajPatternGetPattern (pattern); should return string representation of pattern it has Acd would need propably new file type, patlist. It should be defined in the programs acd file, whether the pattern is regex or prosite. This would allow the reading (and compiling the patterns) in acd command. acdGetPatlist(); Comments? -- Henrikki Almusa From pmr at ebi.ac.uk Wed Jun 16 06:38:19 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 16 Jun 2004 11:38:19 +0100 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg In-Reply-To: <200406161330.27542.henrikki.almusa@helsinki.fi> References: <200406141220.41863.henrikki.almusa@helsinki.fi> <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> <200406161330.27542.henrikki.almusa@helsinki.fi> Message-ID: <40D0231B.4020106@ebi.ac.uk> Henrikki Almusa wrote: > Acd would need propably new file type, patlist. It should be defined in the > programs acd file, whether the pattern is regex or prosite. This would allow > the reading (and compiling the patterns) in acd command. ... or we can define a knowntype attribute for the string that says the program will accept a pattern (of some kind) or an @file. That avoids defining a new ACD type, but can still be used in GUIs and web service/workflow wrappers to validate the pattern. regards, Peter Rice From henrikki.almusa at helsinki.fi Mon Jun 21 06:54:36 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 21 Jun 2004 13:54:36 +0300 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg In-Reply-To: <40D0231B.4020106@ebi.ac.uk> References: <200406141220.41863.henrikki.almusa@helsinki.fi> <200406161330.27542.henrikki.almusa@helsinki.fi> <40D0231B.4020106@ebi.ac.uk> Message-ID: <200406211354.36787.henrikki.almusa@helsinki.fi> On Wednesday 16 June 2004 13:38, Peter Rice wrote: > Henrikki Almusa wrote: > > Acd would need propably new file type, patlist. It should be defined in > > the programs acd file, whether the pattern is regex or prosite. This > > would allow the reading (and compiling the patterns) in acd command. > > ... or we can define a knowntype attribute for the string that says the > program will accept a pattern (of some kind) or an @file. That avoids > defining a new ACD type, but can still be used in GUIs and web > service/workflow wrappers to validate the pattern. Sure. Then parsing the file needs another function. ajParsePatternFile(patlist,filename,type); type would be ajint How about the rest? If good, any existing ajax file to use or new? -- Henrikki Almusa From gbottu at ben.vub.ac.be Thu Jun 24 08:49:38 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 24 Jun 2004 14:49:38 +0200 Subject: question about nullok in outfile Message-ID: <20040624124938.GA23332@bigben.ulb.ac.be> Dear colleagues, I noticed a change of behaviour for the case when you have an ACD object of type outfile with attribute "nullok: Y" and without "default", when the user puts nothing on the command line. With EMBOSS 2.6.0 no output file was created. I think this is the behaviour that one should expect, since the on-line ACD manual says "Can accept a null filename as 'no file'". Since EMBOSS 2.8.0 however an output file is always created. In the case that there are several outfile objects it can have a name like "xxx.out2". Is this change in behaviour intended or is it a bug introduced together with some other change ? Sincerely, Guy Bottu, BEN From henrikki.almusa at helsinki.fi Mon Jun 28 04:20:54 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 28 Jun 2004 11:20:54 +0300 Subject: Patten lists ajax header, dirst draft Message-ID: <200406281120.54203.henrikki.almusa@helsinki.fi> Hello Heres a first draft for ajpat.h. Now this is just for comment on command in there. I have done some work to .c as well, but thats not finished yet. But this is for comments. #ifdef __cplusplus extern "C" { #endif #ifndef ajpat_h #define ajpat_h typedef struct AjSPattern { AjPStr name; AjPStr origpat; AjPStr propat; AjPRegex regexpat; ajint mismatch; } AjOPattern; #define AjPPattern AjOPattern* struct AjSPatlist { AjPList patlist; AjIList iter; ajint type; } AjPOPatlist; // type can 1: regex, 2: prosite (protein) 3: prosite like (nucleotide) #define AjPPatlist AjOPatlist* // Pattern