From ayates at ebi.ac.uk  Mon Jan  4 04:47:58 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 4 Jan 2010 09:47:58 +0000
Subject: [Biojava-dev] biojava hackathon
In-Reply-To: <59a41c430912210820p59ae6b46wa239ae78328098d8@mail.gmail.com>
References: <dd8886300912210723r2b22847dq48db52e14fcb1a0a@mail.gmail.com>
	<59a41c430912210820p59ae6b46wa239ae78328098d8@mail.gmail.com>
Message-ID: <31FC6A52-DE16-47B1-86E7-D5C49EA6C6FA@ebi.ac.uk>

Other hotels available near the campus are:

http://www.redlionhinxton.co.uk/ (the nearest non WT owned  
accommodation)

http://www.johnbarleycorn.co.uk/ (in the next village along)

http://www.duxfordlodgehotel.co.uk/ (see above)

http://www.wtconference.org/ (owned by WT & sometimes will offer  
accommodation)

However one problem with all of these are the costs involved; if you  
can get into the Travelodge Andreas mentioned it's normally quite a  
bit cheaper but do check carefully. Spending ?5 more per night to get  
into one of the other places can be worth it.

Andy

On 21 Dec 2009, at 16:20, Andreas Prlic wrote:

> A few people asked me where to stay and I suggested to book the
> Travelodge in Hills road. It is a plain and cheap hotel (for
> Cambridge), walking distance to the train station, town center (20
> min) and close to one of the stops of the Genome Campus bus routes.
>
> Andreas
>
> On Mon, Dec 21, 2009 at 7:23 AM, Johan Henriksson  
> <mahogny at areta.org> wrote:
>> Hello,
>> has anyone done their homework and figured out which hotels are the  
>> best.
>> maybe someone working there knows the "standard" ones?
>>
>> it seems I can join in. have not decided exactly what I will work  
>> on but
>> surely not the protein stuff. either improving the core or the
>> algorithms/data structures. I have experimented a bit with  
>> alternative ways
>> of dealing with annotation and sequence data, maybe it can be of use.
>>
>> /Johan
>>
>> --
>> -----------------------------------------------------------
>> Johan Henriksson
>> PhD student, Karolinska Institutet
>> http://mahogny.areta.org  http://www.endrov.net
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev



From holland at eaglegenomics.com  Mon Jan  4 05:57:54 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 4 Jan 2010 10:57:54 +0000
Subject: [Biojava-dev] BioJava 2010 Hackathon
Message-ID: <E304F7F2-09B7-4C46-92F9-F9CA6E68C5EC@eaglegenomics.com>

Hi all,

For those attending the 2010 BioJava hackathon at the Wellcome Trust Genome Campus, near Cambridge, all details can be found on this wiki:

  http://biojava.org/wiki/BioJava:Hackathon2010

If your name is not listed on the wiki but you are planning on attending, please let us know by Jan 12th latest. Due to security arrangements at the campus it is not possible to just turn up on the day.

Subjects for the hackathon are open for discussion on the wiki.

Looking forward to seeing you all there!

cheers,
Richard

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From jolyon.holdstock at ogt.co.uk  Wed Jan 13 07:49:17 2010
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Wed, 13 Jan 2010 12:49:17 -0000
Subject: [Biojava-dev] Script for cookbook
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F02C64D8C@EUCLID.internal.ogtip.com>

Hi,

 

I was going to add the following script to the annotation section of the
cookbook. 

It takes an EMBL or Genbank file and outputs information about each CDS
feature.

 

I just wanted to check this was OK and also is this the most efficient
way of doing this?

 

Cheers,

 

Jolyon

 

[CODE]

import java.io.*;

import java.util.*;

import org.biojava.bio.*;

import org.biojava.bio.seq.*;

import org.biojava.bio.seq.io.*;

import org.biojavax.*;

import org.biojavax.ontology.*;

import org.biojavax.bio.*;

import org.biojavax.bio.seq.*;

 

public class ExtractInformation {

  //Create the RichSequence object

  RichSequence richSeq;

  public ExtractInformation(String fileName){

    //Load the sequence file

    try {

      richSeq = RichSequence.IOTools.readGenbankDNA(new
BufferedReader(new FileReader(fileName)),null).nextRichSequence();

    }

    catch(FileNotFoundException fnfe){

      System.out.println("FilwNotFoundException: " + fnfe);

    }

    catch(BioException bioe1){

      System.err.println("Not a Genbank sequence trying EMBL");

      try  {

        richSeq = RichSequence.IOTools.readGenbankDNA(new
BufferedReader(new FileReader(fileName)),null).nextRichSequence();

      }

      catch(BioException bioe2){

        System.err.println("Not an EMBL sequence either");

        System.exit(1);

      }

      catch(FileNotFoundException fnfe){

        System.out.println("FilwNotFoundException: " + fnfe);

      }

    }

    //Filter the sequence on CDS features

    FeatureFilter ff = new FeatureFilter.ByType("CDS");

    FeatureHolder fh = richSeq.filter(ff);

 

    //Iterate through the CDS features

    for (Iterator <RichFeature> i = fh.features(); i.hasNext();){

      RichFeature rf = i.next();

      

      //Get the strand orientation of the feature

      char featureStrand = rf.getStrand().getToken();

 

      //Get the location of the feature

      String featureLocation = rf.getLocation().toString();

      

      //Get the annotation of the feature

      RichAnnotation ra = (RichAnnotation)rf.getAnnotation();

 

      //Create the required ComparableTerms

      ComparableTerm geneTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");

      ComparableTerm locusTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("locus_tag");

      ComparableTerm productTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("product");

      ComparableTerm synonymTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene_synonym");

      ComparableTerm proteinIDTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("protein_id");

      

      //Create empty strings

      String gene = "";

      String locus = "";

      String product = "";

      String geneSynonym = "";

      String proteinID = "";

 

      //Iterate through the notes in the annotation 

      for (Iterator <Note> it = ra.getNoteSet().iterator();
it.hasNext();){

        Note note = it.next();

      

      //Check each note to see if it matches one of the required
ComparableTerms

        if(note.getTerm().equals(locusTerm)){

          locus = note.getValue().toString();

        }

        if(note.getTerm().equals(productTerm)){

          product = note.getValue().toString();

        }

        if(note.getTerm().equals(geneTerm)){

          gene = note.getValue().toString();

        }

        if(note.getTerm().equals(synonymTerm)){

          geneSynonym = note.getValue().toString();

        }

        if(note.getTerm().equals(proteinIDTerm)){

          proteinID = note.getValue().toString();

        }

      }

      //Outout the feature information

      System.out.println(locus + "  " + gene + "  " + geneSynonym + "  "
+ proteinID + "  " + product +"  " + featureStrand +"  Chr1:" +
featureLocation);

    }

  }

 

  public static void main(String args []){

    if (args.length != 1){

      System.out.println("Usage: java ExtractInformation <file in
Genbank or EMBL format>");

      System.exit(1);

    }

    else {

      new ExtractInformation(args[0]);

    }

  }

}

[/CODE]

 

Dr. Jolyon Holdstock                                       
Senior Computational Biologist,

Oxford Gene Technology,                                   
Begbroke Science Park,                                     
Sandy Lane, Yarnton,                                           
Oxford, OX5 1PF, UK.                                             

T: +44 (0)1865 856 852                                     
F: +44 (0)1865 842 116                                     
E: jolyon.holdstock at ogt.co.uk <mailto:nicola.booton-mander at ogt.co.uk>

W: www.ogt.co.uk <blocked::http://www.ogt.co.uk/>     

                                             

Looking to outsource your microarray studies? Look no further.
Click here to tour our facilities
<http://www.ogt.co.uk/highthroughputservices.html> 

Click here to request a quotation
<http://www.ogt.co.uk/htsquotationrequest.asp> 

 

Scientific pedigree delivering high quality microarray results to you:

*         Service capacity >1000 samples per week

*         Rigorous QC <http://www.ogt.co.uk/hts_qc.html>  from sample to
result

*         Applications <http://www.ogt.co.uk/hts_apps.html>  available
include aCGH, CNV, methylation studies and miRNA



Oxford Gene Technology (Operations) Ltd. Registered in England No:
03845432 Begbroke Science Park Sandy Lane Yarnton Oxford OX5 1PF  

Confidentiality Notice: The contents of this email from Oxford Gene
Technology are confidential and intended solely for the person to whom
it is addressed. It may contain privileged and confidential information.
If you are not the intended recipient you must not read, copy,
distribute, discuss or take any action in reliance on it. If you have
received this email in error please advise the sender so that we can
arrange for proper delivery. Then please delete the message from your
inbox. Thank you.

