From jw12 at sanger.ac.uk Thu Feb 2 04:45:27 2012 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 2 Feb 2012 09:45:27 +0000 Subject: [Biojava-l] Only 10 days left to register for DAS Workshop 2012 Message-ID: <4628F603-166D-4A9B-AEB3-4696E91431CD@sanger.ac.uk> Only 10 days left to register for DAS Workshop 2012 DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Learn of and contribute to current developments in DAS such as: DAS in the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative annotation projects, DAS alternative formats. Registration is open for the 2012 DAS workshop (27-29 February) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Please register early as places will be limited. Registration closes 10 February 2012 - 12:00. If you are interested in giving a 15 minute talk on the second day please email Jonathan Warren using jonathan.warren at sanger.ac.uk Many thanks The Sanger/EBI DAS team. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From andreas at sdsc.edu Tue Feb 7 01:55:29 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 6 Feb 2012 22:55:29 -0800 Subject: [Biojava-l] Google Summer of Code 2012 Message-ID: Hi, This is an early heads-up that Google has announced that there will be another Summer of Code this year [1][2]. We will try to participate again from the side of BioJava. Around March 16th we should know if we have been accepted as an organisation, after which we can start discussing student proposals. In the meanwhile would-be students are invited to start thinking about potential projects. Here a couple of dates: ? February 27 ? March 9: Google will accept applications from open source projects. ? March 12 ? 15: Google program administrators review organization applications. ? March 16: List of accepted mentoring organizations published on http://www.google-melange.com ? March 17-25: Would-be student participants discuss application/project ideas with mentoring organizations. ? March 26-April 6: Student application period ? April 23: Accepted student proposals announced at http://www.google-melange.com ? May 21: Students begin coding Andreas more infos: [1] - http://google-opensource.blogspot.com/2012/02/google-summer-of-code-2012-is-on.html [2] - http://code.google.com/p/google-summer-of-code/wiki/ProgramPresentations From sfrees at ramapo.edu Thu Feb 16 09:24:56 2012 From: sfrees at ramapo.edu (Scott Frees) Date: Thu, 16 Feb 2012 09:24:56 -0500 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB Message-ID: Hello ? I have developed an application that searches and compares g-quadruplexes within mRNA. The web application has been running without any problems on several different web servers for over a year. Suddenly, just this week, it is unable to download sequence data using GenbankRichSequenceDB ? has anyone else has had this problem? We are using BioJava 1.8.1 Below is the exception trace, and the code that follows is a small test app that generates the exception. This code worked without any problems prior to Tuesday this week, and we haven't made any modification to our application. ------------------------------------------------------ org.biojava.bio.BioException: Failed to read Genbank sequence at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) at Tester.main(Tester.java:11) Caused by: org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) ... 1 more Caused by: org.biojava.bio.seq.io.ParseException: A Exception Has Occurred During Parsing. Please submit the details that follow to biojava-l at biojava.org or post a bug report to http://bugzilla.open-bio.org/ Format_object=org.biojavax.bio.seq.io.GenbankFormat Accession=null Id=null Comments=Bad section Parse_block= Stack trace follows .... at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 2 more Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -4 at java.lang.String.substring(Unknown Source) at java.lang.String.substring(Unknown Source) at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) ... 4 more ----------------------------- import org.biojava.bio.BioException; import org.biojava.bio.seq.db.IllegalIDException; import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; import org.biojavax.bio.seq.RichSequence; public class Tester { public static void main(String args[]) { String id = "NM_001110.2"; // Issue occurs with any ID GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); try { RichSequence rs = ncbi.getRichSequence(id); System.out.println(rs.seqString()); } catch (IllegalIDException e) { e.printStackTrace(); } catch (BioException e) { e.printStackTrace(); } } } From gwaldon at geneinfinity.org Thu Feb 16 20:53:36 2012 From: gwaldon at geneinfinity.org (George Waldon) Date: Thu, 16 Feb 2012 19:53:36 -0600 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: References: Message-ID: <20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> Hello Scott, This appears to be an exception thrown by the parser. Is-there a way you can fetch the sequence(s) as a text file before the exception occurs? It would be interesting to see if you can reproduce the exception; you can send me the file if you want. Regards, George Quoting Scott Frees : > Hello - > > I have developed an application that searches and compares > g-quadruplexes within mRNA. The web application has been running > without any problems on several different web servers for over a year. > Suddenly, just this week, it is unable to download sequence data > using GenbankRichSequenceDB - has anyone else has had this problem? > > We are using BioJava 1.8.1 > > Below is the exception trace, and the code that follows is a small > test app that generates the exception. This code worked without any > problems prior to Tuesday this week, and we haven't made any > modification to our application. > ------------------------------------------------------ > org.biojava.bio.BioException: Failed to read Genbank sequence > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) > at Tester.main(Tester.java:11) > Caused by: org.biojava.bio.BioException: Could not read sequence > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) > ... 1 more > Caused by: org.biojava.bio.seq.io.ParseException: > > A Exception Has Occurred During Parsing. > Please submit the details that follow to biojava-l at biojava.org or post > a bug report to http://bugzilla.open-bio.org/ > > Format_object=org.biojavax.bio.seq.io.GenbankFormat > Accession=null > Id=null > Comments=Bad section > Parse_block= > Stack trace follows .... > > at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) > at > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) > ... 2 more > Caused by: java.lang.StringIndexOutOfBoundsException: String index out > of range: -4 > at java.lang.String.substring(Unknown Source) > at java.lang.String.substring(Unknown Source) > at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) > ... 4 more > ----------------------------- > > > import org.biojava.bio.BioException; > import org.biojava.bio.seq.db.IllegalIDException; > import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; > import org.biojavax.bio.seq.RichSequence; > > public class Tester { > public static void main(String args[]) { > String id = "NM_001110.2"; // Issue occurs with any ID > GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); > try { > RichSequence rs = ncbi.getRichSequence(id); > System.out.println(rs.seqString()); > } catch (IllegalIDException e) { > e.printStackTrace(); > } catch (BioException e) { > e.printStackTrace(); > } > } > } > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -------------------------------- George Waldon From sfrees at ramapo.edu Thu Feb 16 22:25:03 2012 From: sfrees at ramapo.edu (Scott Frees) Date: Thu, 16 Feb 2012 22:25:03 -0500 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> References: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> Message-ID: George - Thanks for your response. I think I tracked down the problem. When building the FetchURL, GenbankRichSequenceDB uses "genbank" as the db. In the org.biojava.bio.seq.db.FetchURL constructor, rettype and retmode are specifically not set when given "genbank" - see lines 54-55 commented out. // rettype = format; // retmode = format; Entrez recently updated their API (http://www.ncbi.nlm.nih.gov/books/NBK25501/) on Wednesday and in the release notes they say they've