From service at birthdayalarm.com Wed Oct 11 00:21:20 2006 From: service at birthdayalarm.com (NandaKumar Sreedharan) Date: Wed, 11 Oct 2006 04:21:20 +0000 Subject: [Biojava-l] Calendar Message-ID: <200610110451.k9B4pNga015117@portal.open-bio.org> Hi, I am creating a birthday calendar of all my friends and family. Can you please click on the link below to enter your birthday for me. http://www.birthdayalarm.com/bd2/74713512a732679238b1279483798c781990119d1719 Thanks, NandaKumar From rajeee_sss at yahoo.com Wed Oct 11 03:41:21 2006 From: rajeee_sss at yahoo.com (Rajeswari) Date: Wed, 11 Oct 2006 00:41:21 -0700 (PDT) Subject: [Biojava-l] how can i read a genbank Message-ID: <20061011074121.38573.qmail@web30012.mail.mud.yahoo.com> Dear developers., I got the biojava program to read a genbank file from biojava.org. it is as follows: import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; import java.io.*; import org.biojava.bio.*; import java.util.*; public class genbank1 { public static void main(String[] args) { BufferedReader br = null; try { FileReader f=new FileReader(mygen.java); br = new BufferedReader(f); } catch (FileNotFoundException ex) { ex.printStackTrace(); System.exit(-1); } SequenceIterator sequences = SeqIOTools.readGenbank(br); while(sequences.hasNext()) { try { Sequence seq = sequences.nextSequence(); } catch(BioException ex) { ex.printStackTrace(); } catch(NoSuchElementException ex) { ex.printStackTrace(); } } } } And i saved it as genbank1.java it was compiled with javac genbank1.java and when i try to execute it shows no classfoundException. i run the pro as follows: c:\jdk1.4\bin\java genbank1 mygen.java mygen.java consists of the genbank file. i think the error may be deu to the genbank file. can anybody tell me how to do this pro correct? and provide me the exact format of a genbank file with extension. regards s.rajee --------------------------------- Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail. From markjschreiber at gmail.com Wed Oct 11 09:33:28 2006 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 11 Oct 2006 21:33:28 +0800 Subject: [Biojava-l] how can i read a genbank In-Reply-To: <20061011074121.38573.qmail@web30012.mail.mud.yahoo.com> References: <20061011074121.38573.qmail@web30012.mail.mud.yahoo.com> Message-ID: <93b45ca50610110633q3b7d93bw7233cfa4cdbbd9d3@mail.gmail.com> This sounds like a problem with your classpath. For advice on setting your classpath take a look at http://biojava.org/wiki/BioJava:GetStarted - Mark On 10/11/06, Rajeswari wrote: > Dear developers., > > I got the biojava program to read a genbank file from biojava.org. > > it is as follows: > > import org.biojava.bio.seq.*; > import org.biojava.bio.seq.io.*; > import java.io.*; > import org.biojava.bio.*; > import java.util.*; > > public class genbank1 > { > public static void main(String[] args) > { > BufferedReader br = null; > > try > { > FileReader f=new FileReader(mygen.java); > br = new BufferedReader(f); > > } > catch (FileNotFoundException ex) > { > ex.printStackTrace(); > System.exit(-1); > } > > > SequenceIterator sequences = SeqIOTools.readGenbank(br); > > while(sequences.hasNext()) > { > try > { > > Sequence seq = sequences.nextSequence(); > > > } > catch(BioException ex) > { > ex.printStackTrace(); > } > catch(NoSuchElementException ex) > { > ex.printStackTrace(); > } > } > } > } > > > And i saved it as genbank1.java > > it was compiled with javac genbank1.java > > > and when i try to execute it shows no classfoundException. > > > i run the pro as follows: > > c:\jdk1.4\bin\java genbank1 mygen.java > > mygen.java consists of the genbank file. > > > > i think the error may be deu to the genbank file. > > > can anybody tell me how to do this pro correct? and provide me the exact format of a genbank file with extension. > > > > regards > s.rajee > > > --------------------------------- > Do you Yahoo!? > Everyone is raving about the all-new Yahoo! Mail. > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From emd at sanger.ac.uk Thu Oct 12 05:44:31 2006 From: emd at sanger.ac.uk (Ed Dicks) Date: Thu, 12 Oct 2006 10:44:31 +0100 (BST) Subject: [Biojava-l] advice on ABIFParser Message-ID: Hi, Can anyone give me some advice on using; org.biojava.bio.program.abi.ABIFParser I'm working with an ab1 sequence trace file and trying to pull out the value of a data item defined with a tag - index pair. my sample code is; (trying to pull out the mobility file name) ABIFParser abiParse=new ABIFParser("temp.ab1"); ABIFParser.DataAccess a1=abiParse.getDataAccess(); ABIFParser.TaggedDataRecord r1=abiParse.getDataRecord("PDMF",1); System.err.println("r1 ok "+r1.toString()); The output looks like... r1 ok org.biojava.bio.program.abi.ABIFParser$TaggedDataRecord at 80474d4[ tagName = PDMF tagNumber = 1 dataType = PSTRING elementLength = 1 numberOfElements= 21 recordLength = 21 dataRecord = 0x0001265A crypticVariable = 0 ] now I've done "strings temp.ab1" to verify the tag "PDMF" is present. What's going on here is that ABIFParser reads the data item into a long variable (field dataRecord) but the PSTRING is length 21 which is too big for a long. I have succesfully pulled out strings that are length <= 8 but this one just seems too big, can anyone give me some advice on this. Thanks Ed --------------------------------------------------------- Dr Ed Dicks Cancer Genome Project (Team 78) The Wellcome Trust Sanger Institute Hinxton, Cambs. CB10 1SA Tel: +44 1223 494967 --------------------------------------------------------- From russ at kepler-eng.com Thu Oct 12 09:38:41 2006 From: russ at kepler-eng.com (Russ Kepler) Date: Thu, 12 Oct 2006 07:38:41 -0600 Subject: [Biojava-l] advice on ABIFParser In-Reply-To: References: Message-ID: <200610120738.41125.russ@kepler-eng.com> On Thursday 12 October 2006 03:44 am, Ed Dicks wrote: > now I've done "strings temp.ab1" to verify the tag "PDMF" is present. > What's going on here is that ABIFParser reads the data item into a long > variable (field dataRecord) but the PSTRING is length 21 which is too big > for a long. I have succesfully pulled out strings that are length <= 8 but > this one just seems too big, can anyone give me some advice on this. The TaggedDataRecord is really a pointer when the data size is > 4 bytes, what you'll have to do is to loop like this: ABIFParser abiParse=new ABIFParser("temp.ab1"); ABIFParser.DataAccess a1=abiParse.getDataAccess(); ABIFParser.TaggedDataRecord r1=abiParse.getDataRecord("PDMF",1); System.err.println("r1 ok "+r1.toString()); a1.seek(r1.dataRecord); int