 

 

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From holland at eaglegenomics.com  Wed Jan 13 08:22:16 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 13 Jan 2010 13:22:16 +0000
Subject: [Biojava-dev] Script for cookbook
In-Reply-To: <588D0DD225D05746B5D8CAE1BE971F3F02C64D8C@EUCLID.internal.ogtip.com>
References: <588D0DD225D05746B5D8CAE1BE971F3F02C64D8C@EUCLID.internal.ogtip.com>
Message-ID: <982845F6-0845-474A-BEBD-C5D336C03F42@eaglegenomics.com>

Just a few minor points, otherwise all good:

 1. Your 'trying EMBL' code just tries Genbank again!
 2. Typo in the FileNotFoundException message.
 3. Check to see that your ComparableTerm retrieval statements using RichObjectFactory are not already defined as constants in RichSequence.Terms or GenbankFormat.Terms. If they are, use the constants instead as this makes the code clearer.
 4. Your system.out line that prints the results has Chr1 hardcoded - should this be a parameter, or read from the file maybe?

cheers,
Richard

On 13 Jan 2010, at 12:49, Jolyon Holdstock wrote:

> Hi,
> 
> 
> 
> I was going to add the following script to the annotation section of the
> cookbook. 
> 
> It takes an EMBL or Genbank file and outputs information about each CDS
> feature.
> 
> 
> 
> I just wanted to check this was OK and also is this the most efficient
> way of doing this?
> 
> 
> 
> Cheers,
> 
> 
> 
> Jolyon
> 
> 
> 
> [CODE]
> 
> import java.io.*;
> 
> import java.util.*;
> 
> import org.biojava.bio.*;
> 
> import org.biojava.bio.seq.*;
> 
> import org.biojava.bio.seq.io.*;
> 
> import org.biojavax.*;
> 
> import org.biojavax.ontology.*;
> 
> import org.biojavax.bio.*;
> 
> import org.biojavax.bio.seq.*;
> 
> 
> 
> public class ExtractInformation {
> 
>  //Create the RichSequence object
> 
>  RichSequence richSeq;
> 
>  public ExtractInformation(String fileName){
> 
>    //Load the sequence file
> 
>    try {
> 
>      richSeq = RichSequence.IOTools.readGenbankDNA(new
> BufferedReader(new FileReader(fileName)),null).nextRichSequence();
> 
>    }
> 
>    catch(FileNotFoundException fnfe){
> 
>      System.out.println("FilwNotFoundException: " + fnfe);
> 
>    }
> 
>    catch(BioException bioe1){
> 
>      System.err.println("Not a Genbank sequence trying EMBL");
> 
>      try  {
> 
>        richSeq = RichSequence.IOTools.readGenbankDNA(new
> BufferedReader(new FileReader(fileName)),null).nextRichSequence();
> 
>      }
> 
>      catch(BioException bioe2){
> 
>        System.err.println("Not an EMBL sequence either");
> 
>        System.exit(1);
> 
>      }
> 
>      catch(FileNotFoundException fnfe){
> 
>        System.out.println("FilwNotFoundException: " + fnfe);
> 
>      }
> 
>    }
> 
>    //Filter the sequence on CDS features
> 
>    FeatureFilter ff = new FeatureFilter.ByType("CDS");
> 
>    FeatureHolder fh = richSeq.filter(ff);
> 
> 
> 
>    //Iterate through the CDS features
> 
>    for (Iterator <RichFeature> i = fh.features(); i.hasNext();){
> 
>      RichFeature rf = i.next();
> 
> 
> 
>      //Get the strand orientation of the feature
> 
>      char featureStrand = rf.getStrand().getToken();
> 
> 
> 
>      //Get the location of the feature
> 
>      String featureLocation = rf.getLocation().toString();
> 
> 
> 
>      //Get the annotation of the feature
> 
>      RichAnnotation ra = (RichAnnotation)rf.getAnnotation();
> 
> 
> 
>      //Create the required ComparableTerms
> 
>      ComparableTerm geneTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");
> 
>      ComparableTerm locusTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("locus_tag");
> 
>      ComparableTerm productTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("product");
> 
>      ComparableTerm synonymTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene_synonym");
> 
>      ComparableTerm proteinIDTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("protein_id");
> 
> 
> 
>      //Create empty strings
> 
>      String gene = "";
> 
>      String locus = "";
> 
>      String product = "";
> 
>      String geneSynonym = "";
> 
>      String proteinID = "";
> 
> 
> 
>      //Iterate through the notes in the annotation 
> 
>      for (Iterator <Note> it = ra.getNoteSet().iterator();
> it.hasNext();){
> 
>        Note note = it.next();
> 
> 
> 
>      //Check each note to see if it matches one of the required
> ComparableTerms
> 
>        if(note.getTerm().equals(locusTerm)){
> 
>          locus = note.getValue().toString();
> 
>        }
> 
>        if(note.getTerm().equals(productTerm)){
> 
>          product = note.getValue().toString();
> 
>        }
> 
>        if(note.getTerm().equals(geneTerm)){
> 
>          gene = note.getValue().toString();
> 
>        }
> 
>        if(note.getTerm().equals(synonymTerm)){
> 
>          geneSynonym = note.getValue().toString();
> 
>        }
> 
>        if(note.getTerm().equals(proteinIDTerm)){
> 
>          proteinID = note.getValue().toString();
> 
>        }
> 
>      }
> 
>      //Outout the feature information
> 
>      System.out.println(locus + "  " + gene + "  " + geneSynonym + "  "
> + proteinID + "  " + product +"  " + featureStrand +"  Chr1:" +
> featureLocation);
> 
>    }
> 
>  }
> 
> 
> 
>  public static void main(String args []){
> 
>    if (args.length != 1){
> 
>      System.out.println("Usage: java ExtractInformation <file in
> Genbank or EMBL format>");
> 
>      System.exit(1);
> 
>    }
> 
>    else {
> 
>      new ExtractInformation(args[0]);
> 
>    }
> 
>  }
> 
> }
> 
> [/CODE]
> 
> 
> 
> Dr. Jolyon Holdstock                                       
> Senior Computational Biologist,
> 
> Oxford Gene Technology,                                   
> Begbroke Science Park,                                     
> Sandy Lane, Yarnton,                                           
> Oxford, OX5 1PF, UK.                                             
> 
> T: +44 (0)1865 856 852                                     
> F: +44 (0)1865 842 116                                     
> E: jolyon.holdstock at ogt.co.uk <mailto:nicola.booton-mander at ogt.co.uk>
> 
> W: www.ogt.co.uk <blocked::http://www.ogt.co.uk/>     
> 
> 
> 
> Looking to outsource your microarray studies? Look no further.
> Click here to tour our facilities
> <http://www.ogt.co.uk/highthroughputservices.html> 
> 
> Click here to request a quotation
> <http://www.ogt.co.uk/htsquotationrequest.asp> 
> 
> 
> 
> Scientific pedigree delivering high quality microarray results to you:
> 
> *         Service capacity >1000 samples per week
> 
> *         Rigorous QC <http://www.ogt.co.uk/hts_qc.html>  from sample to
> result
> 
> *         Applications <http://www.ogt.co.uk/hts_apps.html>  available
> include aCGH, CNV, methylation studies and miRNA
> 
> 
> 
> Oxford Gene Technology (Operations) Ltd. Registered in England No:
> 03845432 Begbroke Science Park Sandy Lane Yarnton Oxford OX5 1PF  
> 
> Confidentiality Notice: The contents of this email from Oxford Gene
> Technology are confidential and intended solely for the person to whom
> it is addressed. It may contain privileged and confidential information.
> If you are not the intended recipient you must not read, copy,
> distribute, discuss or take any action in reliance on it. If you have
> received this email in error please advise the sender so that we can
> arrange for proper delivery. Then please delete the message from your
> inbox. Thank you.
> 
> 
> 
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From genjasp at gmail.com  Wed Jan 13 09:14:26 2010
From: genjasp at gmail.com (Alessandro Cipriani)
Date: Wed, 13 Jan 2010 15:14:26 +0100
Subject: [Biojava-dev] Script for cookbook
In-Reply-To: <982845F6-0845-474A-BEBD-C5D336C03F42@eaglegenomics.com>
References: <588D0DD225D05746B5D8CAE1BE971F3F02C64D8C@EUCLID.internal.ogtip.com>
	<982845F6-0845-474A-BEBD-C5D336C03F42@eaglegenomics.com>
Message-ID: <46b9a2151001130614i1d1b057xfdffa8f0051d0b89@mail.gmail.com>

Hi,
i think it is not a good practice:
-to insert a try/catch block into anothet try/catch block.
-to import all lib even  unrequired
-to make all methods public

otherwise it seems to be ok!