handling functions AjPPattern ajPatternNew (AjPStr name,AjPStr pat,int mismatch); ajPatternDel (AjPPattern thys); AjPStr ajPatternGetName (AjPPattern thys); ajint ajPatternGetType (AjPPattern thys); ajint ajPatternGetMismatch (AjPPattern thys); AjPStr ajPatternGetPro (AjPPattern thys); AjPStr ajPatternGetOrigPro (AjPPattern thys); AjPRegex ajPatternGetRegex (AjPPattern thys); AjPStr ajPatternGetPattern (AjPPattern thys); // Patlist handling functions AjPPatlist ajPatlistNew (void); ajPatlistDel (AjPPatlist thys); void ajParsePatternFile (AjPPatlist thys, AjPStr inf, ajint type); ajBool ajPatlistGetNext (AjPPatlist thys, AjPPAttern pattern); void ajPatlistRewind (AjPPatlist thys); ajint ajPatlistGetType (AjPPatlist thys); void ajPatlistAdd (AjPPatlist thys, AjPPattern pat); void ajPatlistSetType (AjPPatlist thys, ajint type); #endif #ifdef __cplusplus } #endif -- Henrikki Almusa From henrikki.almusa at helsinki.fi Mon Jun 28 07:46:31 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 28 Jun 2004 14:46:31 +0300 Subject: Patten lists ajax header, dirst draft In-Reply-To: <200406281120.54203.henrikki.almusa@helsinki.fi> References: <200406281120.54203.henrikki.almusa@helsinki.fi> Message-ID: <200406281446.31435.henrikki.almusa@helsinki.fi> On Monday 28 June 2004 11:20, Henrikki Almusa wrote: > typedef struct AjSPattern { > AjPStr name; > AjPStr origpat; > AjPStr propat; > AjPRegex regexpat; > ajint mismatch; > } AjOPattern; One question to those, that might know more about the workings of prosite pattern searching (fuzz*). There are functions (in nucleus/embpat.c): void embPatCompile(ajint type, AjPStr pattern, AjPStr opattern, ajint* plen, ajint** buf, EmbOPatBYPNode* off, ajuint** sotable, ajuint* solimit, ajint* m, AjPStr* regexp, ajint*** skipm, ajint mismatch); void embPatFuzzSearch(ajint type, ajint begin, AjPStr pattern, AjPStr opattern, AjPStr name, AjPStr text, AjPList *l, ajint plen, ajint mismatch, AjBool left, AjBool right, ajint *buf, EmbOPatBYPNode *off, ajuint *sotable, ajint solimit, AjPStr regexp, ajint **skipm, ajint *hits, ajint m, void **tidy); Now in fuzznuc they both use the same values for pretty much everything. So does this mean that all of those (f.ex. *off, *sotable, solimit) are something that should be saved? Because in that case, the above struct for pattern won't work. There should be additional stucture to compas everything that is needed from complile function to search. Regards, -- Henrikki Almusa From henrikki.almusa at helsinki.fi Tue Jun 29 06:43:12 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 29 Jun 2004 13:43:12 +0300 Subject: Patten lists ajax header, dirst draft In-Reply-To: <200406281120.54203.henrikki.almusa@helsinki.fi> References: <200406281120.54203.henrikki.almusa@helsinki.fi> Message-ID: <200406291343.12877.henrikki.almusa@helsinki.fi> Hello, Heres a revised version of the files 'ajpat.c' and 'ajpat.h' (attached). These are first draft on .c and some modification on .h due reasons that I found when writing .c. I would like comments on them (there are some amount of comments missing from functions). I'm pretty sure there are bugs to be found in there, since its just compiled (compiles with one warning) and not tested. And I do have few questions. 1. Prosite patterns. This is problematic and the pattern system in these files won't (probably) work with them. Should the prosite patterns get a new struct or what could be done with them? 2. How to do the overloading on for these, so that @filename would be accepted (in regs and fuzzes)? I don't exactly understand how to do so. Is there a similar example somewhere in the emboss that I could look at? I'm going to go on holiday next week, so I'll be unable to work with this after that for a while. Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.c Type: text/x-csrc Size: 7778 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040629/2cca8e04/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.h Type: text/x-chdr Size: 2097 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040629/2cca8e04/attachment-0001.bin From henrikki.almusa at helsinki.fi Wed Jun 30 09:32:40 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 30 Jun 2004 16:32:40 +0300 Subject: Patten lists ajax header, dirst draft In-Reply-To: <200406291343.12877.henrikki.almusa@helsinki.fi> References: <200406281120.54203.henrikki.almusa@helsinki.fi> <200406291343.12877.henrikki.almusa@helsinki.fi> Message-ID: <200406301632.40816.henrikki.almusa@helsinki.fi> Hello again, Heres second draft of the files. I have made the struct holding pattern now so, that it hold void* instead of regex or string. This allows it to be used for holding other types of patterns (if they come from somewhere). I've tested parsing function and that seems to be working now. I'm thinking that the type information perhaps should be in pattern struct itself, since its really needed in ajPatternGetCompiledPattern and ajPatternDel. Also some kind of checking might be needed on file parsing. I seem to have problems in reading the information of the pattern struct though. I have tried to use this in dreg with AjPStr file; file=ajStrNewC("pattern.file"); plist=ajPatlistNew(); ajParsePatternFile(plist,file,1); while (ajPatlistGetNext(plist,&pat)) { ajFmtPrint ("name: %S\n",ajPatternGetName(name)); ajFmtPrint ("pattern: %S\n",ajPatternGetPattern(pat)); } But this segfaults on ajFmtPrint for some reason. #0 0x400ee6ff in cvt_uS () from /work/hena/emboss-2.8.0/lib/libajax.so.0 #1 0x400ef39e in ajFmtVfmt () from /work/hena/emboss-2.8.0/lib/libajax.so.0 #2 0x400eec7c in ajFmtPrint () from /work/hena/emboss-2.8.0/lib/libajax.so.0 #3 0x080487b1 in main () #4 0x40452a67 in __libc_start_main () from /lib/i686/libc.so.6 My two other question remain still. So any comments etc. -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.c Type: text/x-csrc Size: 7123 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040630/a95bece1/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.h Type: text/x-chdr Size: 2007 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20040630/a95bece1/attachment-0001.bin From support_dept at researchingpeople.biz Tue Jun 1 00:56:13 2004 From: support_dept at researchingpeople.biz (support_dept at researchingpeople.biz) Date: Mon, 31 May 2004 16:56:13 -0800 Subject: Someone is researching: emboss-dev@embnet.org Message-ID: ****NOT COMMERCIAL EMAIL**** Someone is researching your background via our website. 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A Daily Automatic New Connection Search is like a manual search except that it occurs automatically every day. After the search completes our system sends you an automatic email to confirm that the search has been performed. If any search results are found a link will be included in the email for your convenience. You can change the searches you want our system to perform through our automatic searching page. These searches occur daily and only search through connections that have been submitted since the last automatic search. Sincerely, Awareness Department From Harold at tlcfan.com Thu Jun 3 03:08:30 2004 From: Harold at tlcfan.com (Marissa Laird) Date: Thu, 03 Jun 2004 08:08:30 +0500 Subject: Cheapp Soft-offfers - very big disccounts! robe Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hoop.gif Type: image/gif Size: 10715 bytes Desc: not available URL: From americanbiotechnology at earthlink.net Fri Jun 4 23:25:02 2004 From: americanbiotechnology at earthlink.net (americanbiotechnology at earthlink.net) Date: 04 Jun 2004 16:25:02 -0700 Subject: American Biotechnology News Message-ID: <20040604162449.6D377C379F52743B@earthlink.net> An HTML attachment was scrubbed... URL: From syec.support.dept at learning-web.biz Tue Jun 8 01:05:00 2004 From: syec.support.dept at learning-web.biz (SYEC Support Dept.) Date: Mon, 7 Jun 2004 18:05:00 -0700 Subject: Someone is searching for opinions about: emboss-dev@embnet.org Message-ID: <200406080105.i58150qa028354@homer.learning-web.biz> Advisory - A user is trying to share experiences and opinions about you in our online community. To view all of the postings about you at our website use this link: http://4.shyx.us/lx.php?a=search&b=5&c=emboss-dev at embnet.org IMPORTANT - If you prefer not to be notified by our website in the future when postings are mode about you, just add your email address to our Do Not Email List. Our