count = (int) r1.numberOfElements; StringBuffer sb = new StringBuffer(count); for (int i = 0; i < count; ) { sb.append(a1.readChar()); } System.out.println("Dye mobility: "+sb.toString()); Really your basic seek & read loop. Look in ABIFChromatogram.parseBaseCalls() for a fuller example, but this will get you started. From andreas.draeger at uni-tuebingen.de Fri Oct 13 03:56:39 2006 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Fri, 13 Oct 2006 09:56:39 +0200 Subject: [Biojava-l] Java(TM) Message-ID: <452F46B7.2020207@uni-tuebingen.de> Hi all, Yesterday our institution, the University of T?bingen, Germany, received an email from SUN. The email started by saying that SUN is pleased to see projects written in their programing language "Java" that we provide at our institution. However, they wanted us to rename our Evoulutionary Algorithms package "JavaEvA" to something like "JEvA" and our Neural Network project "JavaNNS" should also be renamed to something else like "JNNS". The reason for this is that SUN owns a trademark on the name "Java" and no other institution or company is supposed to use this name for its own purposes or software packages, even if this is a non profit and/or open source project as JavaEvA and JavaNNS. We might later even get a dissuasion letter if we do not follow the instructions in the email. I do not exactly know how SUN and the BioJava project are connected. However, in the worst case someday we could also receive a writing like that. To summarize: we should be aware that possibly the name "BioJava" has to be changed to something else like "JBio" or "BioJ" or what ever SUN might suggest as soon as they recognize our project. If there is already an agreement with SUN about that, I am not well informed and curious to know about it. Otherwise you are now informed about what happened to us in T?bingen. Sincerely, Andreas Dr?ger -- Dipl.Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From mark.schreiber at novartis.com Fri Oct 13 05:05:55 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 13 Oct 2006 17:05:55 +0800 Subject: [Biojava-l] Java(TM) Message-ID: Hi - This issue has been mentioned before however we have never been instructed by Sun to modify the name. This doesn't mean it cannot happen, however several people in Sun know about the project (Joshua Bloch apparently even mentioned it in a talk) and it has been featured in news stories on their own websites. Sun even provided open-bio with some servers and I think have shipped biojava on some machines that are 'prepackaged' with bio applications. All of this doesn't prevent them from asking us to change the name and they are infact legally within their rights to request it. While it may not be possible to own the word Java due to the large Island already having the same name it is possible to register it for trade in computation related activities. Given that open-bio is not likely to want to get into litigation with Sun then I suspect we would need to change the name. The most problematic part would be modifying package names. Perhaps we (meaning open-bio collectively and the biojava core people) could attempt to pre-empt this a little by talking with Sun directly to see what our options are. Any thoughts? - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com www.dengueinfo.org phone +65 6722 2973 fax +65 6722 2910 Andreas Dr?ger Sent by: biojava-l-bounces at lists.open-bio.org 10/13/2006 03:56 PM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Java(TM) Hi all, Yesterday our institution, the University of T?bingen, Germany, received an email from SUN. The email started by saying that SUN is pleased to see projects written in their programing language "Java" that we provide at our institution. However, they wanted us to rename our Evoulutionary Algorithms package "JavaEvA" to something like "JEvA" and our Neural Network project "JavaNNS" should also be renamed to something else like "JNNS". The reason for this is that SUN owns a trademark on the name "Java" and no other institution or company is supposed to use this name for its own purposes or software packages, even if this is a non profit and/or open source project as JavaEvA and JavaNNS. We might later even get a dissuasion letter if we do not follow the instructions in the email. I do not exactly know how SUN and the BioJava project are connected. However, in the worst case someday we could also receive a writing like that. To summarize: we should be aware that possibly the name "BioJava" has to be changed to something else like "JBio" or "BioJ" or what ever SUN might suggest as soon as they recognize our project. If there is already an agreement with SUN about that, I am not well informed and curious to know about it. Otherwise you are now informed about what happened to us in T?bingen. Sincerely, Andreas Dr?ger -- Dipl.Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From hlapp at gmx.net Wed Oct 18 16:29:20 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 18 Oct 2006 16:29:20 -0400 Subject: [Biojava-l] NESCent Phyloinformatics Hackathon Message-ID: (this has been silently discarded by the mailing list, apologies if you have received this before) The National Evolutionary Synthesis Center (NESCent) in collaboration with Arlin Stoltzfus (U. Maryland, NIST), Aaron Mackey (GSK), Rutger Vos (UBC), and Mark Holder (FSU) sponsors a Phyloinformatics Hackathon to take place Dec 11-15 in Durham, NC. The (wiki) website with more information and a formal proposal is at https://www.nescent.org/wg_phyloinformatics/ In short, the goal is to leverage the Bio* toolkits to provide the "glue" for evolutionary analyses of various types that depend on automation, interoperability, and data integration. CALL FOR INPUT: The specific objectives are driven by "use cases", that is, specific target problems of interest to evolutionary biologists (click 'Use Cases' at the above website). We invite community input in order to focus efforts on the most urgent or pervasive problems. The wiki for the hackathon allows direct editing of the use cases after registration. You may also upload data files, or add comments to the "Forum" page. Alternatively, send email to hlapp at nescent.org. You may also contact any of the organizers with questions or comments. ATTENDANCE: The hackathon is scheduled for Dec 11-15, 2006 in Durham NC. Space is limited, and attendance is by invitation. If you have not been contacted but desire to attend, please contact Hilmar Lapp (hlapp at nescent.org). ORGANIZERS: Hilmar Lapp (NESCent; hlapp at nescent.org) Aaron Mackey (GSK; aaron.j.mackey at gsk.com) Mark Holder (FSU; mholder at scs.fsu.edu) Arlin Stoltzfus (CARB, NIST; arlin.stoltzfus at nist.gov) Todd Vision (NESCent; tjv at bio.unc.edu) Rutger Vos (UBC; rvosa at sfu.ca) From CARMELK at il.ibm.com Thu Oct 19 08:44:43 2006 From: CARMELK at il.ibm.com (Carmel Kent) Date: Thu, 19 Oct 2006 14:44:43 +0200 Subject: [Biojava-l] can BioJava do alignment ? Message-ID: Hello, I'm interested in a Java package for sequence alignment. I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can only create objects that are representations of alignments generated by third-party software. I had an impression that BioJava 1.5 can do alignment itself (e.g., I saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class named org.biojava.bio.alignment.NeedlemanWunch) I have two questions: is this true ? I mean, does BioJava 1.5 contain the alignment algorithm, itself ? if it does, I downloaded the CVS view of BioJava 1.5, but could not find any javadocs or the alignment package source. Where can I find it ? Thanks very much, Carmel Kent Research Staff Member Healthcare I/T Research IBM Research Laboratory in Haifa Tel. +972-4-8281059 Email: carmelk at il.ibm.com From rmedrado at gmail.com Thu Oct 19 13:45:24 2006 From: rmedrado at gmail.com (Ramon Medrado) Date: Thu, 19 Oct 2006 14:45:24 -0300 Subject: [Biojava-l] can BioJava do alignment ? In-Reply-To: References: Message-ID: <37ba4b050610191045q30a6282bjce052e31e1463cea@mail.gmail.com> Hi, The information is true. Biojava 1.5 has the main algorithms of alignment as NeedlemanWunch, SmithWaterman and other implementations that are encapsulated on package org.biojava.bio.alignment All source is disponible in this link : http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz and the jar file is disponible in: http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar and the javadoc: http://www.biojava.org/download/bj15b/doc/doc.tar.gz I wait to have helped -- Ramon Undergraduate Student of Computer Science Universidade Estadual de Santa Cruz - Brasil 2006/10/19, Carmel Kent : > > > Hello, > > I'm interested in a Java package for sequence alignment. > I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can > only create objects that are representations of alignments generated by > third-party software. > > I had an impression that BioJava 1.5 can do alignment itself (e.g., I > saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class > named org.biojava.bio.alignment.NeedlemanWunch) > > I have two questions: > > is this true ? I mean, does BioJava 1.5 contain the alignment > algorithm, > itself ? if it does, I downloaded the CVS view of BioJava 1.5, but could not find > any javadocs or the alignment package source. Where can I find it ? > > > Thanks very much, > > > Carmel Kent > Research Staff Member > Healthcare I/T Research > IBM Research Laboratory in Haifa > Tel. +972-4-8281059 > Email: carmelk at il.ibm.com > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From mark.schreiber at novartis.com Thu Oct 19 21:57:09 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 20 Oct 2006 09:57:09 +0800 Subject: [Biojava-l] can BioJava do alignment ? Message-ID: Hi - You can also perform an alignment using HMMs in biojava 1.3 and 1.4. See the example at (http://biojava.org/wiki/BioJava:CookBook:DP:PairWise). This is actually the most flexible way to do it. - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com www.dengueinfo.org phone +65 6722 2973 fax +65 6722 2910 "Ramon Medrado" Sent by: biojava-l-bounces at lists.open-bio.org 10/20/2006 01:45 AM To: biojava cc: (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] can BioJava do alignment ? Hi, The information is true. Biojava 1.5 has the main algorithms of alignment as NeedlemanWunch, SmithWaterman and other implementations that are encapsulated on package org.biojava.bio.alignment All source is disponible in this link : http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz and the jar file is disponible in: http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar and the javadoc: http://www.biojava.org/download/bj15b/doc/doc.tar.gz I wait to have helped -- Ramon Undergraduate Student of Computer Science Universidade Estadual de Santa Cruz - Brasil 2006/10/19, Carmel Kent : > > > Hello, > > I'm interested in a Java package for sequence alignment. > I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can > only create objects that are representations of alignments generated by > third-party software. > > I had an impression that BioJava 1.5 can do alignment itself (e.g., I > saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class > named org.biojava.bio.alignment.NeedlemanWunch) > > I have two questions: > > is this true ? I mean, does BioJava 1.5 contain the alignment > algorithm, > itself ? if it does, I downloaded the CVS view of BioJava 1.5, but could not find > any javadocs or the alignment package source. Where can I find it ? > > > Thanks very much, > > > Carmel Kent > Research Staff Member > Healthcare I/T Research > IBM Research Laboratory in Haifa > Tel. +972-4-8281059 > Email: carmelk at il.ibm.com > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From n.haigh at sheffield.ac.uk Wed Oct 25 09:54:26 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Wed, 25 Oct 2006 13:54:26 +0000 Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests Message-ID: <453F6C92.6020207@sheffield.ac.uk> I have recently installed some more software for which there are bioperl-run tests and run the test suite with several versions of the software I could find. I've added info to http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any fails in any of the versions I tested I've noted them together with versions that were ok (if any). There maybe another 6 or so programs I'm trying to get hold of to run further tests - I'll update when I get them. Nath From n.haigh at sheffield.ac.uk Thu Oct 26 04:46:13 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Thu, 26 Oct 2006 09:46:13 +0100 Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests In-Reply-To: <453F6C92.6020207@sheffield.ac.uk> References: <453F6C92.6020207@sheffield.ac.uk> Message-ID: <454075D5.2030005@sheffield.ac.uk> Nathan S. Haigh wrote: > I have recently installed some more software for which there are > bioperl-run tests and run the test suite with several versions of the > software I could find. I've added info to > http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any > fails in any of the versions I tested I've noted them together with > versions that were ok (if any). > > There maybe another 6 or so programs I'm trying to get hold of to run > further tests - I'll update when I get them. > Nath > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > My aplogies, this should have gone to the Bioperl mailing list! :o) From henrich at embl.de Mon Oct 23 05:57:14 2006 From: henrich at embl.de (ThorstenInAnger) Date: Mon, 23 Oct 2006 02:57:14 -0700 (PDT) Subject: [Biojava-l] fasta description line Message-ID: <6950970.post@talk.nabble.com> Hi, I want to do something very simple: - get id and sequence from a database - create a sequence object - write it out as fasta format file (with a defined description line) this is my code: rs = stmt.executeQuery(query); Feature.Template templ = new Feature.Template(); //fill in the template Annotation an = new SimpleAnnotation(); templ.location = Location.empty; while (rs.next()) { mepdId = rs.getInt(1); mepdName = rs.getString(2); seq = rs.getString(3); seqObj = DNATools.createDNASequence(seq, mepdName); an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description here"); templ.annotation = an; seqObj.createFeature(templ); SeqIOTools.writeFasta(fastaFos, seqObj); //db.addSequence(seqObj); } It works fine, but there is no description line in the resulting file! How can I change the fasta description line? Also I am using deprecated methods, but could not find out what to use instead: FastaFormat.PROPERTY_DESCRIPTIONLINE SeqIOTools.writeFasta All tutorials I found are using the deprecated. Cheers, Thorsten -- View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970 Sent from the BioJava mailing list archive at Nabble.com. From sgerster at student.ethz.ch Tue Oct 31 03:04:33 2006 From: sgerster at student.ethz.ch (Gerster Sarah) Date: Tue, 31 Oct 2006 09:04:33 +0100 Subject: [Biojava-l] pK values Message-ID: Hi! I want to compute the pI of some sequences. I looked at "IsoelectricPointCalc.java". Where do the values for the pks come from? are they defined as constants somewhere? I couldn't find them... I wanted to see if the values are the same ones than the ones that I am supposed to use. And another question> reading in sequences from an xml file... Is there something that I can use, or do I have to write it on my own? Cheers Sarah From markjschreiber at gmail.com Tue Oct 31 04:37:24 2006 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 31 Oct 2006 17:37:24 +0800 Subject: [Biojava-l] fasta description line In-Reply-To: <6950970.post@talk.nabble.com> References: <6950970.post@talk.nabble.com> Message-ID: <93b45ca50610310137u68700b06se364f99da69feb47@mail.gmail.com> Hi - If you are using biojava 1.5 beta (recommended) you should use RichSequence.IOTools to write the fasta (strongly recommended). With the new org.biojavax.bio.seq.io.FastaFormat object the description line is constructed from: richSequence.getIdentifier() richSequence.getNamespace().getName(); richSequence.getAccession() richSequence.getVersion() richSequence.getName() richSequence.getDescription() - Mark On 10/23/06, ThorstenInAnger wrote: > > Hi, > > I want to do something very simple: > > - get id and sequence from a database > - create a sequence object > - write it out as fasta format file (with a defined description line) > > this is my code: > rs = stmt.executeQuery(query); > Feature.Template templ = new Feature.Template(); > > //fill in the template > Annotation an = new SimpleAnnotation(); > templ.location = Location.empty; > > while (rs.next()) { > mepdId = rs.getInt(1); > mepdName = rs.getString(2); > seq = rs.getString(3); > seqObj = DNATools.createDNASequence(seq, mepdName); > an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description > here"); > templ.annotation = an; > seqObj.createFeature(templ); > SeqIOTools.writeFasta(fastaFos, seqObj); > //db.addSequence(seqObj); > } > > It works fine, but there is no description line in the resulting file! > How can I change the fasta description line? > > Also I am using deprecated methods, but could not find out what to use > instead: > FastaFormat.PROPERTY_DESCRIPTIONLINE > SeqIOTools.writeFasta > All tutorials I found are using the deprecated. > > Cheers, > > Thorsten > > -- > View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970 > Sent from the BioJava mailing list archive at Nabble.com. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From markjschreiber at gmail.com Tue Oct 31 04:27:29 2006 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 31 Oct 2006 17:27:29 +0800 Subject: [Biojava-l] pK values In-Reply-To: References: Message-ID: <93b45ca50610310127h75010e56ne31e188294e23803@mail.gmail.com> Hi - The values are calculated using the SymbolPropertyTable returned by ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK); This table gets it's values from the resource file org/biojava/bio/symbol/ResidueProperties.xml The pK values were added by david huen (I think). To read XML sequence files try one of the methods in RichSequence.IOTools from biojava 1.5 beta. - Mark On 10/31/06, Gerster Sarah wrote: > Hi! > > I want to compute the pI of some sequences. I looked at "IsoelectricPointCalc.java". Where do the values for the pks come from? are they defined as constants somewhere? I couldn't find them... I wanted to see if the values are the same ones than the ones that I am supposed to use. > > And another question> reading in sequences from an xml file... Is there something that I can use, or do I have to write it on my own? > > Cheers > > Sarah > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From smh1008 at cam.ac.uk Tue Oct 31 07:21:43 2006 From: smh1008 at cam.ac.uk (David Huen) Date: 31 Oct 2006 12:21:43 +0000 Subject: [Biojava-l] pK values In-Reply-To: <93b45ca50610310127h75010e56ne31e188294e23803@mail.gmail.com> References: <93b45ca50610310127h75010e56ne31e188294e23803@mail.gmail.com> Message-ID: On Oct 31 2006, Mark Schreiber wrote: >Hi - > >The values are calculated using the SymbolPropertyTable returned by >ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK); > >This table gets it's values from the resource file >org/biojava/bio/symbol/ResidueProperties.xml > >The pK values were added by david huen (I think). > I used the same pK values as those used by GCG to maintian cross-compability. Regards, David From service at birthdayalarm.com Wed Oct 11 04:21:20 2006 From: service at birthdayalarm.com (NandaKumar Sreedharan) Date: Wed, 11 Oct 2006 04:21:20 +0000 Subject: [Biojava-l] Calendar Message-ID: <200610110451.k9B4pNga015117@portal.open-bio.org> Hi, I am creating a birthday calendar of all my friends and family. Can you please click on the link below to enter your birthday for me. http://www.birthdayalarm.com/bd2/74713512a732679238b1279483798c781990119d1719 Thanks, NandaKumar From rajeee_sss at yahoo.com Wed Oct 11 07:41:21 2006 From: rajeee_sss at yahoo.com (Rajeswari) Date: Wed, 11 Oct 2006 00:41:21 -0700 (PDT) Subject: [Biojava-l] how can i read a genbank Message-ID: <20061011074121.38573.qmail@web30012.mail.mud.yahoo.com> Dear developers., I got the biojava program to read a genbank file from biojava.org. it is as follows: import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; import java.io.