set defaults on each database for retmode. I'm new to biojava and entrez, but I can only assume that the "genbank" db used to return sequences as text always, which is why FetchURL doesn't include the parameter in the URL it builds. It looks like the default now is XML - which breaks the GenbankRichSequenceDB parser. I proved it out by subclassing GenbankRichSequenceDB to set the retmode parameter as text, and the problem is resolved. @Override protected URL getAddress(String id) throws MalformedURLException { FetchURL seqURL = new FetchURL("Genbank", "text"); String baseurl = seqURL.getbaseURL(); String db = seqURL.getDB(); // added retmode=text String url = baseurl+db+"&id="+id+"&rettype=gb&retmode=text&tool="+getTool()+"&email="+getEmail(); return new URL(url); } I think a more elegant solution would be to simply fix FetchURL to use the retmode parameter Regards - Scott On Thu, Feb 16, 2012 at 8:53 PM, George Waldon wrote: > Hello Scott, > > This appears to be an exception thrown by the parser. Is-there a way you can > fetch the sequence(s) as a text file before the exception occurs? It would > be interesting to see if you can reproduce the exception; you can send me > the file if you want. > > Regards, > George > > Quoting Scott Frees : > >> Hello - >> >> I have developed an application that searches and compares >> g-quadruplexes within mRNA. ?The web application has been running >> without any problems on several different web servers for over a year. >> ?Suddenly, just this week, it is unable to download sequence data >> using GenbankRichSequenceDB - has anyone else has had this problem? >> >> We are using BioJava 1.8.1 >> >> Below is the exception trace, and the code that follows is a small >> test app that generates the exception. ?This code worked without any >> problems prior to Tuesday this week, and we haven't made any >> modification to our application. >> ------------------------------------------------------ >> org.biojava.bio.BioException: Failed to read Genbank sequence >> ? ? ? ?at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) >> ? ? ? ?at Tester.main(Tester.java:11) >> Caused by: org.biojava.bio.BioException: Could not read sequence >> ? ? ? ?at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >> ? ? ? ?at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) >> ? ? ? ?... 1 more >> Caused by: org.biojava.bio.seq.io.ParseException: >> >> A Exception Has Occurred During Parsing. >> Please submit the details that follow to biojava-l at biojava.org or post >> a bug report to http://bugzilla.open-bio.org/ >> >> Format_object=org.biojavax.bio.seq.io.GenbankFormat >> Accession=null >> Id=null >> Comments=Bad section >> Parse_block= >> Stack trace follows .... >> >> ? ? ? ?at >> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) >> ? ? ? ?at >> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) >> ? ? ? ?at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >> ? ? ? ?... 2 more >> Caused by: java.lang.StringIndexOutOfBoundsException: String index out >> of range: -4 >> ? ? ? ?at java.lang.String.substring(Unknown Source) >> ? ? ? ?at java.lang.String.substring(Unknown Source) >> ? ? ? ?at >> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) >> ? ? ? ?... 4 more >> ----------------------------- >> >> >> import org.biojava.bio.BioException; >> import org.biojava.bio.seq.db.IllegalIDException; >> import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; >> import org.biojavax.bio.seq.RichSequence; >> >> public class Tester { >> ? ? ? ?public static void main(String args[]) { >> ? ? ? ? ? ? ? ?String id = "NM_001110.2"; ?// Issue occurs with any ID >> ? ? ? ? ? ? ? ?GenbankRichSequenceDB ?ncbi = new GenbankRichSequenceDB(); >> ? ? ? ? ? ? ? ?try { >> ? ? ? ? ? ? ? ? ? ? ? ?RichSequence rs = ncbi.getRichSequence(id); >> ? ? ? ? ? ? ? ? ? ? ? ?System.out.println(rs.seqString()); >> ? ? ? ? ? ? ? ?} catch (IllegalIDException e) { >> ? ? ? ? ? ? ? ? ? ? ? ?e.printStackTrace(); >> ? ? ? ? ? ? ? ?} catch (BioException e) { >> ? ? ? ? ? ? ? ? ? ? ? ?e.printStackTrace(); >> ? ? ? ? ? ? ? ?} >> ? ? ? ?} >> } >> >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > > -------------------------------- > George Waldon > > From gwaldon at geneinfinity.org Fri Feb 17 12:56:06 2012 From: gwaldon at geneinfinity.org (George Waldon) Date: Fri, 17 Feb 2012 11:56:06 -0600 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: References: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> Message-ID: <20120217115606.20971rxmiucjxwbo@gator1273.hostgator.com> Hi Scott, Yes, well done. You need to fix rettype too. So, if I have it correct, we should uncomment and have: rettype = "gb" retmode = "txt" and existing code should not be broken. What do you think? I can commit if you do not have a developer account. Thanks, - George Quoting Scott Frees : > George - Thanks for your response. > > I think I tracked down the problem. When building the FetchURL, > GenbankRichSequenceDB uses "genbank" as the db. In the > org.biojava.bio.seq.db.FetchURL constructor, rettype and retmode are > specifically not set when given "genbank" - see lines 54-55 commented > out. > > // rettype = format; > // retmode = format; > > Entrez recently updated their API > (http://www.ncbi.nlm.nih.gov/books/NBK25501/) on Wednesday and in the > release notes they say they've set defaults on each database for > retmode. I'm new to biojava and entrez, but I can only assume that > the "genbank" db used to return sequences as text always, which is why > FetchURL doesn't include the parameter in the URL it builds. It looks > like the default now is XML - which breaks the GenbankRichSequenceDB > parser. > > I proved it out by subclassing GenbankRichSequenceDB to set the > retmode parameter as text, and the problem is resolved. > > @Override > protected URL getAddress(String id) throws MalformedURLException { > FetchURL seqURL = new FetchURL("Genbank", "text"); > String baseurl = seqURL.getbaseURL(); > String db = seqURL.getDB(); > // added retmode=text > String url = > baseurl+db+"&id="+id+"&rettype=gb&retmode=text&tool="+getTool()+"&email="+getEmail(); > return new URL(url); > } > > I think a more elegant solution would be to simply fix FetchURL to use > the retmode parameter > > Regards - > Scott > > On Thu, Feb 16, 2012 at 8:53 PM, George Waldon > wrote: >> Hello Scott, >> >> This appears to be an exception thrown by the parser. Is-there a way you can >> fetch the sequence(s) as a text file before the exception occurs? It would >> be interesting to see if you can reproduce the exception; you can send me >> the file if you want. >> >> Regards, >> George >> >> Quoting Scott Frees : >> >>> Hello - >>> >>> I have developed an application that searches and compares >>> g-quadruplexes within mRNA.  The web application has been running >>> without any problems on several different web servers for over a year. >>>  Suddenly, just this week, it is unable to download sequence data >>> using GenbankRichSequenceDB - has anyone else has had this problem? >>> >>> We are using BioJava 1.8.1 >>> >>> Below is the exception trace, and the code that follows is a small >>> test app that generates the exception.  This code worked without any >>> problems prior to Tuesday this week, and we haven't made any >>> modification to our application. >>> ------------------------------------------------------ >>> org.biojava.bio.BioException: Failed to read Genbank sequence >>>        at >>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) >>>        at Tester.main(Tester.java:11) >>> Caused by: org.biojava.bio.BioException: Could not read sequence >>>        at >>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >>>        at >>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) >>>        ... 1 more >>> Caused by: org.biojava.bio.seq.io.ParseException: >>> >>> A Exception Has Occurred During Parsing. >>> Please submit the details that follow to biojava-l at biojava.org or post >>> a bug report to http://bugzilla.open-bio.org/ >>> >>> Format_object=org.biojavax.bio.seq.io.GenbankFormat >>> Accession=null >>> Id=null >>> Comments=Bad section >>> Parse_block= >>> Stack trace follows .... >>> >>>        at >>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) >>>        at >>> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) >>>        at >>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >>>        ... 