website will never send email to an address that appears on our Do Not Email List. To add to Do Not Email List click here: http://2.shyx.biz/lx.php?a=donotemail&b=emboss-dev at embnet.org Best Regards, Support Department From henrikki.almusa at helsinki.fi Mon Jun 14 09:20:41 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 14 Jun 2004 12:20:41 +0300 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg Message-ID: <200406141220.41863.henrikki.almusa@helsinki.fi> Hello, There might be a need for doing sequences with a list of patterns. Now at the moment there is only tfscan and patmatmotifs that uses list of patterns to search in seqeunces. The problem is that tfscan uses only fixed sequences and patmatmotifs uses a directory of files. I propose to modify reg and fuzz pattern searches to read a "fasta format of pattern" file. Example file using dreg might be >pat1 [ac]{2}gg >pat2 [gc]{3}att Pattern could span multiple lines. I would be willing to try out some changes in fuzz group as start. Should the code that reads the pattern file reading be coded somewhere else (eg not in fuzznuc.c)? Any feedback or suggestions etc would be welcome -- Henrikki Almusa From gwilliam at hgmp.mrc.ac.uk Mon Jun 14 09:26:09 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Mon, 14 Jun 2004 10:26:09 +0100 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg References: <200406141220.41863.henrikki.almusa@helsinki.fi> Message-ID: <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> Should the file of patterns allow each pattern to have its own allowed number of mismatches? >pat1 ggataata[ac]{2}gg >pat2 gcggcatgtagc[gc]{3}att Gary Henrikki Almusa wrote: > > Hello, > > There might be a need for doing sequences with a list of patterns. Now at the > moment there is only tfscan and patmatmotifs that uses list of patterns to > search in seqeunces. The problem is that tfscan uses only fixed sequences and > patmatmotifs uses a directory of files. > > I propose to modify reg and fuzz pattern searches to read a "fasta format of > pattern" file. Example file using dreg might be > > >pat1 > [ac]{2}gg > >pat2 > [gc]{3}att > > Pattern could span multiple lines. > > I would be willing to try out some changes in fuzz group as start. Should the > code that reads the pattern file reading be coded somewhere else (eg not in > fuzznuc.c)? > > Any feedback or suggestions etc would be welcome > -- > Henrikki Almusa -- 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 gwilliam at hgmp.mrc.ac.uk Wed Jun 16 10:25:18 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 16 Jun 2004 11:25:18 +0100 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg References: <200406141220.41863.henrikki.almusa@helsinki.fi> <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> <200406161305.17606.henrikki.almusa@helsinki.fi> Message-ID: <40D0200E.A52A3D58@hgmp.mrc.ac.uk> Henrikki, Would it be a good idea to overload the pattern qualifier of fuzz(nuc|pro|tran) and [pd]reg so that they understand '@filename' to be a pattern list filename, in the same way as restrict will either read a comma-delimited list of enzyme names or a '@filename' of a list of enzymes? So: fuzznuc could then be run as normal: fuzznuc em:hsfau -patt 'acgacga[gc]' -out test.out or with a pattern list: fuzznuc em:hsfau -patt '@patfile' -out test.out Gary Henrikki Almusa wrote: > > On Monday 14 June 2004 12:26, Gary Williams, Tel 01223 494522 wrote: > > Should the file of patterns allow each pattern to have its own allowed > > number of mismatches? > > > > >pat1 > > > > ggataata[ac]{2}gg > > > > >pat2 > > > > gcggcatgtagc[gc]{3}att > > No reason why not. > > Now the coding itself. Since reading that file is pretty low level stuff, it > should probably be in "ajax/" dir? My obj c abilities are not perhaps that > good. Anyone willing to help on the .c side? > > What might be needed in .h (names can be changed). This mainly is for using > the pattern in program. This is now currently just what I could come up with, > so I can go completely off here :). > > struct AjSPattern { > AjPStr name; > AjPStr opropat; > AjPStr propat; > AjPRegex regexpat; > ajint mismatch; > } AjOPattern; > #define AjPPattern AjOPattern* > > struct