*; import org.biojava.bio.*; import java.util.*; public class genbank1 { public static void main(String[] args) { BufferedReader br = null; try { FileReader f=new FileReader(mygen.java); br = new BufferedReader(f); } catch (FileNotFoundException ex) { ex.printStackTrace(); System.exit(-1); } SequenceIterator sequences = SeqIOTools.readGenbank(br); while(sequences.hasNext()) { try { Sequence seq = sequences.nextSequence(); } catch(BioException ex) { ex.printStackTrace(); } catch(NoSuchElementException ex) { ex.printStackTrace(); } } } } And i saved it as genbank1.java it was compiled with javac genbank1.java and when i try to execute it shows no classfoundException. i run the pro as follows: c:\jdk1.4\bin\java genbank1 mygen.java mygen.java consists of the genbank file. i think the error may be deu to the genbank file. can anybody tell me how to do this pro correct? and provide me the exact format of a genbank file with extension. regards s.rajee --------------------------------- Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail. From markjschreiber at gmail.com Wed Oct 11 13:33:28 2006 From: markjschreiber at gmail.com (Mark Schreiber) Date: Wed, 11 Oct 2006 21:33:28 +0800 Subject: [Biojava-l] how can i read a genbank In-Reply-To: <20061011074121.38573.qmail@web30012.mail.mud.yahoo.com> References: <20061011074121.38573.qmail@web30012.mail.mud.yahoo.com> Message-ID: <93b45ca50610110633q3b7d93bw7233cfa4cdbbd9d3@mail.gmail.com> This sounds like a problem with your classpath. For advice on setting your classpath take a look at http://biojava.org/wiki/BioJava:GetStarted - Mark On 10/11/06, Rajeswari wrote: > Dear developers., > > I got the biojava program to read a genbank file from biojava.org. > > it is as follows: > > import org.biojava.bio.seq.*; > import org.biojava.bio.seq.io.*; > import java.io.*; > import org.biojava.bio.*; > import java.util.*; > > public class genbank1 > { > public static void main(String[] args) > { > BufferedReader br = null; > > try > { > FileReader f=new FileReader(mygen.java); > br = new BufferedReader(f); > > } > catch (FileNotFoundException ex) > { > ex.printStackTrace(); > System.exit(-1); > } > > > SequenceIterator sequences = SeqIOTools.readGenbank(br); > > while(sequences.hasNext()) > { > try > { > > Sequence seq = sequences.nextSequence(); > > > } > catch(BioException ex) > { > ex.printStackTrace(); > } > catch(NoSuchElementException ex) > { > ex.printStackTrace(); > } > } > } > } > > > And i saved it as genbank1.java > > it was compiled with javac genbank1.java > > > and when i try to execute it shows no classfoundException. > > > i run the pro as follows: > > c:\jdk1.4\bin\java genbank1 mygen.java > > mygen.java consists of the genbank file. > > > > i think the error may be deu to the genbank file. > > > can anybody tell me how to do this pro correct? and provide me the exact format of a genbank file with extension. > > > > regards > s.rajee > > > --------------------------------- > Do you Yahoo!? > Everyone is raving about the all-new Yahoo! Mail. > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From emd at sanger.ac.uk Thu Oct 12 09:44:31 2006 From: emd at sanger.ac.uk (Ed Dicks) Date: Thu, 12 Oct 2006 10:44:31 +0100 (BST) Subject: [Biojava-l] advice on ABIFParser Message-ID: Hi, Can anyone give me some advice on using; org.biojava.bio.program.abi.ABIFParser I'm working with an ab1 sequence trace file and trying to pull out the value of a data item defined with a tag - index pair. my sample code is; (trying to pull out the mobility file name) ABIFParser abiParse=new ABIFParser("temp.ab1"); ABIFParser.DataAccess a1=abiParse.getDataAccess(); ABIFParser.TaggedDataRecord r1=abiParse.getDataRecord("PDMF",1); System.err.println("r1 ok "+r1.toString()); The output looks like... r1 ok org.biojava.bio.program.abi.ABIFParser$TaggedDataRecord at 80474d4[ tagName = PDMF tagNumber = 1 dataType = PSTRING elementLength = 1 numberOfElements= 21 recordLength = 21 dataRecord = 0x0001265A crypticVariable = 0 ] now I've done "strings temp.ab1" to verify the tag "PDMF" is present. What's going on here is that ABIFParser reads the data item into a long variable (field dataRecord) but the PSTRING is length 21 which is too big for a long. I have succesfully pulled out strings that are length <= 8 but this one just seems too big, can anyone give me some advice on this. Thanks Ed --------------------------------------------------------- Dr Ed Dicks Cancer Genome Project (Team 78) The Wellcome Trust Sanger Institute Hinxton, Cambs. CB10 1SA Tel: +44 1223 494967 --------------------------------------------------------- From russ at kepler-eng.com Thu Oct 12 13:38:41 2006 From: russ at kepler-eng.com (Russ Kepler) Date: Thu, 12 Oct 2006 07:38:41 -0600 Subject: [Biojava-l] advice on ABIFParser In-Reply-To: References: Message-ID: <200610120738.41125.russ@kepler-eng.com> On Thursday 12 October 2006 03:44 am, Ed Dicks wrote: > now I've done "strings temp.ab1" to verify the tag "PDMF" is present. > What's going on here is that ABIFParser reads the data item into a long > variable (field dataRecord) but the PSTRING is length 21 which is too big > for a long. I have succesfully pulled out strings that are length <= 8 but > this one just seems too big, can anyone give me some advice on this. The TaggedDataRecord is really a pointer when the data size is > 4 bytes, what you'll have to do is to loop like this: ABIFParser abiParse=new ABIFParser("temp.ab1"); ABIFParser.DataAccess a1=abiParse.getDataAccess(); ABIFParser.TaggedDataRecord r1=abiParse.getDataRecord("PDMF",1); System.err.println("r1 ok "+r1.toString()); a1.seek(r1.dataRecord); int count = (int) r1.numberOfElements; StringBuffer sb = new StringBuffer(count); for (int i = 0; i < count; ) { sb.append(a1.readChar()); } System.out.println("Dye