Regards

Alex


2010/1/13 Richard Holland <holland at eaglegenomics.com>:
> Just a few minor points, otherwise all good:
>
> ?1. Your 'trying EMBL' code just tries Genbank again!
> ?2. Typo in the FileNotFoundException message.
> ?3. Check to see that your ComparableTerm retrieval statements using RichObjectFactory are not already defined as constants in RichSequence.Terms or GenbankFormat.Terms. If they are, use the constants instead as this makes the code clearer.
> ?4. Your system.out line that prints the results has Chr1 hardcoded - should this be a parameter, or read from the file maybe?
>
> cheers,
> Richard
>
> On 13 Jan 2010, at 12:49, Jolyon Holdstock wrote:
>
>> Hi,
>>
>>
>>
>> I was going to add the following script to the annotation section of the
>> cookbook.
>>
>> It takes an EMBL or Genbank file and outputs information about each CDS
>> feature.
>>
>>
>>
>> I just wanted to check this was OK and also is this the most efficient
>> way of doing this?
>>
>>
>>
>> Cheers,
>>
>>
>>
>> Jolyon
>>
>>
>>
>> [CODE]
>>
>> import java.io.*;
>>
>> import java.util.*;
>>
>> import org.biojava.bio.*;
>>
>> import org.biojava.bio.seq.*;
>>
>> import org.biojava.bio.seq.io.*;
>>
>> import org.biojavax.*;
>>
>> import org.biojavax.ontology.*;
>>
>> import org.biojavax.bio.*;
>>
>> import org.biojavax.bio.seq.*;
>>
>>
>>
>> public class ExtractInformation {
>>
>> ?//Create the RichSequence object
>>
>> ?RichSequence richSeq;
>>
>> ?public ExtractInformation(String fileName){
>>
>> ? ?//Load the sequence file
>>
>> ? ?try {
>>
>> ? ? ?richSeq = RichSequence.IOTools.readGenbankDNA(new
>> BufferedReader(new FileReader(fileName)),null).nextRichSequence();
>>
>> ? ?}
>>
>> ? ?catch(FileNotFoundException fnfe){
>>
>> ? ? ?System.out.println("FilwNotFoundException: " + fnfe);
>>
>> ? ?}
>>
>> ? ?catch(BioException bioe1){
>>
>> ? ? ?System.err.println("Not a Genbank sequence trying EMBL");
>>
>> ? ? ?try ?{
>>
>> ? ? ? ?richSeq = RichSequence.IOTools.readGenbankDNA(new
>> BufferedReader(new FileReader(fileName)),null).nextRichSequence();
>>
>> ? ? ?}
>>
>> ? ? ?catch(BioException bioe2){
>>
>> ? ? ? ?System.err.println("Not an EMBL sequence either");
>>
>> ? ? ? ?System.exit(1);
>>
>> ? ? ?}
>>
>> ? ? ?catch(FileNotFoundException fnfe){
>>
>> ? ? ? ?System.out.println("FilwNotFoundException: " + fnfe);
>>
>> ? ? ?}
>>
>> ? ?}
>>
>> ? ?//Filter the sequence on CDS features
>>
>> ? ?FeatureFilter ff = new FeatureFilter.ByType("CDS");
>>
>> ? ?FeatureHolder fh = richSeq.filter(ff);
>>
>>
>>
>> ? ?//Iterate through the CDS features
>>
>> ? ?for (Iterator <RichFeature> i = fh.features(); i.hasNext();){
>>
>> ? ? ?RichFeature rf = i.next();
>>
>>
>>
>> ? ? ?//Get the strand orientation of the feature
>>
>> ? ? ?char featureStrand = rf.getStrand().getToken();
>>
>>
>>
>> ? ? ?//Get the location of the feature
>>
>> ? ? ?String featureLocation = rf.getLocation().toString();
>>
>>
>>
>> ? ? ?//Get the annotation of the feature
>>
>> ? ? ?RichAnnotation ra = (RichAnnotation)rf.getAnnotation();
>>
>>
>>
>> ? ? ?//Create the required ComparableTerms
>>
>> ? ? ?ComparableTerm geneTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");
>>
>> ? ? ?ComparableTerm locusTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("locus_tag");
>>
>> ? ? ?ComparableTerm productTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("product");
>>
>> ? ? ?ComparableTerm synonymTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene_synonym");
>>
>> ? ? ?ComparableTerm proteinIDTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("protein_id");
>>
>>
>>
>> ? ? ?//Create empty strings
>>
>> ? ? ?String gene = "";
>>
>> ? ? ?String locus = "";
>>
>> ? ? ?String product = "";
>>
>> ? ? ?String geneSynonym = "";
>>
>> ? ? ?String proteinID = "";
>>
>>
>>
>> ? ? ?//Iterate through the notes in the annotation
>>
>> ? ? ?for (Iterator <Note> it = ra.getNoteSet().iterator();
>> it.hasNext();){
>>
>> ? ? ? ?Note note = it.next();
>>
>>
>>
>> ? ? ?//Check each note to see if it matches one of the required
>> ComparableTerms
>>
>> ? ? ? ?if(note.getTerm().equals(locusTerm)){
>>
>> ? ? ? ? ?locus = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ? ?if(note.getTerm().equals(productTerm)){
>>
>> ? ? ? ? ?product = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ? ?if(note.getTerm().equals(geneTerm)){
>>
>> ? ? ? ? ?gene = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ? ?if(note.getTerm().equals(synonymTerm)){
>>
>> ? ? ? ? ?geneSynonym = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ? ?if(note.getTerm().equals(proteinIDTerm)){
>>
>> ? ? ? ? ?proteinID = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ?}
>>
>> ? ? ?//Outout the feature information
>>
>> ? ? ?System.out.println(locus + " ?" + gene + " ?" + geneSynonym + " ?"
>> + proteinID + " ?" + product +" ?" + featureStrand +" ?Chr1:" +
>> featureLocation);
>>
>> ? ?}
>>
>> ?}
>>
>>
>>
>> ?public static void main(String args []){
>>
>> ? ?if (args.length != 1){
>>
>> ? ? ?System.out.println("Usage: java ExtractInformation <file in
>> Genbank or EMBL format>");
>>
>> ? ? ?System.exit(1);
>>
>> ? ?}
>>
>> ? ?else {
>>
>> ? ? ?new ExtractInformation(args[0]);
>>
>> ? ?}
>>
>> ?}
>>
>> }
>>
>> [/CODE]
>>
>>
>>
>> Dr. Jolyon Holdstock
>> Senior Computational Biologist,
>>
>> Oxford Gene Technology,
>> Begbroke Science Park,
>> Sandy Lane, Yarnton,
>> Oxford, OX5 1PF, UK.
>>
>> T: +44 (0)1865 856 852
>> F: +44 (0)1865 842 116
>> E: jolyon.holdstock at ogt.co.uk <mailto:nicola.booton-mander at ogt.co.uk>
>>
>> W: www.ogt.co.uk <blocked::http://www.ogt.co.uk/>
>>
>>
>>
>> Looking to outsource your microarray studies? Look no further.
>> Click here to tour our facilities
>> <http://www.ogt.co.uk/highthroughputservices.html>
>>
>> Click here to request a quotation
>> <http://www.ogt.co.uk/htsquotationrequest.asp>
>>
>>
>>
>> Scientific pedigree delivering high quality microarray results to you:
>>
>> * ? ? ? ? Service capacity >1000 samples per week
>>
>> * ? ? ? ? Rigorous QC <http://www.ogt.co.uk/hts_qc.html> ?from sample to
>> result
>>
>> * ? ? ? ? Applications <http://www.ogt.co.uk/hts_apps.html> ?available
>> include aCGH, CNV, methylation studies and miRNA
>>
>>
>>
>> Oxford Gene Technology (Operations) Ltd. Registered in England No:
>> 03845432 Begbroke Science Park Sandy Lane Yarnton Oxford OX5 1PF
>>
>> Confidentiality Notice: The contents of this email from Oxford Gene
>> Technology are confidential and intended solely for the person to whom
>> it is addressed. It may contain privileged and confidential information.
>> If you are not the intended recipient you must not read, copy,
>> distribute, discuss or take any action in reliance on it. If you have
>> received this email in error please advise the sender so that we can
>> arrange for proper delivery. Then please delete the message from your
>> inbox. Thank you.
>>
>>
>>
>>
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From mahogny at areta.org  Sun Jan 17 12:52:45 2010
From: mahogny at areta.org (Johan Henriksson)
Date: Sun, 17 Jan 2010 18:52:45 +0100
Subject: [Biojava-dev] biojava hackathon
In-Reply-To: <dd8886300912210723r2b22847dq48db52e14fcb1a0a@mail.gmail.com>
References: <dd8886300912210723r2b22847dq48db52e14fcb1a0a@mail.gmail.com>
Message-ID: <dd8886301001170952k2684c4f4xf6e53951b063dbe8@mail.gmail.com>

sorry, I will not be able to attend the hackathon this year for a whole lot
of reasons. in addition, sorry for telling this so late.

I'm looking forward to the next one though; happy hacking to the rest of
you!

/Johan

-- 
-----------------------------------------------------------
Johan Henriksson
PhD student, Karolinska Institutet
http://mahogny.areta.org  http://www.endrov.net

From heuermh at acm.org  Mon Jan 18 23:54:21 2010
From: heuermh at acm.org (Michael Heuer)
Date: Mon, 18 Jan 2010 23:54:21 -0500 (EST)
Subject: [Biojava-dev] hackathon task list, pom refactoring, &c.
In-Reply-To: <E304F7F2-09B7-4C46-92F9-F9CA6E68C5EC@eaglegenomics.com>
Message-ID: <Pine.GSO.4.44.1001182335530.409-100000@shell3.shore.net>

Hello Hackathon participants,

Might we start a task list for the hackathon tomorrow, on the biojava
wiki perhaps?  It would be nice to be able to contribute to the list of
tasks and to claim tasks to work on from off-site.

Today I refactored and cleaned up all the maven poms.  Build and test
works for me on linux, win, and mac with commandline maven.  Eclipse via
m2eclipse is good for almost everything, but has trouble firing off the
maven-jaxb2-plugin code generation step.

If you want to give it a try, version maven 3.0.6-alpha is a lot
more picky about reproducable builds than earlier versions, and
complained a ton when I first started.  Now the only warning is the
deprecated maven1 repo link at java.net.

I have set up cia.vc to post svn commit notification via IRC to #biojava
on irc.freenode.net.  I'll also be on there most of the day tomorrow, or
available on google chat.

Ah, with the blogs and the twitter and stuff, I can't keep up.  ;)

   michael


From heuermh at acm.org  Tue Jan 19 00:02:28 2010
From: heuermh at acm.org (Michael Heuer)
Date: Tue, 19 Jan 2010 00:02:28 -0500 (EST)
Subject: [Biojava-dev] [Biojava-l] BioJava Hackathon - Day 1
In-Reply-To: <95988839-75A3-4087-8071-5A19BEECDD04@eaglegenomics.com>
Message-ID: <Pine.GSO.4.44.1001182354410.409-100000@shell3.shore.net>

On Mon, 18 Jan 2010, Richard Holland wrote:

> ...
>
> Also by making the new SymbolList implement the standard List
> interface from Collections, it can be used in nice Java shortcuts such
> as the new foreach loops, and standard iterators can be used (instead of
> the current SymbolListIterator method). Collections API can also be used
> then to do things like subsets or reverses.