AjSPatlist { > AjPList patlist; > ajint type; # 0 regex, 1 prosite > } AjPOPatlist; > #define AjPPatlist AjOPatlist* > > AjBool ajPatlistGetNext (patlist, &pattern); > void ajPatlistRewind (patlist); > ajint ajPatlistGetType (patlist); > > AjPStr ajPatternGetName (pattern); > ajint ajPatternGetType (pattern); > whether propat is not NULL in struct should work > ajint ajPatternGetMismatch (pattern); > AjPStr ajPatternGetPro (pattern); > AjPStr ajPatternGetOrigPro (pattern); > AjPRegex ajPatternGetRegex (pattern); > AjPStr ajPatternGetPattern (pattern); > should return string representation of pattern it has > > Acd would need propably new file type, patlist. It should be defined in the > programs acd file, whether the pattern is regex or prosite. This would allow > the reading (and compiling the patterns) in acd command. > > acdGetPatlist(); > > Comments? > -- > Henrikki Almusa -- 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 Wed Jun 16 10:30:27 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 16 Jun 2004 13:30:27 +0300 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg In-Reply-To: <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> References: <200406141220.41863.henrikki.almusa@helsinki.fi> <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> Message-ID: <200406161330.27542.henrikki.almusa@helsinki.fi> On Monday 14 June 2004 12:26, Gary Williams, Tel 01223 494522 wrote: > Should the file of patterns allow each pattern to have its own allowed > number of mismatches? > > >pat1 > > ggataata[ac]{2}gg > > >pat2 > > gcggcatgtagc[gc]{3}att No reason why not. Now the coding itself. Since reading that file is pretty low level stuff, it should probably be in "ajax/" dir? My obj c abilities are not perhaps that good. Anyone willing to help on the .c side? What might be needed in .h (names can be changed). This mainly is for using the pattern in program. This is now currently just what I could come up with, so I can go completely off here :). struct AjSPattern { AjPStr name; AjPStr opropat; AjPStr propat; AjPRegex regexpat; ajint mismatch; } AjOPattern; #define AjPPattern AjOPattern* struct AjSPatlist { AjPList patlist; ajint type; # 0 regex, 1 prosite } AjPOPatlist; #define AjPPatlist AjOPatlist* AjBool ajPatlistGetNext (patlist, &pattern); void ajPatlistRewind (patlist); ajint ajPatlistGetType (patlist); AjPStr ajPatternGetName (pattern); ajint ajPatternGetType (pattern); whether propat is not NULL in struct should work ajint ajPatternGetMismatch (pattern); AjPStr ajPatternGetPro (pattern); AjPStr ajPatternGetOrigPro (pattern); AjPRegex ajPatternGetRegex (pattern); AjPStr ajPatternGetPattern (pattern); should return string representation of pattern it has Acd would need propably new file type, patlist. It should be defined in the programs acd file, whether the pattern is regex or prosite. This would allow the reading (and compiling the patterns) in acd command. acdGetPatlist(); Comments? -- Henrikki Almusa From pmr at ebi.ac.uk Wed Jun 16 10:38:19 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 16 Jun 2004 11:38:19 +0100 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg In-Reply-To: <200406161330.27542.henrikki.almusa@helsinki.fi> References: <200406141220.41863.henrikki.almusa@helsinki.fi> <40CD6F31.D42BE6FB@hgmp.mrc.ac.uk> <200406161330.27542.henrikki.almusa@helsinki.fi> Message-ID: <40D0231B.4020106@ebi.ac.uk> Henrikki Almusa wrote: > Acd would need propably new file type, patlist. It should be defined in the > programs acd file, whether the pattern is regex or prosite. This would allow > the reading (and compiling the patterns) in acd command. ... or we can define a knowntype attribute for the string that says the program will accept a pattern (of some kind) or an @file. That avoids defining a new ACD type, but can still be used in GUIs and web service/workflow wrappers to validate the pattern. regards, Peter Rice From henrikki.almusa at helsinki.fi Mon Jun 21 10:54:36 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 21 Jun 2004 13:54:36 +0300 Subject: Pattern lists and fuzz(nuc|pro|tran) and [pd]reg In-Reply-To: <40D0231B.4020106@ebi.ac.uk> References: <200406141220.41863.henrikki.almusa@helsinki.fi> <200406161330.27542.henrikki.almusa@helsinki.fi> <40D0231B.4020106@ebi.ac.uk> Message-ID: <200406211354.36787.henrikki.almusa@helsinki.fi> On Wednesday 16 June 2004 13:38, Peter Rice wrote: > Henrikki Almusa wrote: > > Acd would need propably new file type, patlist. It should be defined in > > the programs acd file, whether the pattern is regex or prosite. This > > would allow the reading (and compiling the patterns) in acd command. > > ... or we can define a knowntype attribute for the string that says the > program will accept a pattern (of some kind) or an @file. That avoids > defining a new ACD type, but can still be used in GUIs and web > service/workflow wrappers to validate the pattern. Sure. Then parsing the file needs another function. ajParsePatternFile(patlist,filename,type); type would be ajint How about the rest? If good, any existing ajax file to use or new? -- Henrikki Almusa From gbottu at ben.vub.ac.be Thu Jun 24 12:49:38 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 24 Jun 2004 14:49:38 +0200 Subject: question about nullok in outfile Message-ID: <20040624124938.GA23332@bigben.ulb.ac.be> Dear colleagues, I noticed a change of behaviour for the case when you have an ACD object of type outfile with attribute "nullok: Y" and without "default", when the user puts nothing on the command line. With EMBOSS 2.6.0 no output file was created. I think this is the behaviour that one should expect, since the on-line ACD manual says "Can accept a null filename as 'no file'". Since EMBOSS 2.8.0 however an output file is always created. In the case that there are several outfile objects it can have a name like "xxx.out2". Is this change in behaviour intended or is it a bug introduced together with some other change ? Sincerely, Guy Bottu, BEN From henrikki.almusa at helsinki.fi Mon Jun 28 08:20:54 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 28 Jun 2004 11:20:54 +0300 Subject: Patten lists ajax header, dirst draft Message-ID: <200406281120.54203.henrikki.almusa@helsinki.fi> Hello Heres a first draft for ajpat.h. Now this is just for comment on command in there. I have done some work to .c as well, but thats not finished yet. But this is for comments. #ifdef __cplusplus extern "C" { #endif #ifndef ajpat_h #define ajpat_h typedef struct AjSPattern { AjPStr name; AjPStr origpat; AjPStr propat; AjPRegex regexpat; ajint mismatch; } AjOPattern; #define AjPPattern AjOPattern* struct AjSPatlist { AjPList patlist; AjIList iter; ajint type; } AjPOPatlist; // type can 1: regex, 2: prosite (protein) 3: prosite like (nucleotide) #define AjPPatlist AjOPatlist* // Pattern handling functions AjPPattern ajPatternNew (AjPStr name,AjPStr pat,int mismatch); ajPatternDel (AjPPattern thys); AjPStr ajPatternGetName (AjPPattern thys); ajint ajPatternGetType (AjPPattern thys); ajint ajPatternGetMismatch (AjPPattern thys); AjPStr ajPatternGetPro (AjPPattern thys); AjPStr ajPatternGetOrigPro (AjPPattern thys); AjPRegex ajPatternGetRegex (AjPPattern thys); AjPStr ajPatternGetPattern (AjPPattern thys); // Patlist handling functions AjPPatlist ajPatlistNew (void); ajPatlistDel (AjPPatlist thys); void ajParsePatternFile (AjPPatlist thys, AjPStr inf, ajint type); ajBool ajPatlistGetNext (AjPPatlist thys, AjPPAttern pattern); void ajPatlistRewind (AjPPatlist thys); ajint ajPatlistGetType (AjPPatlist thys); void ajPatlistAdd (AjPPatlist thys, AjPPattern pat); void ajPatlistSetType (AjPPatlist thys, ajint type); #endif #ifdef __cplusplus } #endif -- Henrikki Almusa From henrikki.almusa at helsinki.fi Mon Jun 28 11:46:31 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Mon, 28 Jun 2004 14:46:31 +0300 Subject: Patten lists ajax header, dirst draft In-Reply-To: <200406281120.54203.henrikki.almusa@helsinki.fi> References: <200406281120.54203.henrikki.almusa@helsinki.fi> Message-ID: <200406281446.31435.henrikki.almusa@helsinki.fi> On Monday 28 June 2004 11:20, Henrikki Almusa wrote: > typedef struct AjSPattern { > AjPStr name; > AjPStr origpat; > AjPStr propat; > AjPRegex regexpat; > ajint mismatch; > } AjOPattern; One question to those, that might know more about the workings of prosite pattern searching (fuzz*). There are functions (in nucleus/embpat.c): void