mobility: "+sb.toString()); Really your basic seek & read loop. Look in ABIFChromatogram.parseBaseCalls() for a fuller example, but this will get you started. From andreas.draeger at uni-tuebingen.de Fri Oct 13 07:56:39 2006 From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=) Date: Fri, 13 Oct 2006 09:56:39 +0200 Subject: [Biojava-l] Java(TM) Message-ID: <452F46B7.2020207@uni-tuebingen.de> Hi all, Yesterday our institution, the University of T?bingen, Germany, received an email from SUN. The email started by saying that SUN is pleased to see projects written in their programing language "Java" that we provide at our institution. However, they wanted us to rename our Evoulutionary Algorithms package "JavaEvA" to something like "JEvA" and our Neural Network project "JavaNNS" should also be renamed to something else like "JNNS". The reason for this is that SUN owns a trademark on the name "Java" and no other institution or company is supposed to use this name for its own purposes or software packages, even if this is a non profit and/or open source project as JavaEvA and JavaNNS. We might later even get a dissuasion letter if we do not follow the instructions in the email. I do not exactly know how SUN and the BioJava project are connected. However, in the worst case someday we could also receive a writing like that. To summarize: we should be aware that possibly the name "BioJava" has to be changed to something else like "JBio" or "BioJ" or what ever SUN might suggest as soon as they recognize our project. If there is already an agreement with SUN about that, I am not well informed and curious to know about it. Otherwise you are now informed about what happened to us in T?bingen. Sincerely, Andreas Dr?ger -- Dipl.Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 From mark.schreiber at novartis.com Fri Oct 13 09:05:55 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 13 Oct 2006 17:05:55 +0800 Subject: [Biojava-l] Java(TM) Message-ID: Hi - This issue has been mentioned before however we have never been instructed by Sun to modify the name. This doesn't mean it cannot happen, however several people in Sun know about the project (Joshua Bloch apparently even mentioned it in a talk) and it has been featured in news stories on their own websites. Sun even provided open-bio with some servers and I think have shipped biojava on some machines that are 'prepackaged' with bio applications. All of this doesn't prevent them from asking us to change the name and they are infact legally within their rights to request it. While it may not be possible to own the word Java due to the large Island already having the same name it is possible to register it for trade in computation related activities. Given that open-bio is not likely to want to get into litigation with Sun then I suspect we would need to change the name. The most problematic part would be modifying package names. Perhaps we (meaning open-bio collectively and the biojava core people) could attempt to pre-empt this a little by talking with Sun directly to see what our options are. Any thoughts? - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com www.dengueinfo.org phone +65 6722 2973 fax +65 6722 2910 Andreas Dr?ger Sent by: biojava-l-bounces at lists.open-bio.org 10/13/2006 03:56 PM To: biojava-l at biojava.org cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Java(TM) Hi all, Yesterday our institution, the University of T?bingen, Germany, received an email from SUN. The email started by saying that SUN is pleased to see projects written in their programing language "Java" that we provide at our institution. However, they wanted us to rename our Evoulutionary Algorithms package "JavaEvA" to something like "JEvA" and our Neural Network project "JavaNNS" should also be renamed to something else like "JNNS". The reason for this is that SUN owns a trademark on the name "Java" and no other institution or company is supposed to use this name for its own purposes or software packages, even if this is a non profit and/or open source project as JavaEvA and JavaNNS. We might later even get a dissuasion letter if we do not follow the instructions in the email. I do not exactly know how SUN and the BioJava project are connected. However, in the worst case someday we could also receive a writing like that. To summarize: we should be aware that possibly the name "BioJava" has to be changed to something else like "JBio" or "BioJ" or what ever SUN might suggest as soon as they recognize our project. If there is already an agreement with SUN about that, I am not well informed and curious to know about it. Otherwise you are now informed about what happened to us in T?bingen. Sincerely, Andreas Dr?ger -- Dipl.Bioinform. Andreas Dr?ger Eberhard Karls University T?bingen Center for Bioinformatics (ZBIT) Germany Phone: +49-7071-29-70436 Fax: +49-7071-29-5091 _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From hlapp at gmx.net Wed Oct 18 20:29:20 2006 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 18 Oct 2006 16:29:20 -0400 Subject: [Biojava-l] NESCent Phyloinformatics Hackathon Message-ID: (this has been silently discarded by the mailing list, apologies if you have received this before) The National Evolutionary Synthesis Center (NESCent) in collaboration with Arlin Stoltzfus (U. Maryland, NIST), Aaron Mackey (GSK), Rutger Vos (UBC), and Mark Holder (FSU) sponsors a Phyloinformatics Hackathon to take place Dec 11-15 in Durham, NC. The (wiki) website with more information and a formal proposal is at https://www.nescent.org/wg_phyloinformatics/ In short, the goal is to leverage the Bio* toolkits to provide the "glue" for evolutionary analyses of various types that depend on automation, interoperability, and data integration. CALL FOR INPUT: The specific objectives are driven by "use cases", that is, specific target problems of interest to evolutionary biologists (click 'Use Cases' at the above website). We invite community input in order to focus efforts on the most urgent or pervasive problems. The wiki for the hackathon allows direct editing of the use cases after registration. You may also upload data files, or add comments to the "Forum" page. Alternatively, send email to hlapp at nescent.org. You may also contact any of the organizers with questions or comments. ATTENDANCE: The hackathon is scheduled for Dec 11-15, 2006 in Durham NC. Space is limited, and attendance is by invitation. If you have not been contacted but desire to attend, please contact Hilmar Lapp (hlapp at