2 more >>> Caused by: java.lang.StringIndexOutOfBoundsException: String index out >>> of range: -4 >>>        at java.lang.String.substring(Unknown Source) >>>        at java.lang.String.substring(Unknown Source) >>>        at >>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) >>>        ... 4 more >>> ----------------------------- >>> >>> >>> import org.biojava.bio.BioException; >>> import org.biojava.bio.seq.db.IllegalIDException; >>> import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; >>> import org.biojavax.bio.seq.RichSequence; >>> >>> public class Tester { >>>        public static void main(String args[]) { >>>                String id = >>> "NM_001110.2";  // Issue occurs with any ID >>>               >>>  GenbankRichSequenceDB  ncbi = new >>> GenbankRichSequenceDB(); >>>                try { >>>                   >>>      RichSequence rs = ncbi.getRichSequence(id); >>>                   >>>      System.out.println(rs.seqString()); >>>                } catch >>> (IllegalIDException e) { >>>                   >>>      e.printStackTrace(); >>>                } catch >>> (BioException e) { >>>                   >>>      e.printStackTrace(); >>>                } >>>        } >>> } >>> >>> _______________________________________________ >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >> >> >> >> -------------------------------- >> George Waldon >> >> > -------------------------------- George Waldon From sfrees at ramapo.edu Fri Feb 17 13:06:11 2012 From: sfrees at ramapo.edu (Scott Frees) Date: Fri, 17 Feb 2012 13:06:11 -0500 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: <17423_1329501371_4F3E94BB_17423_6399_1_20120217115606.20971rxmiucjxwbo@gator1273.hostgator.com> References: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> <17423_1329501371_4F3E94BB_17423_6399_1_20120217115606.20971rxmiucjxwbo@gator1273.hostgator.com> Message-ID: George - That looks right to me. I don't have a developer account, so it would be great if you could check that in. Thanks! Scott On Fri, Feb 17, 2012 at 12:56 PM, George Waldon wrote: > Hi Scott, > > Yes, well done. You need to fix rettype too. So, if I have it correct, we > should uncomment and have: > > rettype = "gb" > retmode = "txt" > > and existing code should not be broken. What do you think? I can commit if > you do not have a developer account. > > Thanks, > - George > > Quoting Scott Frees : > >> George - Thanks for your response. >> >> I think I tracked down the problem. ?When building the FetchURL, >> GenbankRichSequenceDB uses "genbank" as the db. ?In the >> org.biojava.bio.seq.db.FetchURL constructor, rettype and retmode are >> specifically not set when given "genbank" - see lines 54-55 commented >> out. >> >> ? ? ? ? ? ? ? ?// ? ? ?rettype = format; >> ? ? ? ? ? ? ? ?// ? ? ?retmode = format; >> >> Entrez recently updated their API >> (http://www.ncbi.nlm.nih.gov/books/NBK25501/) on Wednesday and in the >> release notes they say they've set defaults on each database for >> retmode. ?I'm new to biojava and entrez, but I can only assume that >> the "genbank" db used to return sequences as text always, which is why >> FetchURL doesn't include the parameter in the URL it builds. ?It looks >> like the default now is XML - which breaks the GenbankRichSequenceDB >> parser. >> >> I proved it out by subclassing GenbankRichSequenceDB to set the >> retmode parameter as text, and the problem is resolved. >> >> @Override >> protected URL getAddress(String id) throws MalformedURLException { >> ? ? ? ?FetchURL seqURL = new FetchURL("Genbank", "text"); >> ? ? ? ?String baseurl = seqURL.getbaseURL(); >> ? ? ? ?String db = seqURL.getDB(); >> ? ? ? ?// added retmode=text >> ? ? ? ?String url = >> >> baseurl+db+"&id="+id+"&rettype=gb&retmode=text&tool="+getTool()+"&email="+getEmail(); >> ? ? ? ?return new URL(url); >> } >> >> I think a more elegant solution would be to simply fix FetchURL to use >> the retmode parameter >> >> Regards - >> Scott >> >> On Thu, Feb 16, 2012 at 8:53 PM, George Waldon >> wrote: >>> >>> Hello Scott, >>> >>> This appears to be an exception thrown by the parser. Is-there a way you >>> can >>> fetch the sequence(s) as a text file before the exception occurs? It >>> would >>> be interesting to see if you can reproduce the exception; you can send me >>> the file if you want. >>> >>> Regards, >>> George >>> >>> Quoting Scott Frees : >>> >>>> Hello - >>>> >>>> I have developed an application that searches and compares >>>> g-quadruplexes within mRNA.  The web application has been running >>>> >>>> without any problems on several different web servers for over a year. >>>>  Suddenly, just this week, it is unable to download sequence data >>>> >>>> using GenbankRichSequenceDB - has anyone else has had this problem? >>>> >>>> We are using BioJava 1.8.1 >>>> >>>> Below is the exception trace, and the code that follows is a small >>>> test app that generates the exception.  This code worked without >>>> any >>>> >>>> problems prior to Tuesday this week, and we haven't made any >>>> modification to our application. >>>> ------------------------------------------------------ >>>> org.biojava.bio.BioException: Failed to read Genbank sequence >>>>        at >>>> >>>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) >>>>        at Tester.main(Tester.java:11) >>>> >>>> Caused by: org.biojava.bio.BioException: Could not read sequence >>>>        at >>>> >>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >>>>        at >>>> >>>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) >>>>        ... 1 more >>>> >>>> Caused by: org.biojava.bio.seq.io.ParseException: >>>> >>>> A Exception Has Occurred During Parsing. >>>> Please submit the details that follow to biojava-l at biojava.org or post >>>> a bug report to http://bugzilla.open-bio.org/ >>>> >>>> Format_object=org.biojavax.bio.seq.io.GenbankFormat >>>> Accession=null >>>> Id=null >>>> Comments=Bad section >>>> Parse_block= >>>> Stack trace follows .... >>>> >>>>        at >>>> >>>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) >>>>        at >>>> >>>> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) >>>>        at >>>> >>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >>>>        ... 2 more >>>> >>>> Caused by: java.lang.StringIndexOutOfBoundsException: String index out >>>> of range: -4 >>>>        at java.lang.String.substring(Unknown Source) >>>>        at java.lang.String.substring(Unknown Source) >>>>        at >>>> >>>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) >>>>        ... 4 more >>>> >>>> ----------------------------- >>>> >>>> >>>> import org.biojava.bio.BioException; >>>> import org.biojava.bio.seq.db.IllegalIDException; >>>> import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; >>>> import org.biojavax.bio.seq.RichSequence; >>>> >>>> public class Tester { >>>>        public static void main(String args[]) { >>>>                String id = >>>> "NM_001110.2";  // Issue occurs with any ID >>>>               >>>>  GenbankRichSequenceDB  ncbi = new GenbankRichSequenceDB(); >>>>                try { >>>>                     >>>>    RichSequence rs = ncbi.getRichSequence(id); >>>>                     >>>>    System.out.println(rs.seqString()); >>>>                } catch >>>> (IllegalIDException e) { >>>>                     >>>>    e.printStackTrace(); >>>>                } catch >>>> (BioException e) { >>>>                     >>>>    e.printStackTrace(); >>>>                } >>>>        } >>>> } >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>> >>> >>> >>> >>> -------------------------------- >>> George Waldon >>> >>> >> > > > > -------------------------------- > George Waldon > > From gwaldon at geneinfinity.org Sat Feb 18 20:53:24 2012 From: gwaldon at geneinfinity.org (George Waldon) Date: Sat, 18 Feb 2012 19:53:24 -0600 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: References: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> <17423_1329501371_4F3E94BB_17423_6399_1_20120217115606.20971rxmiucjxwbo@gator1273.hostgator.com> Message-ID: <20120218195324.10467cih0sgpmgi8@gator1273.hostgator.com> Hi Scott, Sorry for the delay in response. It was a little more complicated than expected and I hope the fix does not break any code around. I added a test for GenbankRichSequenceDB. Everything should be committed by now and you can check out the result on the BioJava server. Let me know if you get any problems or unexpected issues. Thank you, George Quoting Scott Frees : > George - > > That looks right to me. I don't have a developer account, so it would > be great if you could check that in. > > Thanks! > Scott > > On Fri, Feb 17, 2012 at 12:56 PM, George Waldon > wrote: >> Hi Scott, >> >> Yes, well done. You need to fix rettype too. So, if I have it correct, we >> should uncomment and have: >> >> rettype = "gb" >> retmode = "txt" >> >> and existing code should not be broken. What do you think? I can commit if >> you do not have a developer account. >> >> Thanks, >> - George >> >> Quoting Scott Frees : >> >>> George - Thanks for your response. >>> >>> I think I tracked down the problem.  