embPatCompile(ajint type, AjPStr pattern, AjPStr opattern, ajint* plen, ajint** buf, EmbOPatBYPNode* off, ajuint** sotable, ajuint* solimit, ajint* m, AjPStr* regexp, ajint*** skipm, ajint mismatch); void embPatFuzzSearch(ajint type, ajint begin, AjPStr pattern, AjPStr opattern, AjPStr name, AjPStr text, AjPList *l, ajint plen, ajint mismatch, AjBool left, AjBool right, ajint *buf, EmbOPatBYPNode *off, ajuint *sotable, ajint solimit, AjPStr regexp, ajint **skipm, ajint *hits, ajint m, void **tidy); Now in fuzznuc they both use the same values for pretty much everything. So does this mean that all of those (f.ex. *off, *sotable, solimit) are something that should be saved? Because in that case, the above struct for pattern won't work. There should be additional stucture to compas everything that is needed from complile function to search. Regards, -- Henrikki Almusa From henrikki.almusa at helsinki.fi Tue Jun 29 10:43:12 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 29 Jun 2004 13:43:12 +0300 Subject: Patten lists ajax header, dirst draft In-Reply-To: <200406281120.54203.henrikki.almusa@helsinki.fi> References: <200406281120.54203.henrikki.almusa@helsinki.fi> Message-ID: <200406291343.12877.henrikki.almusa@helsinki.fi> Hello, Heres a revised version of the files 'ajpat.c' and 'ajpat.h' (attached). These are first draft on .c and some modification on .h due reasons that I found when writing .c. I would like comments on them (there are some amount of comments missing from functions). I'm pretty sure there are bugs to be found in there, since its just compiled (compiles with one warning) and not tested. And I do have few questions. 1. Prosite patterns. This is problematic and the pattern system in these files won't (probably) work with them. Should the prosite patterns get a new struct or what could be done with them? 2. How to do the overloading on for these, so that @filename would be accepted (in regs and fuzzes)? I don't exactly understand how to do so. Is there a similar example somewhere in the emboss that I could look at? I'm going to go on holiday next week, so I'll be unable to work with this after that for a while. Thanks, -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.c Type: text/x-csrc Size: 7778 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ajpat.h Type: text/x-chdr Size: 2097 bytes Desc: not available URL: From henrikki.almusa at helsinki.fi Wed Jun 30 13:32:40 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 30 Jun 2004 16:32:40 +0300 Subject: Patten lists ajax header, dirst draft In-Reply-To: <200406291343.12877.henrikki.almusa@helsinki.fi> References: <200406281120.54203.henrikki.almusa@helsinki.fi> <200406291343.12877.henrikki.almusa@helsinki.fi> Message-ID: <200406301632.40816.henrikki.almusa@helsinki.fi> Hello again, Heres second draft of the files. I have made the struct holding pattern now so, that it hold void* instead of regex or string. This allows it to be used for holding other types of patterns (if they come from somewhere). I've tested parsing function and that seems to be working now. I'm thinking that the type information perhaps should be in pattern struct itself, since its really needed in ajPatternGetCompiledPattern and ajPatternDel. Also some kind of checking might be needed on file parsing. I seem to have problems in reading the information of the pattern struct though. I have tried to use this in dreg with AjPStr file; file=ajStrNewC("pattern.file"); plist=ajPatlistNew(); ajParsePatternFile(plist,file,1); while (ajPatlistGetNext(plist,&pat)) { ajFmtPrint ("name: %S\n",ajPatternGetName(name)); ajFmtPrint ("pattern: %S\n",ajPatternGetPattern(pat)); } But this segfaults on ajFmtPrint for some reason. #0 0x400ee6ff in cvt_uS () from /work/hena/emboss-2.8.0/lib/libajax.so.0 #1 0x400ef39e in ajFmtVfmt () from /work/hena/emboss-2.8.0/lib/libajax.so.0 #2 0x400eec7c in ajFmtPrint () from /work/hena/emboss-2.8.0/lib/libajax.so.0 #3 0x080487b1 in main () #4 0x40452a67 in __libc_start_main () from /lib/i686/libc.so.6 My two other question remain still. So any comments etc. -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... 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