Is this a good idea?  It might preclude some efficient implementation
strategies, such as ParallelArray from JSR166

http://gee.cs.oswego.edu/dl/jsr166/dist/extra166ydocs/extra166y/ParallelArray.html

Would Iterable be sufficient enough?

Also, List indexing is not compatible with typical sequence feature
indexing.

   michael


From holland at eaglegenomics.com  Tue Jan 19 00:45:14 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 19 Jan 2010 05:45:14 +0000
Subject: [Biojava-dev] [Biojava-l] BioJava Hackathon - Day 1
In-Reply-To: <Pine.GSO.4.44.1001182354410.409-100000@shell3.shore.net>
References: <Pine.GSO.4.44.1001182354410.409-100000@shell3.shore.net>
Message-ID: <56B4AA4E-FF88-4D4E-BD95-49B76194FA82@eaglegenomics.com>

Good point - Iterable would probably be fine.

On 19 Jan 2010, at 05:02, Michael Heuer wrote:

> On Mon, 18 Jan 2010, Richard Holland wrote:
> 
>> ...
>> 
>> Also by making the new SymbolList implement the standard List
>> interface from Collections, it can be used in nice Java shortcuts such
>> as the new foreach loops, and standard iterators can be used (instead of
>> the current SymbolListIterator method). Collections API can also be used
>> then to do things like subsets or reverses.
> 
> Is this a good idea?  It might preclude some efficient implementation
> strategies, such as ParallelArray from JSR166
> 
> http://gee.cs.oswego.edu/dl/jsr166/dist/extra166ydocs/extra166y/ParallelArray.html
> 
> Would Iterable be sufficient enough?
> 
> Also, List indexing is not compatible with typical sequence feature
> indexing.
> 
>   michael
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/



From ayates at ebi.ac.uk  Tue Jan 19 03:50:49 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 19 Jan 2010 08:50:49 +0000
Subject: [Biojava-dev] [Biojava-l] BioJava Hackathon - Day 1
In-Reply-To: <56B4AA4E-FF88-4D4E-BD95-49B76194FA82@eaglegenomics.com>
References: <Pine.GSO.4.44.1001182354410.409-100000@shell3.shore.net>
	<56B4AA4E-FF88-4D4E-BD95-49B76194FA82@eaglegenomics.com>
Message-ID: <25714175-4B75-4D30-AA42-E0176060DCAB@ebi.ac.uk>

This somewhat targets what this new version should be about; making  
the most of Java5+ features (Iterable & generics being the first  
things that spring to mind).


On 19 Jan 2010, at 05:45, Richard Holland wrote:

> Good point - Iterable would probably be fine.
>
> On 19 Jan 2010, at 05:02, Michael Heuer wrote:
>
>> On Mon, 18 Jan 2010, Richard Holland wrote:
>>
>>> ...
>>>
>>> Also by making the new SymbolList implement the standard List
>>> interface from Collections, it can be used in nice Java shortcuts  
>>> such
>>> as the new foreach loops, and standard iterators can be used  
>>> (instead of
>>> the current SymbolListIterator method). Collections API can also  
>>> be used
>>> then to do things like subsets or reverses.
>>
>> Is this a good idea?  It might preclude some efficient implementation
>> strategies, such as ParallelArray from JSR166
>>
>> http://gee.cs.oswego.edu/dl/jsr166/dist/extra166ydocs/extra166y/ParallelArray.html
>>
>> Would Iterable be sufficient enough?
>>
>> Also, List indexing is not compatible with typical sequence feature
>> indexing.
>>
>>  michael
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From andy.law at roslin.ed.ac.uk  Tue Jan 19 04:23:26 2010
From: andy.law at roslin.ed.ac.uk (Andy Law (RI))
Date: Tue, 19 Jan 2010 09:23:26 +0000
Subject: [Biojava-dev] hackathon task list, pom refactoring, &c.
In-Reply-To: <Pine.GSO.4.44.1001182335530.409-100000@shell3.shore.net>
References: <Pine.GSO.4.44.1001182335530.409-100000@shell3.shore.net>
Message-ID: <6B943C9E-98E1-4788-8860-2B6AC266421C@roslin.ed.ac.uk>


On 19 Jan 2010, at 04:54, Michael Heuer wrote:


>
> I have set up cia.vc to post svn commit notification via IRC to  
> #biojava
> on irc.freenode.net.  I'll also be on there most of the day  
> tomorrow, or
> available on google chat.
>
> Ah, with the blogs and the twitter and stuff, I can't keep up.  ;)


Sheesh! What was ever wrong with posting occasional notes via email?



Later,

Andy
--------
Yada, yada, yada...
The University of Edinburgh is a charitable body, registered in  
Scotland, with registration number SC005336
Disclaimer: This e-mail and any attachments are confidential and  
intended solely for the use of the recipient(s) to whom they are  
addressed. If you have received it in error, please destroy all copies  
and inform the sender.




From jw12 at sanger.ac.uk  Tue Jan 19 05:41:12 2010
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Tue, 19 Jan 2010 10:41:12 +0000
Subject: [Biojava-dev] DAS Workshop Registrations now Open (workshop date
	7-9 April 2010)
Message-ID: <9EDF4E46-15F8-434E-B557-2DE5906C4182@sanger.ac.uk>

If you don't know about DAS and wish to know how to distribute your  
latest biological annotation to the world then the upcoming DAS  
workshop maybe for you.
If you know about DAS and are maybe a DAS client developer then the  
upcoming DAS workshop is for you (as you will need to know about the  
upcoming DAS 1.6 Specification and how it may affect your software).

For information on the workshop and registration please go to:

http://www.ebi.ac.uk/training/handson/DAS_070410.html



Jonathan Warren
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk








-- 
 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 heuermh at acm.org  Tue Jan 19 19:52:29 2010
From: heuermh at acm.org (Michael Heuer)
Date: Tue, 19 Jan 2010 19:52:29 -0500 (EST)
Subject: [Biojava-dev] sequence-core tests currently do not compile
In-Reply-To: <6B943C9E-98E1-4788-8860-2B6AC266421C@roslin.ed.ac.uk>
Message-ID: <Pine.GSO.4.44.1001191950560.15376-100000@shell3.shore.net>


Module sequence-core tests currently do not compile

[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-compiler-plugin:2.0.2:testCompile
(default-testCompile) on project sequence-co
re: Compilation failure: Compilation failure:
C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[8,7]
class DNATests
is public, should be declared in a file named DNATests.java

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[45,9]
cannot find sy
mbol
symbol  : class Sequence
location: class org.biojava3.core.DNATests

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[45,28]
cannot find s
ymbol
symbol  : class DNACompound
location: class org.biojava3.core.DNATests

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[40,17]
cannot find s
ymbol
symbol  : class BadSequence
location: class org.biojava3.core.DNATests

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[12,15]
getSeq(java.l
ang.String) in org.biojava3.core.DNATests cannot be applied to ()

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[18,15]
getSeq(java.l
ang.String) in org.biojava3.core.DNATests cannot be applied to ()

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[24,15]
getSeq(java.l
ang.String) in org.biojava3.core.DNATests cannot be applied to ()

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[37,16]
cannot find s
ymbol
symbol  : variable toString
location: class java.lang.String

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[47,15]
cannot find s
ymbol
symbol  : class DNASequence
location: class org.biojava3.core.DNATests


From ayates at ebi.ac.uk  Wed Jan 20 04:55:31 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 20 Jan 2010 09:55:31 +0000
Subject: [Biojava-dev] sequence-core tests currently do not compile
In-Reply-To: <Pine.GSO.4.44.1001191950560.15376-100000@shell3.shore.net>
References: <Pine.GSO.4.44.1001191950560.15376-100000@shell3.shore.net>
Message-ID: <9981AAC1-1197-4DF7-B347-5ADE4E0C03C0@ebi.ac.uk>

Hmmm interesting. That should have all been commented out I thought. I  
will fix & commit back
On 20 Jan 2010, at 00:52, Michael Heuer wrote:

>
> Module sequence-core tests currently do not compile
>
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-compiler-plugin:2.0.2:testCompile
> (default-testCompile) on project sequence-co
> re: Compilation failure: Compilation failure:
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[8,7]
> class DNATests
> is public, should be declared in a file named DNATests.java
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[45,9]
> cannot find sy
> mbol
> symbol  : class Sequence
> location: class org.biojava3.core.DNATests
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[45,28]
> cannot find s
> ymbol
> symbol  : class DNACompound
> location: class org.biojava3.core.DNATests
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[40,17]
> cannot find s
> ymbol
> symbol  : class BadSequence
> location: class org.biojava3.core.DNATests
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[12,15]
> getSeq(java.l
> ang.String) in org.biojava3.core.DNATests cannot be applied to ()
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[18,15]
> getSeq(java.l
> ang.String) in org.biojava3.core.DNATests cannot be applied to ()
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[24,15]
> getSeq(java.l
> ang.String) in org.biojava3.core.DNATests cannot be applied to ()
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[37,16]
> cannot find s
> ymbol
> symbol  : variable toString
> location: class java.lang.String
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[47,15]
> cannot find s
> ymbol
> symbol  : class DNASequence
> location: class org.biojava3.core.DNATests
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From HWillis at scripps.edu  Tue Jan 26 13:09:36 2010
From: HWillis at scripps.edu (Scooter Willis)
Date: Tue, 26 Jan 2010 13:09:36 -0500
Subject: [Biojava-dev] Code Update
Message-ID: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>


I checked in updates with test cases for Fasta fileparsing where the main focus is on the fasta header.  The test cases are based on the wikipedia examples so results will vary with actual files. It is very easy now to do a custom header parser so we have lots of flexibility.  I also started the code for the file pointer sequence proxy where the key usage is creating a sequence with the header and storing a reference to the file and offset in the file for the start of the sequence. When a method is called related to getting a sequence/subsequence the init() method is called to load the sequence data via RandomAccessFile with a seek to the offset. It turns out that none of the java io classes will actually return an offset index of the actual bytes read. This also gets complicated with the readline() methods where the CR and/or LF is stripped off when the string is returned so you can't keep track of it externally. I copied the BufferedReader.java class to BufferedReaderBytesRead.java and keep track of the file pointer internally. This code still needs to be tested. This should be a great way to load large date sets with minimal memory. To complete this approach I will probably do a collection that is proxy aware that can go through and free up storage by returning a sequence to its proxy state.