When building the FetchURL, >>> GenbankRichSequenceDB uses "genbank" as the db.  In the >>> org.biojava.bio.seq.db.FetchURL constructor, rettype and retmode are >>> specifically not set when given "genbank" - see lines 54-55 commented >>> out. >>> >>>                //   >>>    rettype = format; >>>                //   >>>    retmode = format; >>> >>> Entrez recently updated their API >>> (http://www.ncbi.nlm.nih.gov/books/NBK25501/) on Wednesday and in the >>> release notes they say they've set defaults on each database for >>> retmode.  I'm new to biojava and entrez, but I can only assume that >>> the "genbank" db used to return sequences as text always, which is why >>> FetchURL doesn't include the parameter in the URL it builds.  It looks >>> like the default now is XML - which breaks the GenbankRichSequenceDB >>> parser. >>> >>> I proved it out by subclassing GenbankRichSequenceDB to set the >>> retmode parameter as text, and the problem is resolved. >>> >>> @Override >>> protected URL getAddress(String id) throws MalformedURLException { >>>        FetchURL seqURL = new >>> FetchURL("Genbank", "text"); >>>        String baseurl = seqURL.getbaseURL(); >>>        String db = seqURL.getDB(); >>>        // added retmode=text >>>        String url = >>> >>> baseurl+db+"&id="+id+"&rettype=gb&retmode=text&tool="+getTool()+"&email="+getEmail(); >>>        return new URL(url); >>> } >>> >>> I think a more elegant solution would be to simply fix FetchURL to use >>> the retmode parameter >>> >>> Regards - >>> Scott >>> >>> On Thu, Feb 16, 2012 at 8:53 PM, George Waldon >>> wrote: >>>> >>>> Hello Scott, >>>> >>>> This appears to be an exception thrown by the parser. Is-there a way you >>>> can >>>> fetch the sequence(s) as a text file before the exception occurs? It >>>> would >>>> be interesting to see if you can reproduce the exception; you can send me >>>> the file if you want. >>>> >>>> Regards, >>>> George >>>> >>>> Quoting Scott Frees : >>>> >>>>> Hello - >>>>> >>>>> I have developed an application that searches and compares >>>>> g-quadruplexes within mRNA.  The web application has been running >>>>> >>>>> without any problems on several different web servers for over a year. >>>>>  Suddenly, just this week, it is unable to download sequence data >>>>> >>>>> using GenbankRichSequenceDB - has anyone else has had this problem? >>>>> >>>>> We are using BioJava 1.8.1 >>>>> >>>>> Below is the exception trace, and the code that follows is a small >>>>> test app that generates the exception.  This code worked without >>>>> any >>>>> >>>>> problems prior to Tuesday this week, and we haven't made any >>>>> modification to our application. >>>>> ------------------------------------------------------ >>>>> org.biojava.bio.BioException: Failed to read Genbank sequence >>>>>        at >>>>> >>>>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) >>>>>        at Tester.main(Tester.java:11) >>>>> >>>>> Caused by: org.biojava.bio.BioException: Could not read sequence >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >>>>>        at >>>>> >>>>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) >>>>>        ... 1 more >>>>> >>>>> Caused by: org.biojava.bio.seq.io.ParseException: >>>>> >>>>> A Exception Has Occurred During Parsing. >>>>> Please submit the details that follow to biojava-l at biojava.org or post >>>>> a bug report to http://bugzilla.open-bio.org/ >>>>> >>>>> Format_object=org.biojavax.bio.seq.io.GenbankFormat >>>>> Accession=null >>>>> Id=null >>>>> Comments=Bad section >>>>> Parse_block= >>>>> Stack trace follows .... >>>>> >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >>>>>        ... 2 more >>>>> >>>>> Caused by: java.lang.StringIndexOutOfBoundsException: String index out >>>>> of range: -4 >>>>>        at java.lang.String.substring(Unknown Source) >>>>>        at java.lang.String.substring(Unknown Source) >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) >>>>>        ... 4 more >>>>> >>>>> ----------------------------- >>>>> >>>>> >>>>> import org.biojava.bio.BioException; >>>>> import org.biojava.bio.seq.db.IllegalIDException; >>>>> import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; >>>>> import org.biojavax.bio.seq.RichSequence; >>>>> >>>>> public class Tester { >>>>>        public static void main(String args[]) { >>>>>                String id = >>>>> "NM_001110.2";  // Issue occurs with any ID >>>>>               >>>>>  GenbankRichSequenceDB  ncbi = new GenbankRichSequenceDB(); >>>>>                try { >>>>>                     >>>>>    RichSequence rs = ncbi.getRichSequence(id); >>>>>                     >>>>>    System.out.println(rs.seqString()); >>>>>                } catch >>>>> (IllegalIDException e) { >>>>>                     >>>>>    e.printStackTrace(); >>>>>                } catch >>>>> (BioException e) { >>>>>                     >>>>>    e.printStackTrace(); >>>>>                } >>>>>        } >>>>> } >>>>> >>>>> _______________________________________________ >>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>>> >>>> >>>> >>>> >>>> -------------------------------- >>>> George Waldon >>>> >>>> >>> >> >> >> >> -------------------------------- >> George Waldon >> >> > -------------------------------- George Waldon From tariq_cp at hotmail.com Fri Feb 24 06:41:50 2012 From: tariq_cp at hotmail.com (Muhammad Tariq Pervez) Date: Fri, 24 Feb 2012 11:41:50 +0000 Subject: [Biojava-l] How to get guide tree,root MSA and lineage file Message-ID: hi all, I am working on a research project. To build simulated/true MSA through iSG2.1 is its part. But i don't how to get/build guide tree, root MSA and lineage files. These files are basic requirements of iSG for building true alignment. Guide trees are built by almost all MSA methods but i am confused what guide tree should be used for iSG and what is root MSA etc. Your help will be very beneficial for the research work. Best Regards. Muhammad Tariq Pervez Ph.D (Bioinformatics Scholar) From andreas at sdsc.edu Sat Feb 25 18:24:12 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Sat, 25 Feb 2012 15:24:12 -0800 Subject: [Biojava-l] How to get guide tree,root MSA and lineage file In-Reply-To: References: Message-ID: Hi Muhammad, not sure if you are talking about biojava... The alignment module currently does not print out this internal data, but it should be easy to add. Take a look at the GuideTree class for example. The alignment module is using the forester library for some of the calculations, wich might provide some additional utility methods which you might find useful. Andreas On Fri, Feb 24, 2012 at 3:41 AM, Muhammad Tariq Pervez wrote: > > hi all, > I am working on a research project. To build simulated/true MSA through iSG2.1 is its part. But i don't how to get/build guide tree, root MSA and lineage files. These files are basic requirements of iSG for building true alignment. Guide trees are built by almost all MSA methods but i am confused what guide tree should be used for iSG and what is root MSA etc. > Your help will be very beneficial for the research work. > > Best Regards. > > > Muhammad Tariq Pervez > > Ph.D (Bioinformatics Scholar) > > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l From jw12 at sanger.ac.uk Thu Feb 2 09:45:27 2012 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 2 Feb 2012 09:45:27 +0000 Subject: [Biojava-l] Only 10 days left to register for DAS Workshop 2012 Message-ID: <4628F603-166D-4A9B-AEB3-4696E91431CD@sanger.ac.uk> Only 10 days left to register for DAS Workshop 2012 DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Learn of and contribute to current developments in DAS such as: DAS in the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative annotation projects, DAS alternative formats. Registration is open for the 2012 DAS workshop (27-29 February) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Please register early as places will be limited. Registration closes 10 February 2012 - 12:00. If you are interested in giving a 15 minute talk on the second day please email Jonathan Warren using jonathan.warren at sanger.ac.uk Many thanks The Sanger/EBI DAS team. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From andreas at sdsc.edu Tue Feb 7 06:55:29 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Mon, 6 Feb 2012 22:55:29 -0800 Subject: [Biojava-l] Google Summer of Code 2012 Message-ID: Hi, This is an early heads-up that Google has announced that there will be another Summer of Code this year [1][2]. We will try to participate again from the side of BioJava. Around March 16th we should know if we have been accepted as an organisation, after which we can start discussing student proposals. In the meanwhile would-be students are invited to start thinking about potential projects. Here a couple of dates: ? February 27 ? March 9: Google will accept applications from open source projects. ? March 12 ? 15: Google program administrators review organization applications. ? March 16: List of accepted mentoring organizations published on http://www.google-melange.com ? March 17-25: Would-be student participants discuss application/project ideas with mentoring organizations. ? March 26-April 6: Student application period ? April 23: Accepted student proposals announced at http://www.google-melange.com ? May 21: Students begin coding Andreas more infos: [1] - http://google-opensource.blogspot.com/2012/02/google-summer-of-code-2012-is-on.html [2] - http://code.google.com/p/google-summer-of-code/wiki/ProgramPresentations From sfrees at ramapo.edu Thu Feb 16 14:24:56 2012 From: sfrees at ramapo.edu (Scott Frees) Date: Thu, 16 Feb 2012 09:24:56 -0500 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB Message-ID: Hello ? I have developed an application that searches and compares g-quadruplexes within mRNA. The web application has been running without any problems on several different web servers for over a year. Suddenly, just this week, it is unable to download sequence data using GenbankRichSequenceDB ? has anyone else has had this problem? We are using BioJava 1.8.1 Below is the exception trace, and the code that follows is a small test app that generates the exception. This code worked without any problems prior to Tuesday this week, and we haven't made any modification to our application. ------------------------------------------------------ org.biojava.bio.BioException: Failed to read Genbank sequence at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) at Tester.main(Tester.java:11) Caused by: org.biojava.bio.BioException: Could not read sequence at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) ... 1 more Caused by: org.biojava.bio.seq.io.ParseException: A Exception Has Occurred During Parsing. Please submit the details that follow to biojava-l at biojava.org or post a bug report to http://bugzilla.open-bio.org/ Format_object=org.biojavax.bio.seq.io.GenbankFormat Accession=null Id=null Comments=Bad section Parse_block= Stack trace follows .... at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ... 2 more Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: -4 at java.lang.String.substring(Unknown Source) at java.lang.String.substring(Unknown Source) at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) ... 4 more ----------------------------- import org.biojava.bio.BioException; import org.biojava.bio.seq.db.IllegalIDException; import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; import org.biojavax.bio.seq.RichSequence; public class Tester { public static void main(String args[]) { String id = "NM_001110.2"; // Issue occurs with any ID GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); try { RichSequence rs = ncbi.getRichSequence(id); System.out.println(rs.seqString()); } catch (IllegalIDException e) { e.printStackTrace(); } catch (BioException e) { e.printStackTrace(); } } } From gwaldon at geneinfinity.org Fri Feb 17 01:53:36 2012 From: gwaldon at geneinfinity.org (George Waldon) Date: Thu, 16 Feb 2012 19:53:36 -0600 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: References: Message-ID: <20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> Hello Scott, This appears to be an exception thrown by the parser. Is-there a way you can fetch the sequence(s) as a text file before the exception occurs? It would be interesting to see if you can reproduce the exception; you can send me the file if you want. Regards, George Quoting Scott Frees : > Hello - > > I have developed an application that searches and compares > g-quadruplexes within mRNA. The web application has been running > without any problems on several different web servers for over a year. > Suddenly, just this week, it is unable to download sequence data > using GenbankRichSequenceDB - has anyone else has had this problem? > > We are using BioJava 1.8.1 > > Below is the exception trace, and the code that follows is a small > test app that generates the exception. This code worked without any > problems prior to Tuesday this week, and we haven't made any > modification to our application. > ------------------------------------------------------ > org.biojava.bio.BioException: Failed to read Genbank sequence > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) > at Tester.main(Tester.java:11) > Caused by: org.biojava.bio.BioException: Could not read sequence > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) > at > org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) > ... 1 more > Caused by: org.biojava.bio.seq.io.ParseException: > > A Exception Has Occurred During Parsing. > Please submit the details that follow to biojava-l at biojava.org or post > a bug report to http://bugzilla.open-bio.org/ > > Format_object=org.biojavax.bio.seq.io.GenbankFormat > Accession=null > Id=null > Comments=Bad section > Parse_block= > Stack trace follows .... > > at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) > at > org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) > at > org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) > ... 2 more > Caused by: java.lang.StringIndexOutOfBoundsException: String index out > of range: -4 > at java.lang.String.substring(Unknown Source) > at java.lang.String.substring(Unknown Source) > at org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) > ... 4 more > ----------------------------- > > > import org.biojava.bio.BioException; > import org.biojava.bio.seq.db.IllegalIDException; > import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; > import org.biojavax.bio.seq.RichSequence; > > public class Tester { > public static void main(String args[]) { > String id = "NM_001110.2"; // Issue occurs with any ID > GenbankRichSequenceDB ncbi = new GenbankRichSequenceDB(); > try { > RichSequence rs = ncbi.getRichSequence(id); > System.out.println(rs.seqString()); > } catch (IllegalIDException e) { > e.printStackTrace(); > } catch (BioException e) { > e.printStackTrace(); > } > } > } > > _______________________________________________ > Biojava-l mailing list - Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -------------------------------- George Waldon From sfrees at ramapo.edu Fri Feb 17 03:25:03 2012 From: sfrees at ramapo.edu (Scott Frees) Date: Thu, 16 Feb 2012 22:25:03 -0500 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> References: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> Message-ID: George - Thanks for your response. I think I tracked down the problem. When building the FetchURL, GenbankRichSequenceDB uses "genbank" as the db. In the org.biojava.bio.seq.db.FetchURL constructor, rettype and retmode are specifically not set when given "genbank" - see lines 54-55 commented out. // rettype = format; // retmode = format; Entrez recently updated their API (http://www.ncbi.nlm.nih.gov/books/NBK25501/) on Wednesday and in the release notes they say they've set defaults on each database for