nescent.org). ORGANIZERS: Hilmar Lapp (NESCent; hlapp at nescent.org) Aaron Mackey (GSK; aaron.j.mackey at gsk.com) Mark Holder (FSU; mholder at scs.fsu.edu) Arlin Stoltzfus (CARB, NIST; arlin.stoltzfus at nist.gov) Todd Vision (NESCent; tjv at bio.unc.edu) Rutger Vos (UBC; rvosa at sfu.ca) From CARMELK at il.ibm.com Thu Oct 19 12:44:43 2006 From: CARMELK at il.ibm.com (Carmel Kent) Date: Thu, 19 Oct 2006 14:44:43 +0200 Subject: [Biojava-l] can BioJava do alignment ? Message-ID: Hello, I'm interested in a Java package for sequence alignment. I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can only create objects that are representations of alignments generated by third-party software. I had an impression that BioJava 1.5 can do alignment itself (e.g., I saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class named org.biojava.bio.alignment.NeedlemanWunch) I have two questions: is this true ? I mean, does BioJava 1.5 contain the alignment algorithm, itself ? if it does, I downloaded the CVS view of BioJava 1.5, but could not find any javadocs or the alignment package source. Where can I find it ? Thanks very much, Carmel Kent Research Staff Member Healthcare I/T Research IBM Research Laboratory in Haifa Tel. +972-4-8281059 Email: carmelk at il.ibm.com From rmedrado at gmail.com Thu Oct 19 17:45:24 2006 From: rmedrado at gmail.com (Ramon Medrado) Date: Thu, 19 Oct 2006 14:45:24 -0300 Subject: [Biojava-l] can BioJava do alignment ? In-Reply-To: References: Message-ID: <37ba4b050610191045q30a6282bjce052e31e1463cea@mail.gmail.com> Hi, The information is true. Biojava 1.5 has the main algorithms of alignment as NeedlemanWunch, SmithWaterman and other implementations that are encapsulated on package org.biojava.bio.alignment All source is disponible in this link : http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz and the jar file is disponible in: http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar and the javadoc: http://www.biojava.org/download/bj15b/doc/doc.tar.gz I wait to have helped -- Ramon Undergraduate Student of Computer Science Universidade Estadual de Santa Cruz - Brasil 2006/10/19, Carmel Kent : > > > Hello, > > I'm interested in a Java package for sequence alignment. > I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can > only create objects that are representations of alignments generated by > third-party software. > > I had an impression that BioJava 1.5 can do alignment itself (e.g., I > saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class > named org.biojava.bio.alignment.NeedlemanWunch) > > I have two questions: > > is this true ? I mean, does BioJava 1.5 contain the alignment > algorithm, > itself ? if it does, I downloaded the CVS view of BioJava 1.5, but could not find > any javadocs or the alignment package source. Where can I find it ? > > > Thanks very much, > > > Carmel Kent > Research Staff Member > Healthcare I/T Research > IBM Research Laboratory in Haifa > Tel. +972-4-8281059 > Email: carmelk at il.ibm.com > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From mark.schreiber at novartis.com Fri Oct 20 01:57:09 2006 From: mark.schreiber at novartis.com (mark.schreiber at novartis.com) Date: Fri, 20 Oct 2006 09:57:09 +0800 Subject: [Biojava-l] can BioJava do alignment ? Message-ID: Hi - You can also perform an alignment using HMMs in biojava 1.3 and 1.4. See the example at (http://biojava.org/wiki/BioJava:CookBook:DP:PairWise). This is actually the most flexible way to do it. - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com www.dengueinfo.org phone +65 6722 2973 fax +65 6722 2910 "Ramon Medrado" Sent by: biojava-l-bounces at lists.open-bio.org 10/20/2006 01:45 AM To: biojava cc: (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [Biojava-l] can BioJava do alignment ? Hi, The information is true. Biojava 1.5 has the main algorithms of alignment as NeedlemanWunch, SmithWaterman and other implementations that are encapsulated on package org.biojava.bio.alignment All source is disponible in this link : http://www.biojava.org/download/bj15b/all/biojava-1.5-beta.tar.gz and the jar file is disponible in: http://www.biojava.org/download/bj15b/bin/biojava-1.5-beta.jar and the javadoc: http://www.biojava.org/download/bj15b/doc/doc.tar.gz I wait to have helped -- Ramon Undergraduate Student of Computer Science Universidade Estadual de Santa Cruz - Brasil 2006/10/19, Carmel Kent : > > > Hello, > > I'm interested in a Java package for sequence alignment. > I understood that BioJava 1.3 & 1.4 itself cannot align sequences, it can > only create objects that are representations of alignments generated by > third-party software. > > I had an impression that BioJava 1.5 can do alignment itself (e.g., I > saw in http://biojava.org/wiki/BioJava:CookBook:DP:PairWise2 the class > named org.biojava.bio.alignment.NeedlemanWunch) > > I have two questions: > > is this true ? I mean, does BioJava 1.5 contain the alignment > algorithm, > itself ? if it does, I downloaded the CVS view of BioJava 1.5, but could not find > any javadocs or the alignment package source. Where can I find it ? > > > Thanks very much, > > > Carmel Kent > Research Staff Member > Healthcare I/T Research > IBM Research Laboratory in Haifa > Tel. +972-4-8281059 > Email: carmelk at il.ibm.com > > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l From n.haigh at sheffield.ac.uk Wed Oct 25 13:54:26 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Wed, 25 Oct 2006 13:54:26 +0000 Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests Message-ID: <453F6C92.6020207@sheffield.ac.uk> I have recently installed some more software for which there are bioperl-run tests and run the test suite with several versions of the software I could find. I've added info to http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any fails in any of the versions I tested I've noted them together with versions that were ok (if any). There maybe another 6 or so programs I'm trying to get hold of to run further tests - I'll update when I get them. Nath From n.haigh at sheffield.ac.uk Thu Oct 26 08:46:13 2006 From: n.haigh at sheffield.ac.uk (Nathan Haigh) Date: Thu, 26 Oct 2006 09:46:13 +0100 Subject: [Biojava-l] More extensive Bioperl-run 1.5.2RC2 tests In-Reply-To: <453F6C92.6020207@sheffield.ac.uk> References: <453F6C92.6020207@sheffield.ac.uk> Message-ID: <454075D5.2030005@sheffield.ac.uk> Nathan S. Haigh wrote: > I have recently installed some more software for which there are > bioperl-run tests and run the test suite with