I will work this week on getting some wiki pages created to give examples on using the header parsing interface and proxy sequences. How do we want to organize wiki pages related to biojava3 work? 

Thanks

Scooter

From andreas at sdsc.edu  Tue Jan 26 13:45:59 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 26 Jan 2010 10:45:59 -0800
Subject: [Biojava-dev] Code Update
In-Reply-To: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
References: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
Message-ID: <59a41c431001261045g301d8a48hbd55999cafa5601c@mail.gmail.com>

the cookbook approach seems to work quite well. You could start a new
"Chapter" in the book and make it clear that this will be only
available once biojava 3 has been released (or via SVN checkout)

Andreas

On Tue, Jan 26, 2010 at 10:09 AM, Scooter Willis <HWillis at scripps.edu> wrote:
>
> I checked in updates with test cases for Fasta fileparsing where the main focus is on the fasta header. ?The test cases are based on the wikipedia examples so results will vary with actual files. It is very easy now to do a custom header parser so we have lots of flexibility. ?I also started the code for the file pointer sequence proxy where the key usage is creating a sequence with the header and storing a reference to the file and offset in the file for the start of the sequence. When a method is called related to getting a sequence/subsequence the init() method is called to load the sequence data via RandomAccessFile with a seek to the offset. It turns out that none of the java io classes will actually return an offset index of the actual bytes read. This also gets complicated with the readline() methods where the CR and/or LF is stripped off when the string is returned so you can't keep track of it externally. I copied the BufferedReader.java class to BufferedReaderBytes!
> ?Read.java and keep track of the file pointer internally. This code still needs to be tested. This should be a great way to load large date sets with minimal memory. To complete this approach I will probably do a collection that is proxy aware that can go through and free up storage by returning a sequence to its proxy state.
>
> I will work this week on getting some wiki pages created to give examples on using the header parsing interface and proxy sequences. How do we want to organize wiki pages related to biojava3 work?
>
> Thanks
>
> Scooter
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From ayates at ebi.ac.uk  Tue Jan 26 14:58:43 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 26 Jan 2010 19:58:43 +0000
Subject: [Biojava-dev] Code Update
In-Reply-To: <59a41c431001261045g301d8a48hbd55999cafa5601c@mail.gmail.com>
References: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
	<59a41c431001261045g301d8a48hbd55999cafa5601c@mail.gmail.com>
Message-ID: <7075E1DA-E19E-4AB0-A6DC-DF2A62D7DDE8@ebi.ac.uk>

Talking about code updates I've got DNA -> RNA -> Peptide working  
quite well. It's about a day or two of tinkering away from being  in a  
sensible state. There's also some utilities I've gone & created;  
they've gone into org.biojava3.core.util ... anyone got any better  
suggestions as to where they should live?

Andy

On 26 Jan 2010, at 18:45, Andreas Prlic wrote:

> the cookbook approach seems to work quite well. You could start a new
> "Chapter" in the book and make it clear that this will be only
> available once biojava 3 has been released (or via SVN checkout)
>
> Andreas
>
> On Tue, Jan 26, 2010 at 10:09 AM, Scooter Willis  
> <HWillis at scripps.edu> wrote:
>>
>> I checked in updates with test cases for Fasta fileparsing where  
>> the main focus is on the fasta header.  The test cases are based on  
>> the wikipedia examples so results will vary with actual files. It  
>> is very easy now to do a custom header parser so we have lots of  
>> flexibility.  I also started the code for the file pointer sequence  
>> proxy where the key usage is creating a sequence with the header  
>> and storing a reference to the file and offset in the file for the  
>> start of the sequence. When a method is called related to getting a  
>> sequence/subsequence the init() method is called to load the  
>> sequence data via RandomAccessFile with a seek to the offset. It  
>> turns out that none of the java io classes will actually return an  
>> offset index of the actual bytes read. This also gets complicated  
>> with the readline() methods where the CR and/or LF is stripped off  
>> when the string is returned so you can't keep track of it  
>> externally. I copied the BufferedReader.java class to  
>> BufferedReaderBytes!
>>  Read.java and keep track of the file pointer internally. This code  
>> still needs to be tested. This should be a great way to load large  
>> date sets with minimal memory. To complete this approach I will  
>> probably do a collection that is proxy aware that can go through  
>> and free up storage by returning a sequence to its proxy state.
>>
>> I will work this week on getting some wiki pages created to give  
>> examples on using the header parsing interface and proxy sequences.  
>> How do we want to organize wiki pages related to biojava3 work?
>>
>> Thanks
>>
>> Scooter
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev


From HWillis at scripps.edu  Tue Jan 26 15:17:47 2010
From: HWillis at scripps.edu (Scooter Willis)
Date: Tue, 26 Jan 2010 15:17:47 -0500
Subject: [Biojava-dev] Code Update
In-Reply-To: <7075E1DA-E19E-4AB0-A6DC-DF2A62D7DDE8@ebi.ac.uk>
References: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
	<59a41c431001261045g301d8a48hbd55999cafa5601c@mail.gmail.com>
	<7075E1DA-E19E-4AB0-A6DC-DF2A62D7DDE8@ebi.ac.uk>
Message-ID: <56D4673E-EB91-43BA-BE0F-99BCD202752A@scripps.edu>

Andy

Let me know when you have that in a healthy state and I will work on the gtf/gff3 parser->create gene->transcript->(exon)->to protein code.

Scooter

On Jan 26, 2010, at 2:58 PM, Andy Yates wrote:

> Talking about code updates I've got DNA -> RNA -> Peptide working  
> quite well. It's about a day or two of tinkering away from being  in a  
> sensible state. There's also some utilities I've gone & created;  
> they've gone into org.biojava3.core.util ... anyone got any better  
> suggestions as to where they should live?
> 
> Andy
> 
> On 26 Jan 2010, at 18:45, Andreas Prlic wrote:
> 
>> the cookbook approach seems to work quite well. You could start a new
>> "Chapter" in the book and make it clear that this will be only
>> available once biojava 3 has been released (or via SVN checkout)
>> 
>> Andreas
>> 
>> On Tue, Jan 26, 2010 at 10:09 AM, Scooter Willis  
>> <HWillis at scripps.edu> wrote:
>>> 
>>> I checked in updates with test cases for Fasta fileparsing where  
>>> the main focus is on the fasta header.  The test cases are based on  
>>> the wikipedia examples so results will vary with actual files. It  
>>> is very easy now to do a custom header parser so we have lots of  
>>> flexibility.  I also started the code for the file pointer sequence  
>>> proxy where the key usage is creating a sequence with the header  
>>> and storing a reference to the file and offset in the file for the  
>>> start of the sequence. When a method is called related to getting a  
>>> sequence/subsequence the init() method is called to load the  
>>> sequence data via RandomAccessFile with a seek to the offset. It  
>>> turns out that none of the java io classes will actually return an  
>>> offset index of the actual bytes read. This also gets complicated  
>>> with the readline() methods where the CR and/or LF is stripped off  
>>> when the string is returned so you can't keep track of it  
>>> externally. I copied the BufferedReader.java class to  
>>> BufferedReaderBytes!
>>> Read.java and keep track of the file pointer internally. This code  
>>> still needs to be tested. This should be a great way to load large  
>>> date sets with minimal memory. To complete this approach I will  
>>> probably do a collection that is proxy aware that can go through  
>>> and free up storage by returning a sequence to its proxy state.
>>> 
>>> I will work this week on getting some wiki pages created to give  
>>> examples on using the header parsing interface and proxy sequences.  
>>> How do we want to organize wiki pages related to biojava3 work?
>>> 
>>> Thanks
>>> 
>>> Scooter
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>> 
>> 
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 



From jacobsen at ebi.ac.uk  Wed Jan 27 06:32:31 2010
From: jacobsen at ebi.ac.uk (Jules Jacobsen)
Date: Wed, 27 Jan 2010 11:32:31 +0000
Subject: [Biojava-dev] Code Update
In-Reply-To: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
References: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
Message-ID: <4B60244F.2070603@ebi.ac.uk>

Cool - I've a sudden need for a SELEX reader/parser so will try and 
knock one of those together in the immediate future - might lift some 
code from Jalview for this purpose and see how the new 
MultipleSequenceAlignment class behaves in real life.