retmode. I'm new to biojava and entrez, but I can only assume that the "genbank" db used to return sequences as text always, which is why FetchURL doesn't include the parameter in the URL it builds. It looks like the default now is XML - which breaks the GenbankRichSequenceDB parser. I proved it out by subclassing GenbankRichSequenceDB to set the retmode parameter as text, and the problem is resolved. @Override protected URL getAddress(String id) throws MalformedURLException { FetchURL seqURL = new FetchURL("Genbank", "text"); String baseurl = seqURL.getbaseURL(); String db = seqURL.getDB(); // added retmode=text String url = baseurl+db+"&id="+id+"&rettype=gb&retmode=text&tool="+getTool()+"&email="+getEmail(); return new URL(url); } I think a more elegant solution would be to simply fix FetchURL to use the retmode parameter Regards - Scott On Thu, Feb 16, 2012 at 8:53 PM, George Waldon wrote: > Hello Scott, > > This appears to be an exception thrown by the parser. Is-there a way you can > fetch the sequence(s) as a text file before the exception occurs? It would > be interesting to see if you can reproduce the exception; you can send me > the file if you want. > > Regards, > George > > Quoting Scott Frees : > >> Hello - >> >> I have developed an application that searches and compares >> g-quadruplexes within mRNA. ?The web application has been running >> without any problems on several different web servers for over a year. >> ?Suddenly, just this week, it is unable to download sequence data >> using GenbankRichSequenceDB - has anyone else has had this problem? >> >> We are using BioJava 1.8.1 >> >> Below is the exception trace, and the code that follows is a small >> test app that generates the exception. ?This code worked without any >> problems prior to Tuesday this week, and we haven't made any >> modification to our application. >> ------------------------------------------------------ >> org.biojava.bio.BioException: Failed to read Genbank sequence >> ? ? ? ?at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) >> ? ? ? ?at Tester.main(Tester.java:11) >> Caused by: org.biojava.bio.BioException: Could not read sequence >> ? ? ? ?at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >> ? ? ? ?at >> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) >> ? ? ? ?... 1 more >> Caused by: org.biojava.bio.seq.io.ParseException: >> >> A Exception Has Occurred During Parsing. >> Please submit the details that follow to biojava-l at biojava.org or post >> a bug report to http://bugzilla.open-bio.org/ >> >> Format_object=org.biojavax.bio.seq.io.GenbankFormat >> Accession=null >> Id=null >> Comments=Bad section >> Parse_block= >> Stack trace follows .... >> >> ? ? ? ?at >> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) >> ? ? ? ?at >> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) >> ? ? ? ?at >> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >> ? ? ? ?... 2 more >> Caused by: java.lang.StringIndexOutOfBoundsException: String index out >> of range: -4 >> ? ? ? ?at java.lang.String.substring(Unknown Source) >> ? ? ? ?at java.lang.String.substring(Unknown Source) >> ? ? ? ?at >> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) >> ? ? ? ?... 4 more >> ----------------------------- >> >> >> import org.biojava.bio.BioException; >> import org.biojava.bio.seq.db.IllegalIDException; >> import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; >> import org.biojavax.bio.seq.RichSequence; >> >> public class Tester { >> ? ? ? ?public static void main(String args[]) { >> ? ? ? ? ? ? ? ?String id = "NM_001110.2"; ?// Issue occurs with any ID >> ? ? ? ? ? ? ? ?GenbankRichSequenceDB ?ncbi = new GenbankRichSequenceDB(); >> ? ? ? ? ? ? ? ?try { >> ? ? ? ? ? ? ? ? ? ? ? ?RichSequence rs = ncbi.getRichSequence(id); >> ? ? ? ? ? ? ? ? ? ? ? ?System.out.println(rs.seqString()); >> ? ? ? ? ? ? ? ?} catch (IllegalIDException e) { >> ? ? ? ? ? ? ? ? ? ? ? ?e.printStackTrace(); >> ? ? ? ? ? ? ? ?} catch (BioException e) { >> ? ? ? ? ? ? ? ? ? ? ? ?e.printStackTrace(); >> ? ? ? ? ? ? ? ?} >> ? ? ? ?} >> } >> >> _______________________________________________ >> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > > > -------------------------------- > George Waldon > > From gwaldon at geneinfinity.org Fri Feb 17 17:56:06 2012 From: gwaldon at geneinfinity.org (George Waldon) Date: Fri, 17 Feb 2012 11:56:06 -0600 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: References: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> Message-ID: <20120217115606.20971rxmiucjxwbo@gator1273.hostgator.com> Hi Scott, Yes, well done. You need to fix rettype too. So, if I have it correct, we should uncomment and have: rettype = "gb" retmode = "txt" and existing code should not be broken. What do you think? I can commit if you do not have a developer account. Thanks, - George Quoting Scott Frees : > George - Thanks for your response. > > I think I tracked down the problem. When building the FetchURL, > GenbankRichSequenceDB uses "genbank" as the db. In the > org.biojava.bio.seq.db.FetchURL constructor, rettype and retmode are > specifically not set when given "genbank" - see lines 54-55 commented > out. > > // rettype = format; > // retmode = format; > > Entrez recently updated their API > (http://www.ncbi.nlm.nih.gov/books/NBK25501/) on Wednesday and in the > release notes they say they've set defaults on each database for > retmode. I'm new to biojava and entrez, but I can only assume that > the "genbank" db used to return sequences as text always, which is why > FetchURL doesn't include the parameter in the URL it builds. It looks > like the default now is XML - which breaks the GenbankRichSequenceDB > parser. > > I proved it out by subclassing GenbankRichSequenceDB to set the > retmode parameter as text, and the problem is resolved. > > @Override > protected URL getAddress(String id) throws MalformedURLException { > FetchURL seqURL = new FetchURL("Genbank", "text"); > String baseurl = seqURL.getbaseURL(); > String db = seqURL.getDB(); > // added retmode=text > String url = > baseurl+db+"&id="+id+"&rettype=gb&retmode=text&tool="+getTool()+"&email="+getEmail(); > return new URL(url); > } > > I think a more elegant solution would be to simply fix FetchURL to use > the retmode parameter > > Regards - > Scott > > On Thu, Feb 16, 2012 at 8:53 PM, George Waldon > wrote: >> Hello Scott, >> >> This appears to be an exception thrown by the parser. Is-there a way you can >> fetch the sequence(s) as a text file before the exception occurs? It would >> be interesting to see if you can reproduce the exception; you can send me >> the file if you want. >> >> Regards, >> George >> >> Quoting Scott Frees : >> >>> Hello - >>> >>> I have developed an application that searches and compares >>> g-quadruplexes within mRNA.  The web application has been running >>> without any problems on several different web servers for over a year. >>>  Suddenly, just this week, it is unable to download sequence data >>> using GenbankRichSequenceDB - has anyone else has had this problem? >>> >>> We are using BioJava 1.8.1 >>> >>> Below is the exception trace, and the code that follows is a small >>> test app that generates the exception.  This code worked without any >>> problems prior to Tuesday this week, and we haven't made any >>> modification to our application. >>> ------------------------------------------------------ >>> org.biojava.bio.BioException: Failed to read Genbank sequence >>>        at >>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) >>>        at Tester.main(Tester.java:11) >>> Caused by: org.biojava.bio.BioException: Could not read sequence >>>        at >>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >>>        at >>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) >>>        ... 1 more >>> Caused by: org.biojava.bio.seq.io.ParseException: >>> >>> A Exception Has Occurred During Parsing. >>> Please submit the details that follow to biojava-l at biojava.org or post >>> a bug report to http://bugzilla.open-bio.org/ >>> >>> Format_object=org.biojavax.bio.seq.io.GenbankFormat >>> Accession=null >>> Id=null >>> Comments=Bad section >>> Parse_block= >>> Stack trace follows .... >>> >>>        at >>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) >>>        at >>> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) >>>        at >>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >>>        ... 