several versions of the > software I could find. I've added info to > http://www.bioperl.org/wiki/Release_1.5.2#bioperl-run. If there were any > fails in any of the versions I tested I've noted them together with > versions that were ok (if any). > > There maybe another 6 or so programs I'm trying to get hold of to run > further tests - I'll update when I get them. > Nath > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > My aplogies, this should have gone to the Bioperl mailing list! :o) From henrich at embl.de Mon Oct 23 09:57:14 2006 From: henrich at embl.de (ThorstenInAnger) Date: Mon, 23 Oct 2006 02:57:14 -0700 (PDT) Subject: [Biojava-l] fasta description line Message-ID: <6950970.post@talk.nabble.com> Hi, I want to do something very simple: - get id and sequence from a database - create a sequence object - write it out as fasta format file (with a defined description line) this is my code: rs = stmt.executeQuery(query); Feature.Template templ = new Feature.Template(); //fill in the template Annotation an = new SimpleAnnotation(); templ.location = Location.empty; while (rs.next()) { mepdId = rs.getInt(1); mepdName = rs.getString(2); seq = rs.getString(3); seqObj = DNATools.createDNASequence(seq, mepdName); an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description here"); templ.annotation = an; seqObj.createFeature(templ); SeqIOTools.writeFasta(fastaFos, seqObj); //db.addSequence(seqObj); } It works fine, but there is no description line in the resulting file! How can I change the fasta description line? Also I am using deprecated methods, but could not find out what to use instead: FastaFormat.PROPERTY_DESCRIPTIONLINE SeqIOTools.writeFasta All tutorials I found are using the deprecated. Cheers, Thorsten -- View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970 Sent from the BioJava mailing list archive at Nabble.com. From sgerster at student.ethz.ch Tue Oct 31 08:04:33 2006 From: sgerster at student.ethz.ch (Gerster Sarah) Date: Tue, 31 Oct 2006 09:04:33 +0100 Subject: [Biojava-l] pK values Message-ID: Hi! I want to compute the pI of some sequences. I looked at "IsoelectricPointCalc.java". Where do the values for the pks come from? are they defined as constants somewhere? I couldn't find them... I wanted to see if the values are the same ones than the ones that I am supposed to use. And another question> reading in sequences from an xml file... Is there something that I can use, or do I have to write it on my own? Cheers Sarah From markjschreiber at gmail.com Tue Oct 31 09:37:24 2006 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 31 Oct 2006 17:37:24 +0800 Subject: [Biojava-l] fasta description line In-Reply-To: <6950970.post@talk.nabble.com> References: <6950970.post@talk.nabble.com> Message-ID: <93b45ca50610310137u68700b06se364f99da69feb47@mail.gmail.com> Hi - If you are using biojava 1.5 beta (recommended) you should use RichSequence.IOTools to write the fasta (strongly recommended). With the new org.biojavax.bio.seq.io.FastaFormat object the description line is constructed from: richSequence.getIdentifier() richSequence.getNamespace().getName(); richSequence.getAccession() richSequence.getVersion() richSequence.getName() richSequence.getDescription() - Mark On 10/23/06, ThorstenInAnger wrote: > > Hi, > > I want to do something very simple: > > - get id and sequence from a database > - create a sequence object > - write it out as fasta format file (with a defined description line) > > this is my code: > rs = stmt.executeQuery(query); > Feature.Template templ = new Feature.Template(); > > //fill in the template > Annotation an = new SimpleAnnotation(); > templ.location = Location.empty; > > while (rs.next()) { > mepdId = rs.getInt(1); > mepdName = rs.getString(2); > seq = rs.getString(3); > seqObj = DNATools.createDNASequence(seq, mepdName); > an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description > here"); > templ.annotation = an; > seqObj.createFeature(templ); > SeqIOTools.writeFasta(fastaFos, seqObj); > //db.addSequence(seqObj); > } > > It works fine, but there is no description line in the resulting file! > How can I change the fasta description line? > > Also I am using deprecated methods, but could not find out what to use > instead: > FastaFormat.PROPERTY_DESCRIPTIONLINE > SeqIOTools.writeFasta > All tutorials I found are using the deprecated. > > Cheers, > > Thorsten > > -- > View this message in context: http://www.nabble.com/fasta-description-line-tf2493269.html#a6950970 > Sent from the BioJava mailing list archive at Nabble.com. > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From markjschreiber at gmail.com Tue Oct 31 09:27:29 2006 From: markjschreiber at gmail.com (Mark Schreiber) Date: Tue, 31 Oct 2006 17:27:29 +0800 Subject: [Biojava-l] pK values In-Reply-To: References: Message-ID: <93b45ca50610310127h75010e56ne31e188294e23803@mail.gmail.com> Hi - The values are calculated using the SymbolPropertyTable returned by ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK); This table gets it's values from the resource file org/biojava/bio/symbol/ResidueProperties.xml The pK values were added by david huen (I think). To read XML sequence files try one of the methods in RichSequence.IOTools from biojava 1.5 beta. - Mark On 10/31/06, Gerster Sarah wrote: > Hi! > > I want to compute the pI of some sequences. I looked at "IsoelectricPointCalc.java". Where do the values for the pks come from? are they defined as constants somewhere? I couldn't find them... I wanted to see if the values are the same ones than the ones that I am supposed to use. > > And another question> reading in sequences from an xml file... Is there something that I can use, or do I have to write it on my own? > > Cheers > > Sarah > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > From smh1008 at cam.ac.uk Tue Oct 31 12:21:43 2006 From: smh1008 at cam.ac.uk (David Huen) Date: 31 Oct 2006 12:21:43 +0000 Subject: [Biojava-l] pK values In-Reply-To: <93b45ca50610310127h75010e56ne31e188294e23803@mail.gmail.com> References: <93b45ca50610310127h75010e56ne31e188294e23803@mail.gmail.com> Message-ID: On Oct 31 2006, Mark Schreiber wrote: >Hi - > >The values are calculated using the SymbolPropertyTable returned by >ProteinTools.getSymbolPropertyTable(SymbolPropertyTable.PK); > >This table gets it's values from the resource file >org/biojava/bio/symbol/ResidueProperties.xml > >The pK values were added by david huen (I think). > I used the same pK values as those used by GCG to maintian cross-compability. Regards, David