Plus I've just tweaked the FastaReader and FastaWriter to be setup-neutral.

Jules

On 26/01/2010 18:09, Scooter Willis wrote:
> I checked in updates with test cases for Fasta fileparsing where the main focus is on the fasta header.  The test cases are based on the wikipedia examples so results will vary with actual files. It is very easy now to do a custom header parser so we have lots of flexibility.  I also started the code for the file pointer sequence proxy where the key usage is creating a sequence with the header and storing a reference to the file and offset in the file for the start of the sequence. When a method is called related to getting a sequence/subsequence the init() method is called to load the sequence data via RandomAccessFile with a seek to the offset. It turns out that none of the java io classes will actually return an offset index of the actual bytes read. This also gets complicated with the readline() methods where the CR and/or LF is stripped off when the string is returned so you can't keep track of it externally. I copied the BufferedReader.java class to BufferedReaderBytes!
>   Read.java and keep track of the file pointer internally. This code still needs to be tested. This should be a great way to load large date sets with minimal memory. To complete this approach I will probably do a collection that is proxy aware that can go through and free up storage by returning a sequence to its proxy state.
>
> I will work this week on getting some wiki pages created to give examples on using the header parsing interface and proxy sequences. How do we want to organize wiki pages related to biojava3 work?
>
> Thanks
>
> Scooter
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>    



From chapmanb at 50mail.com  Thu Jan 28 15:35:05 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Thu, 28 Jan 2010 15:35:05 -0500
Subject: [Biojava-dev] OpenBio solution challenge: Project updates at BOSC
	2010
Message-ID: <20100128203505.GG40046@sobchak.mgh.harvard.edu>

Hello all;
The BOSC 2010 organizing committee is hard at work getting prepared for this
July's meeting in Boston:

http://www.open-bio.org/wiki/BOSC_2010

One of the items we've traditionally had at the conference is a project 
update from each of the OpenBio affiliated groups. This year, we're thinking
about organizing these talks around a central theme: the OpenBio solution
challenge. We start with a biological question of general interest, and each
of the project talks would focus around how you would solve that problem 
using your toolkit and programming language.

This is meant to provide a challenge for OpenBio contributors, a nice tutorial
style overview of various projects and approaches for other programmers, and a
fun opportunity to compete and learn from other projects. Conference attendees
will vote on their favorite solution, with the winner receiving fame and
fortune (warning: fortune not guaranteed).

For this to be successful, it of course requires interest and enthusiasm from
y'all fine folks involved with the projects. Specifically:

- Is there interest from your group in participating in the challenge? You'll
  want at least a few people to work on it, and someone to give a presentation 
  at BOSC.

- Do you have suggestions on a good theme or specific biological problem to
  tackle? We'll hope to pick something in a sweet spot that is challenging 
  enough to be of interest, yet reasonable for presentation and preparation.

Let's discuss ideas and get this together. Since the schedule for BOSC is
developing rapidly, please give us an idea if you're interested by
February 12th, and copy responses to the BOSC mailing list as a central 
place for discussion.

bosc at open-bio.org

Thanks,
Brad, Michael, and the BOSC organizing committee

From markw at illuminae.com  Thu Jan 28 16:17:44 2010
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 28 Jan 2010 13:17:44 -0800
Subject: [Biojava-dev] [MOBY-dev] OpenBio solution challenge: Project
 updates at BOSC 2010
In-Reply-To: <20100128203505.GG40046@sobchak.mgh.harvard.edu>
References: <20100128203505.GG40046@sobchak.mgh.harvard.edu>
Message-ID: <op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>


Brad, this sounds exciting!

One thing strikes me, though - by asking for the sub-projects to propose
the "grand challenge" themselves the one thing you can guarantee is that
the "grand challenge" is solvable (or more likely, already solved!)

Other "grand challenge" kinds of meetings have an independent third party
pose the problem that has to be solved, and then all groups work toward a
solution and compare their results.  This would, IMO, be more revealing of
the "state of the art" in each Open-Bio project, and point out where the
weaknesses are that we should be focusing on...  Someone (for example,
you!) could act as the moderator to ensure that the "grand challenge" was
at least a reasonable one, within the scope of what an Open-Bio project
*should* be able to solve...

Just my CAD $0.02

Mark



On Thu, 28 Jan 2010 12:35:05 -0800, Brad Chapman <chapmanb at 50mail.com>  
wrote:

> Hello all;
> The BOSC 2010 organizing committee is hard at work getting prepared for  
> this
> July's meeting in Boston:
>
> http://www.open-bio.org/wiki/BOSC_2010
>
> One of the items we've traditionally had at the conference is a project
> update from each of the OpenBio affiliated groups. This year, we're  
> thinking
> about organizing these talks around a central theme: the OpenBio solution
> challenge. We start with a biological question of general interest, and  
> each
> of the project talks would focus around how you would solve that problem
> using your toolkit and programming language.
>
> This is meant to provide a challenge for OpenBio contributors, a nice  
> tutorial
> style overview of various projects and approaches for other programmers,  
> and a
> fun opportunity to compete and learn from other projects. Conference  
> attendees
> will vote on their favorite solution, with the winner receiving fame and
> fortune (warning: fortune not guaranteed).
>
> For this to be successful, it of course requires interest and enthusiasm  
> from
> y'all fine folks involved with the projects. Specifically:
>
> - Is there interest from your group in participating in the challenge?  
> You'll
>   want at least a few people to work on it, and someone to give a  
> presentation
>   at BOSC.
>
> - Do you have suggestions on a good theme or specific biological problem  
> to
>   tackle? We'll hope to pick something in a sweet spot that is  
> challenging
>   enough to be of interest, yet reasonable for presentation and  
> preparation.
>
> Let's discuss ideas and get this together. Since the schedule for BOSC is
> developing rapidly, please give us an idea if you're interested by
> February 12th, and copy responses to the BOSC mailing list as a central
> place for discussion.
>
> bosc at open-bio.org
>
> Thanks,
> Brad, Michael, and the BOSC organizing committee
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada

From HWillis at scripps.edu  Thu Jan 28 20:03:10 2010
From: HWillis at scripps.edu (Scooter Willis)
Date: Thu, 28 Jan 2010 20:03:10 -0500
Subject: [Biojava-dev] [MOBY-dev] OpenBio solution challenge: Project
 updates at BOSC 2010
In-Reply-To: <op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>
References: <20100128203505.GG40046@sobchak.mgh.harvard.edu>
	<op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <716E205A-5196-409F-A7BC-EF0F52AA997A@scripps.edu>

Brad

I agree with Mark that a particular problem may be biased towards a toolkit/language. Another approach would be to list a collection of problems and each group would then pick a problem to present. Could be a little more interesting to the audience as you are exposed to different problems and the various strengths of each toolkit. This could also help guide future development in the other toolkits as you would benefit from learning about the api and/or programming language. Each group would register a problem that they are going to present. From the group of problems not picked that becomes the surprise challenge where each group has 24 hours to either put together a presentation or an actual solution.

Scooter



On Jan 28, 2010, at 4:17 PM, Mark Wilkinson wrote:

> 
> Brad, this sounds exciting!
> 
> One thing strikes me, though - by asking for the sub-projects to propose
> the "grand challenge" themselves the one thing you can guarantee is that
> the "grand challenge" is solvable (or more likely, already solved!)
> 
> Other "grand challenge" kinds of meetings have an independent third party
> pose the problem that has to be solved, and then all groups work toward a
> solution and compare their results.  This would, IMO, be more revealing of
> the "state of the art" in each Open-Bio project, and point out where the
> weaknesses are that we should be focusing on...  Someone (for example,
> you!) could act as the moderator to ensure that the "grand challenge" was
> at least a reasonable one, within the scope of what an Open-Bio project
> *should* be able to solve...
> 
> Just my CAD $0.02
> 
> Mark
> 
> 
> 
> On Thu, 28 Jan 2010 12:35:05 -0800, Brad Chapman <chapmanb at 50mail.com>  
> wrote:
> 
>> Hello all;
>> The BOSC 2010 organizing committee is hard at work getting prepared for  
>> this
>> July's meeting in Boston:
>> 
>> http://www.open-bio.org/wiki/BOSC_2010
>> 
>> One of the items we've traditionally had at the conference is a project
>> update from each of the OpenBio affiliated groups. This year, we're  
>> thinking
>> about organizing these talks around a central theme: the OpenBio solution
>> challenge. We start with a biological question of general interest, and  
>> each
>> of the project talks would focus around how you would solve that problem
>> using your toolkit and programming language.
>> 
>> This is meant to provide a challenge for OpenBio contributors, a nice  
>> tutorial
>> style overview of various projects and approaches for other programmers,  
>> and a
>> fun opportunity to compete and learn from other projects. Conference  
>> attendees
>> will vote on their favorite solution, with the winner receiving fame and
>> fortune (warning: fortune not guaranteed).
>> 
>> For this to be successful, it of course requires interest and enthusiasm  
>> from
>> y'all fine folks involved with the projects. Specifically:
>> 
>> - Is there interest from your group in participating in the challenge?  
>> You'll
>>  want at least a few people to work on it, and someone to give a  
>> presentation
>>  at BOSC.
>> 
>> - Do you have suggestions on a good theme or specific biological problem  
>> to
>>  tackle? We'll hope to pick something in a sweet spot that is  
>> challenging
>>  enough to be of interest, yet reasonable for presentation and  
>> preparation.
>> 
>> Let's discuss ideas and get this together. Since the schedule for BOSC is
>> developing rapidly, please give us an idea if you're interested by
>> February 12th, and copy responses to the BOSC mailing list as a central
>> place for discussion.
>> 
>> bosc at open-bio.org
>> 
>> Thanks,
>> Brad, Michael, and the BOSC organizing committee
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 
> 
> -- 
> Mark D Wilkinson, PI Bioinformatics
> Assistant Professor, Medical Genetics
> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
> Providence Heart + Lung Institute
> University of British Columbia - St. Paul's Hospital
> Vancouver, BC, Canada
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev



From biopython at maubp.freeserve.co.uk  Fri Jan 29 05:36:40 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 29 Jan 2010 10:36:40 +0000
Subject: [Biojava-dev] [Bioperl-l] [MOBY-dev] OpenBio solution
	challenge: Project updates at BOSC 2010
In-Reply-To: <op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>
References: <20100128203505.GG40046@sobchak.mgh.harvard.edu>
	<op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <320fb6e01001290236l1ad02515w403a19f94dbb6d15@mail.gmail.com>

Hi all,

This is a great topic but should be continue it on just the one mailing list?
Is there a suitable BOSC list, or how about the general Open Bio list?