2 more >>> Caused by: java.lang.StringIndexOutOfBoundsException: String index out >>> of range: -4 >>>        at java.lang.String.substring(Unknown Source) >>>        at java.lang.String.substring(Unknown Source) >>>        at >>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) >>>        ... 4 more >>> ----------------------------- >>> >>> >>> import org.biojava.bio.BioException; >>> import org.biojava.bio.seq.db.IllegalIDException; >>> import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; >>> import org.biojavax.bio.seq.RichSequence; >>> >>> public class Tester { >>>        public static void main(String args[]) { >>>                String id = >>> "NM_001110.2";  // Issue occurs with any ID >>>               >>>  GenbankRichSequenceDB  ncbi = new >>> GenbankRichSequenceDB(); >>>                try { >>>                   >>>      RichSequence rs = ncbi.getRichSequence(id); >>>                   >>>      System.out.println(rs.seqString()); >>>                } catch >>> (IllegalIDException e) { >>>                   >>>      e.printStackTrace(); >>>                } catch >>> (BioException e) { >>>                   >>>      e.printStackTrace(); >>>                } >>>        } >>> } >>> >>> _______________________________________________ >>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >> >> >> >> -------------------------------- >> George Waldon >> >> > -------------------------------- George Waldon From sfrees at ramapo.edu Fri Feb 17 18:06:11 2012 From: sfrees at ramapo.edu (Scott Frees) Date: Fri, 17 Feb 2012 13:06:11 -0500 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: <17423_1329501371_4F3E94BB_17423_6399_1_20120217115606.20971rxmiucjxwbo@gator1273.hostgator.com> References: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> <17423_1329501371_4F3E94BB_17423_6399_1_20120217115606.20971rxmiucjxwbo@gator1273.hostgator.com> Message-ID: George - That looks right to me. I don't have a developer account, so it would be great if you could check that in. Thanks! Scott On Fri, Feb 17, 2012 at 12:56 PM, George Waldon wrote: > Hi Scott, > > Yes, well done. You need to fix rettype too. So, if I have it correct, we > should uncomment and have: > > rettype = "gb" > retmode = "txt" > > and existing code should not be broken. What do you think? I can commit if > you do not have a developer account. > > Thanks, > - George > > Quoting Scott Frees : > >> George - Thanks for your response. >> >> I think I tracked down the problem. ?When building the FetchURL, >> GenbankRichSequenceDB uses "genbank" as the db. ?In the >> org.biojava.bio.seq.db.FetchURL constructor, rettype and retmode are >> specifically not set when given "genbank" - see lines 54-55 commented >> out. >> >> ? ? ? ? ? ? ? ?// ? ? ?rettype = format; >> ? ? ? ? ? ? ? ?// ? ? ?retmode = format; >> >> Entrez recently updated their API >> (http://www.ncbi.nlm.nih.gov/books/NBK25501/) on Wednesday and in the >> release notes they say they've set defaults on each database for >> retmode. ?I'm new to biojava and entrez, but I can only assume that >> the "genbank" db used to return sequences as text always, which is why >> FetchURL doesn't include the parameter in the URL it builds. ?It looks >> like the default now is XML - which breaks the GenbankRichSequenceDB >> parser. >> >> I proved it out by subclassing GenbankRichSequenceDB to set the >> retmode parameter as text, and the problem is resolved. >> >> @Override >> protected URL getAddress(String id) throws MalformedURLException { >> ? ? ? ?FetchURL seqURL = new FetchURL("Genbank", "text"); >> ? ? ? ?String baseurl = seqURL.getbaseURL(); >> ? ? ? ?String db = seqURL.getDB(); >> ? ? ? ?// added retmode=text >> ? ? ? ?String url = >> >> baseurl+db+"&id="+id+"&rettype=gb&retmode=text&tool="+getTool()+"&email="+getEmail(); >> ? ? ? ?return new URL(url); >> } >> >> I think a more elegant solution would be to simply fix FetchURL to use >> the retmode parameter >> >> Regards - >> Scott >> >> On Thu, Feb 16, 2012 at 8:53 PM, George Waldon >> wrote: >>> >>> Hello Scott, >>> >>> This appears to be an exception thrown by the parser. Is-there a way you >>> can >>> fetch the sequence(s) as a text file before the exception occurs? It >>> would >>> be interesting to see if you can reproduce the exception; you can send me >>> the file if you want. >>> >>> Regards, >>> George >>> >>> Quoting Scott Frees : >>> >>>> Hello - >>>> >>>> I have developed an application that searches and compares >>>> g-quadruplexes within mRNA.  The web application has been running >>>> >>>> without any problems on several different web servers for over a year. >>>>  Suddenly, just this week, it is unable to download sequence data >>>> >>>> using GenbankRichSequenceDB - has anyone else has had this problem? >>>> >>>> We are using BioJava 1.8.1 >>>> >>>> Below is the exception trace, and the code that follows is a small >>>> test app that generates the exception.  This code worked without >>>> any >>>> >>>> problems prior to Tuesday this week, and we haven't made any >>>> modification to our application. >>>> ------------------------------------------------------ >>>> org.biojava.bio.BioException: Failed to read Genbank sequence >>>>        at >>>> >>>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) >>>>        at Tester.main(Tester.java:11) >>>> >>>> Caused by: org.biojava.bio.BioException: Could not read sequence >>>>        at >>>> >>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >>>>        at >>>> >>>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) >>>>        ... 1 more >>>> >>>> Caused by: org.biojava.bio.seq.io.ParseException: >>>> >>>> A Exception Has Occurred During Parsing. >>>> Please submit the details that follow to biojava-l at biojava.org or post >>>> a bug report to http://bugzilla.open-bio.org/ >>>> >>>> Format_object=org.biojavax.bio.seq.io.GenbankFormat >>>> Accession=null >>>> Id=null >>>> Comments=Bad section >>>> Parse_block= >>>> Stack trace follows .... >>>> >>>>        at >>>> >>>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) >>>>        at >>>> >>>> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) >>>>        at >>>> >>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >>>>        ... 2 more >>>> >>>> Caused by: java.lang.StringIndexOutOfBoundsException: String index out >>>> of range: -4 >>>>        at java.lang.String.substring(Unknown Source) >>>>        at java.lang.String.substring(Unknown Source) >>>>        at >>>> >>>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) >>>>        ... 4 more >>>> >>>> ----------------------------- >>>> >>>> >>>> import org.biojava.bio.BioException; >>>> import org.biojava.bio.seq.db.IllegalIDException; >>>> import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; >>>> import org.biojavax.bio.seq.RichSequence; >>>> >>>> public class Tester { >>>>        public static void main(String args[]) { >>>>                String id = >>>> "NM_001110.2";  // Issue occurs with any ID >>>>               >>>>  GenbankRichSequenceDB  ncbi = new GenbankRichSequenceDB(); >>>>                try { >>>>                     >>>>    RichSequence rs = ncbi.getRichSequence(id); >>>>                     >>>>    System.out.println(rs.seqString()); >>>>                } catch >>>> (IllegalIDException e) { >>>>                     >>>>    e.printStackTrace(); >>>>                } catch >>>> (BioException e) { >>>>                     >>>>    e.printStackTrace(); >>>>                } >>>>        } >>>> } >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>> >>> >>> >>> >>> -------------------------------- >>> George Waldon >>> >>> >> > > > > -------------------------------- > George Waldon > > From gwaldon at geneinfinity.org Sun Feb 19 01:53:24 2012 From: gwaldon at geneinfinity.org (George Waldon) Date: Sat, 18 Feb 2012 19:53:24 -0600 Subject: [Biojava-l] Parsing exception reading sequence from GenbankRichSequenceDB In-Reply-To: References: <18730_1329443619_4F3DB323_18730_19664_1_20120216195336.67932oqcucuicv8k@gator1273.hostgator.com> <17423_1329501371_4F3E94BB_17423_6399_1_20120217115606.20971rxmiucjxwbo@gator1273.hostgator.com> Message-ID: <20120218195324.10467cih0sgpmgi8@gator1273.hostgator.com> Hi Scott, Sorry for the delay in response. It was a little more complicated than expected and I hope the fix does not break any code around. I added a test for GenbankRichSequenceDB. Everything should be committed by now and you can check out the result on the BioJava server. Let me know if you get any problems or unexpected issues. Thank you, George Quoting Scott Frees : > George - > > That looks right to me. I don't have a developer account, so it would > be great if you could check that in. > > Thanks! > Scott > > On Fri, Feb 17, 2012 at 12:56 PM, George Waldon > wrote: >> Hi Scott, >> >> Yes, well done. You need to fix rettype too. So, if I have it correct, we >> should uncomment and have: >> >> rettype = "gb" >> retmode = "txt" >> >> and existing code should not be broken. What do you think? I can commit if >> you do not have a developer account. >> >> Thanks, >> - George >> >> Quoting Scott Frees : >> >>> George - Thanks for your response. >>> >>> I think I tracked down the problem.  