On Thu, Jan 28, 2010 at 9:17 PM, Mark Wilkinson <markw at illuminae.com> wrote:
>
> Brad, this sounds exciting!
>
> One thing strikes me, though - by asking for the sub-projects to propose
> the "grand challenge" themselves the one thing you can guarantee is that
> the "grand challenge" is solvable (or more likely, already solved!)
>
> Other "grand challenge" kinds of meetings have an independent third party
> pose the problem that has to be solved, and then all groups work toward a
> solution and compare their results. ?This would, IMO, be more revealing of
> the "state of the art" in each Open-Bio project, and point out where the
> weaknesses are that we should be focusing on... ?Someone (for example,
> you!) could act as the moderator to ensure that the "grand challenge" was
> at least a reasonable one, within the scope of what an Open-Bio project
> *should* be able to solve...
>
> Just my CAD $0.02
>
> Mark

One possible problem with having Brad act as moderator is his ties to
Biopython (plus it would be a shame if we'd be one man down for trying
to solve the challenges - grin). Having a project representative "sign off"
on the challenge might work - or simply the whole of the BOSC committee
which is quite balanced. Alternatively some kind of panel of challenges does
seem a good way to reduce individual project bias (as suggest by Scooter),
but there will still need to be a judging committee.

I'm curious what kind of challenges the BOSC committee had in mind -
would something like taking a newly sequence bacteria and producing
an automated annotation as a GenBank, EMBL, or GFF  file be too
ambitious for example? There are already several major projects
to do this e.g. RAST http://rast.nmpdr.org/

Peter
(@Biopython)


From ayates at ebi.ac.uk  Mon Jan  4 09:47:58 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Mon, 4 Jan 2010 09:47:58 +0000
Subject: [Biojava-dev] biojava hackathon
In-Reply-To: <59a41c430912210820p59ae6b46wa239ae78328098d8@mail.gmail.com>
References: <dd8886300912210723r2b22847dq48db52e14fcb1a0a@mail.gmail.com>
	<59a41c430912210820p59ae6b46wa239ae78328098d8@mail.gmail.com>
Message-ID: <31FC6A52-DE16-47B1-86E7-D5C49EA6C6FA@ebi.ac.uk>

Other hotels available near the campus are:

http://www.redlionhinxton.co.uk/ (the nearest non WT owned  
accommodation)

http://www.johnbarleycorn.co.uk/ (in the next village along)

http://www.duxfordlodgehotel.co.uk/ (see above)

http://www.wtconference.org/ (owned by WT & sometimes will offer  
accommodation)

However one problem with all of these are the costs involved; if you  
can get into the Travelodge Andreas mentioned it's normally quite a  
bit cheaper but do check carefully. Spending ?5 more per night to get  
into one of the other places can be worth it.

Andy

On 21 Dec 2009, at 16:20, Andreas Prlic wrote:

> A few people asked me where to stay and I suggested to book the
> Travelodge in Hills road. It is a plain and cheap hotel (for
> Cambridge), walking distance to the train station, town center (20
> min) and close to one of the stops of the Genome Campus bus routes.
>
> Andreas
>
> On Mon, Dec 21, 2009 at 7:23 AM, Johan Henriksson  
> <mahogny at areta.org> wrote:
>> Hello,
>> has anyone done their homework and figured out which hotels are the  
>> best.
>> maybe someone working there knows the "standard" ones?
>>
>> it seems I can join in. have not decided exactly what I will work  
>> on but
>> surely not the protein stuff. either improving the core or the
>> algorithms/data structures. I have experimented a bit with  
>> alternative ways
>> of dealing with annotation and sequence data, maybe it can be of use.
>>
>> /Johan
>>
>> --
>> -----------------------------------------------------------
>> Johan Henriksson
>> PhD student, Karolinska Institutet
>> http://mahogny.areta.org  http://www.endrov.net
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev




From holland at eaglegenomics.com  Mon Jan  4 10:57:54 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Mon, 4 Jan 2010 10:57:54 +0000
Subject: [Biojava-dev] BioJava 2010 Hackathon
Message-ID: <E304F7F2-09B7-4C46-92F9-F9CA6E68C5EC@eaglegenomics.com>

Hi all,

For those attending the 2010 BioJava hackathon at the Wellcome Trust Genome Campus, near Cambridge, all details can be found on this wiki:

  http://biojava.org/wiki/BioJava:Hackathon2010

If your name is not listed on the wiki but you are planning on attending, please let us know by Jan 12th latest. Due to security arrangements at the campus it is not possible to just turn up on the day.

Subjects for the hackathon are open for discussion on the wiki.

Looking forward to seeing you all there!

cheers,
Richard

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From jolyon.holdstock at ogt.co.uk  Wed Jan 13 12:49:17 2010
From: jolyon.holdstock at ogt.co.uk (Jolyon Holdstock)
Date: Wed, 13 Jan 2010 12:49:17 -0000
Subject: [Biojava-dev] Script for cookbook
Message-ID: <588D0DD225D05746B5D8CAE1BE971F3F02C64D8C@EUCLID.internal.ogtip.com>

Hi,

 

I was going to add the following script to the annotation section of the
cookbook. 

It takes an EMBL or Genbank file and outputs information about each CDS
feature.

 

I just wanted to check this was OK and also is this the most efficient
way of doing this?

 

Cheers,

 

Jolyon

 

[CODE]

import java.io.*;

import java.util.*;

import org.biojava.bio.*;

import org.biojava.bio.seq.*;

import org.biojava.bio.seq.io.*;

import org.biojavax.*;

import org.biojavax.ontology.*;

import org.biojavax.bio.*;

import org.biojavax.bio.seq.*;

 

public class ExtractInformation {

  //Create the RichSequence object

  RichSequence richSeq;

  public ExtractInformation(String fileName){

    //Load the sequence file

    try {

      richSeq = RichSequence.IOTools.readGenbankDNA(new
BufferedReader(new FileReader(fileName)),null).nextRichSequence();

    }

    catch(FileNotFoundException fnfe){

      System.out.println("FilwNotFoundException: " + fnfe);

    }

    catch(BioException bioe1){

      System.err.println("Not a Genbank sequence trying EMBL");

      try  {

        richSeq = RichSequence.IOTools.readGenbankDNA(new
BufferedReader(new FileReader(fileName)),null).nextRichSequence();

      }

      catch(BioException bioe2){

        System.err.println("Not an EMBL sequence either");

        System.exit(1);

      }

      catch(FileNotFoundException fnfe){

        System.out.println("FilwNotFoundException: " + fnfe);

      }

    }

    //Filter the sequence on CDS features

    FeatureFilter ff = new FeatureFilter.ByType("CDS");

    FeatureHolder fh = richSeq.filter(ff);

 

    //Iterate through the CDS features

    for (Iterator <RichFeature> i = fh.features(); i.hasNext();){

      RichFeature rf = i.next();

      

      //Get the strand orientation of the feature

      char featureStrand = rf.getStrand().getToken();

 

      //Get the location of the feature

      String featureLocation = rf.getLocation().toString();

      

      //Get the annotation of the feature

      RichAnnotation ra = (RichAnnotation)rf.getAnnotation();

 

      //Create the required ComparableTerms

      ComparableTerm geneTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");

      ComparableTerm locusTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("locus_tag");

      ComparableTerm productTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("product");

      ComparableTerm synonymTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene_synonym");

      ComparableTerm proteinIDTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("protein_id");

      

      //Create empty strings

      String gene = "";

      String locus = "";

      String product = "";

      String geneSynonym = "";

      String proteinID = "";

 

      //Iterate through the notes in the annotation 

      for (Iterator <Note> it = ra.getNoteSet().iterator();
it.hasNext();){

        Note note = it.next();

      

      //Check each note to see if it matches one of the required
ComparableTerms

        if(note.getTerm().equals(locusTerm)){

          locus = note.getValue().toString();

        }

        if(note.getTerm().equals(productTerm)){

          product = note.getValue().toString();

        }

        if(note.getTerm().equals(geneTerm)){

          gene = note.getValue().toString();

        }

        if(note.getTerm().equals(synonymTerm)){

          geneSynonym = note.getValue().toString();

        }

        if(note.getTerm().equals(proteinIDTerm)){

          proteinID = note.getValue().toString();