When building the FetchURL, >>> GenbankRichSequenceDB uses "genbank" as the db.  In the >>> org.biojava.bio.seq.db.FetchURL constructor, rettype and retmode are >>> specifically not set when given "genbank" - see lines 54-55 commented >>> out. >>> >>>                //   >>>    rettype = format; >>>                //   >>>    retmode = format; >>> >>> Entrez recently updated their API >>> (http://www.ncbi.nlm.nih.gov/books/NBK25501/) on Wednesday and in the >>> release notes they say they've set defaults on each database for >>> retmode.  I'm new to biojava and entrez, but I can only assume that >>> the "genbank" db used to return sequences as text always, which is why >>> FetchURL doesn't include the parameter in the URL it builds.  It looks >>> like the default now is XML - which breaks the GenbankRichSequenceDB >>> parser. >>> >>> I proved it out by subclassing GenbankRichSequenceDB to set the >>> retmode parameter as text, and the problem is resolved. >>> >>> @Override >>> protected URL getAddress(String id) throws MalformedURLException { >>>        FetchURL seqURL = new >>> FetchURL("Genbank", "text"); >>>        String baseurl = seqURL.getbaseURL(); >>>        String db = seqURL.getDB(); >>>        // added retmode=text >>>        String url = >>> >>> baseurl+db+"&id="+id+"&rettype=gb&retmode=text&tool="+getTool()+"&email="+getEmail(); >>>        return new URL(url); >>> } >>> >>> I think a more elegant solution would be to simply fix FetchURL to use >>> the retmode parameter >>> >>> Regards - >>> Scott >>> >>> On Thu, Feb 16, 2012 at 8:53 PM, George Waldon >>> wrote: >>>> >>>> Hello Scott, >>>> >>>> This appears to be an exception thrown by the parser. Is-there a way you >>>> can >>>> fetch the sequence(s) as a text file before the exception occurs? It >>>> would >>>> be interesting to see if you can reproduce the exception; you can send me >>>> the file if you want. >>>> >>>> Regards, >>>> George >>>> >>>> Quoting Scott Frees : >>>> >>>>> Hello - >>>>> >>>>> I have developed an application that searches and compares >>>>> g-quadruplexes within mRNA.  The web application has been running >>>>> >>>>> without any problems on several different web servers for over a year. >>>>>  Suddenly, just this week, it is unable to download sequence data >>>>> >>>>> using GenbankRichSequenceDB - has anyone else has had this problem? >>>>> >>>>> We are using BioJava 1.8.1 >>>>> >>>>> Below is the exception trace, and the code that follows is a small >>>>> test app that generates the exception.  This code worked without >>>>> any >>>>> >>>>> problems prior to Tuesday this week, and we haven't made any >>>>> modification to our application. >>>>> ------------------------------------------------------ >>>>> org.biojava.bio.BioException: Failed to read Genbank sequence >>>>>        at >>>>> >>>>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:163) >>>>>        at Tester.main(Tester.java:11) >>>>> >>>>> Caused by: org.biojava.bio.BioException: Could not read sequence >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113) >>>>>        at >>>>> >>>>> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:159) >>>>>        ... 1 more >>>>> >>>>> Caused by: org.biojava.bio.seq.io.ParseException: >>>>> >>>>> A Exception Has Occurred During Parsing. >>>>> Please submit the details that follow to biojava-l at biojava.org or post >>>>> a bug report to http://bugzilla.open-bio.org/ >>>>> >>>>> Format_object=org.biojavax.bio.seq.io.GenbankFormat >>>>> Accession=null >>>>> Id=null >>>>> Comments=Bad section >>>>> Parse_block= >>>>> Stack trace follows .... >>>>> >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:620) >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:279) >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) >>>>>        ... 2 more >>>>> >>>>> Caused by: java.lang.StringIndexOutOfBoundsException: String index out >>>>> of range: -4 >>>>>        at java.lang.String.substring(Unknown Source) >>>>>        at java.lang.String.substring(Unknown Source) >>>>>        at >>>>> >>>>> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:610) >>>>>        ... 4 more >>>>> >>>>> ----------------------------- >>>>> >>>>> >>>>> import org.biojava.bio.BioException; >>>>> import org.biojava.bio.seq.db.IllegalIDException; >>>>> import org.biojavax.bio.db.ncbi.GenbankRichSequenceDB; >>>>> import org.biojavax.bio.seq.RichSequence; >>>>> >>>>> public class Tester { >>>>>        public static void main(String args[]) { >>>>>                String id = >>>>> "NM_001110.2";  // Issue occurs with any ID >>>>>               >>>>>  GenbankRichSequenceDB  ncbi = new GenbankRichSequenceDB(); >>>>>                try { >>>>>                     >>>>>    RichSequence rs = ncbi.getRichSequence(id); >>>>>                     >>>>>    System.out.println(rs.seqString()); >>>>>                } catch >>>>> (IllegalIDException e) { >>>>>                     >>>>>    e.printStackTrace(); >>>>>                } catch >>>>> (BioException e) { >>>>>                     >>>>>    e.printStackTrace(); >>>>>                } >>>>>        } >>>>> } >>>>> >>>>> _______________________________________________ >>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>>>> >>>> >>>> >>>> >>>> -------------------------------- >>>> George Waldon >>>> >>>> >>> >> >> >> >> -------------------------------- >> George Waldon >> >> > -------------------------------- George Waldon From tariq_cp at hotmail.com Fri Feb 24 11:41:50 2012 From: tariq_cp at hotmail.com (Muhammad Tariq Pervez) Date: Fri, 24 Feb 2012 11:41:50 +0000 Subject: [Biojava-l] How to get guide tree,root MSA and lineage file Message-ID: hi all, I am working on a research project. To build simulated/true MSA through iSG2.1 is its part. But i don't how to get/build guide tree, root MSA and lineage files. These files are basic requirements of iSG for building true alignment. Guide trees are built by almost all MSA methods but i am confused what guide tree should be used for iSG and what is root MSA etc. Your help will be very beneficial for the research work. Best Regards. Muhammad Tariq Pervez Ph.D (Bioinformatics Scholar) From andreas at sdsc.edu Sat Feb 25 23:24:12 2012 From: andreas at sdsc.edu (Andreas Prlic) Date: Sat, 25 Feb 2012 15:24:12 -0800 Subject: [Biojava-l] How to get guide tree,root MSA and lineage file In-Reply-To: References: Message-ID: Hi Muhammad, not sure if you are talking about biojava... The alignment module currently does not print out this internal data, but it should be easy to add. Take a look at the GuideTree class for example. The alignment module is using the forester library for some of the calculations, wich might provide some additional utility methods which you might find useful. Andreas On Fri, Feb 24, 2012 at 3:41 AM, Muhammad Tariq Pervez wrote: > > hi all, > I am working on a research project. To build simulated/true MSA through iSG2.1 is its part. But i don't how to get/build guide tree, root MSA and lineage files. These files are basic requirements of iSG for building true alignment. Guide trees are built by almost all MSA methods but i am confused what guide tree should be used for iSG and what is root MSA etc. > Your help will be very beneficial for the research work. > > Best Regards. > > > Muhammad Tariq Pervez > > Ph.D (Bioinformatics Scholar) > > _______________________________________________ > Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l