        }

      }

      //Outout the feature information

      System.out.println(locus + "  " + gene + "  " + geneSynonym + "  "
+ proteinID + "  " + product +"  " + featureStrand +"  Chr1:" +
featureLocation);

    }

  }

 

  public static void main(String args []){

    if (args.length != 1){

      System.out.println("Usage: java ExtractInformation <file in
Genbank or EMBL format>");

      System.exit(1);

    }

    else {

      new ExtractInformation(args[0]);

    }

  }

}

[/CODE]

 

Dr. Jolyon Holdstock                                       
Senior Computational Biologist,

Oxford Gene Technology,                                   
Begbroke Science Park,                                     
Sandy Lane, Yarnton,                                           
Oxford, OX5 1PF, UK.                                             

T: +44 (0)1865 856 852                                     
F: +44 (0)1865 842 116                                     
E: jolyon.holdstock at ogt.co.uk <mailto:nicola.booton-mander at ogt.co.uk>

W: www.ogt.co.uk <blocked::http://www.ogt.co.uk/>     

                                             

Looking to outsource your microarray studies? Look no further.
Click here to tour our facilities
<http://www.ogt.co.uk/highthroughputservices.html> 

Click here to request a quotation
<http://www.ogt.co.uk/htsquotationrequest.asp> 

 

Scientific pedigree delivering high quality microarray results to you:

*         Service capacity >1000 samples per week

*         Rigorous QC <http://www.ogt.co.uk/hts_qc.html>  from sample to
result

*         Applications <http://www.ogt.co.uk/hts_apps.html>  available
include aCGH, CNV, methylation studies and miRNA



Oxford Gene Technology (Operations) Ltd. Registered in England No:
03845432 Begbroke Science Park Sandy Lane Yarnton Oxford OX5 1PF  

Confidentiality Notice: The contents of this email from Oxford Gene
Technology are confidential and intended solely for the person to whom
it is addressed. It may contain privileged and confidential information.
If you are not the intended recipient you must not read, copy,
distribute, discuss or take any action in reliance on it. If you have
received this email in error please advise the sender so that we can
arrange for proper delivery. Then please delete the message from your
inbox. Thank you.

 

 

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From holland at eaglegenomics.com  Wed Jan 13 13:22:16 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 13 Jan 2010 13:22:16 +0000
Subject: [Biojava-dev] Script for cookbook
In-Reply-To: <588D0DD225D05746B5D8CAE1BE971F3F02C64D8C@EUCLID.internal.ogtip.com>
References: <588D0DD225D05746B5D8CAE1BE971F3F02C64D8C@EUCLID.internal.ogtip.com>
Message-ID: <982845F6-0845-474A-BEBD-C5D336C03F42@eaglegenomics.com>

Just a few minor points, otherwise all good:

 1. Your 'trying EMBL' code just tries Genbank again!
 2. Typo in the FileNotFoundException message.
 3. Check to see that your ComparableTerm retrieval statements using RichObjectFactory are not already defined as constants in RichSequence.Terms or GenbankFormat.Terms. If they are, use the constants instead as this makes the code clearer.
 4. Your system.out line that prints the results has Chr1 hardcoded - should this be a parameter, or read from the file maybe?

cheers,
Richard

On 13 Jan 2010, at 12:49, Jolyon Holdstock wrote:

> Hi,
> 
> 
> 
> I was going to add the following script to the annotation section of the
> cookbook. 
> 
> It takes an EMBL or Genbank file and outputs information about each CDS
> feature.
> 
> 
> 
> I just wanted to check this was OK and also is this the most efficient
> way of doing this?
> 
> 
> 
> Cheers,
> 
> 
> 
> Jolyon
> 
> 
> 
> [CODE]
> 
> import java.io.*;
> 
> import java.util.*;
> 
> import org.biojava.bio.*;
> 
> import org.biojava.bio.seq.*;
> 
> import org.biojava.bio.seq.io.*;
> 
> import org.biojavax.*;
> 
> import org.biojavax.ontology.*;
> 
> import org.biojavax.bio.*;
> 
> import org.biojavax.bio.seq.*;
> 
> 
> 
> public class ExtractInformation {
> 
>  //Create the RichSequence object
> 
>  RichSequence richSeq;
> 
>  public ExtractInformation(String fileName){
> 
>    //Load the sequence file
> 
>    try {
> 
>      richSeq = RichSequence.IOTools.readGenbankDNA(new
> BufferedReader(new FileReader(fileName)),null).nextRichSequence();
> 
>    }
> 
>    catch(FileNotFoundException fnfe){
> 
>      System.out.println("FilwNotFoundException: " + fnfe);
> 
>    }
> 
>    catch(BioException bioe1){
> 
>      System.err.println("Not a Genbank sequence trying EMBL");
> 
>      try  {
> 
>        richSeq = RichSequence.IOTools.readGenbankDNA(new
> BufferedReader(new FileReader(fileName)),null).nextRichSequence();
> 
>      }
> 
>      catch(BioException bioe2){
> 
>        System.err.println("Not an EMBL sequence either");
> 
>        System.exit(1);
> 
>      }
> 
>      catch(FileNotFoundException fnfe){
> 
>        System.out.println("FilwNotFoundException: " + fnfe);
> 
>      }
> 
>    }
> 
>    //Filter the sequence on CDS features
> 
>    FeatureFilter ff = new FeatureFilter.ByType("CDS");
> 
>    FeatureHolder fh = richSeq.filter(ff);
> 
> 
> 
>    //Iterate through the CDS features
> 
>    for (Iterator <RichFeature> i = fh.features(); i.hasNext();){
> 
>      RichFeature rf = i.next();
> 
> 
> 
>      //Get the strand orientation of the feature
> 
>      char featureStrand = rf.getStrand().getToken();
> 
> 
> 
>      //Get the location of the feature
> 
>      String featureLocation = rf.getLocation().toString();
> 
> 
> 
>      //Get the annotation of the feature
> 
>      RichAnnotation ra = (RichAnnotation)rf.getAnnotation();
> 
> 
> 
>      //Create the required ComparableTerms
> 
>      ComparableTerm geneTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");
> 
>      ComparableTerm locusTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("locus_tag");
> 
>      ComparableTerm productTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("product");
> 
>      ComparableTerm synonymTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene_synonym");
> 
>      ComparableTerm proteinIDTerm =
> RichObjectFactory.getDefaultOntology().getOrCreateTerm("protein_id");
> 
> 
> 
>      //Create empty strings
> 
>      String gene = "";
> 
>      String locus = "";
> 
>      String product = "";
> 
>      String geneSynonym = "";
> 
>      String proteinID = "";
> 
> 
> 
>      //Iterate through the notes in the annotation 
> 
>      for (Iterator <Note> it = ra.getNoteSet().iterator();
> it.hasNext();){
> 
>        Note note = it.next();
> 
> 
> 
>      //Check each note to see if it matches one of the required
> ComparableTerms
> 
>        if(note.getTerm().equals(locusTerm)){
> 
>          locus = note.getValue().toString();
> 
>        }
> 
>        if(note.getTerm().equals(productTerm)){
> 
>          product = note.getValue().toString();
> 
>        }
> 
>        if(note.getTerm().equals(geneTerm)){
> 
>          gene = note.getValue().toString();
> 
>        }
> 
>        if(note.getTerm().equals(synonymTerm)){
> 
>          geneSynonym = note.getValue().toString();
> 
>        }
> 
>        if(note.getTerm().equals(proteinIDTerm)){
> 
>          proteinID = note.getValue().toString();
> 
>        }
> 
>      }
> 
>      //Outout the feature information
> 
>      System.out.println(locus + "  " + gene + "  " + geneSynonym + "  "
> + proteinID + "  " + product +"  " + featureStrand +"  Chr1:" +
> featureLocation);
> 
>    }
> 
>  }
> 
> 
> 
>  public static void main(String args []){
> 
>    if (args.length != 1){
> 
>      System.out.println("Usage: java ExtractInformation <file in
> Genbank or EMBL format>");
> 
>      System.exit(1);
> 
>    }
> 
>    else {
> 
>      new ExtractInformation(args[0]);
> 
>    }
> 
>  }
> 
> }
> 
> [/CODE]
> 
> 
> 
> Dr. Jolyon Holdstock                                       
> Senior Computational Biologist,
> 
> Oxford Gene Technology,                                   
> Begbroke Science Park,                                     
> Sandy Lane, Yarnton,                                           
> Oxford, OX5 1PF, UK.                                             
> 
> T: +44 (0)1865 856 852                                     
> F: +44 (0)1865 842 116                                     
> E: jolyon.holdstock at ogt.co.uk <mailto:nicola.booton-mander at ogt.co.uk>
> 
> W: www.ogt.co.uk <blocked::http://www.ogt.co.uk/>     
> 
> 
> 
> Looking to outsource your microarray studies? Look no further.
> Click here to tour our facilities
> <http://www.ogt.co.uk/highthroughputservices.html> 
> 
> Click here to request a quotation
> <http://www.ogt.co.uk/htsquotationrequest.asp> 
> 
> 
> 
> Scientific pedigree delivering high quality microarray results to you:
> 
> *         Service capacity >1000 samples per week
> 
> *         Rigorous QC <http://www.ogt.co.uk/hts_qc.html>  from sample to
> result
> 
> *         Applications <http://www.ogt.co.uk/hts_apps.html>  available
> include aCGH, CNV, methylation studies and miRNA
> 
> 
> 
> Oxford Gene Technology (Operations) Ltd. Registered in England No:
> 03845432 Begbroke Science Park Sandy Lane Yarnton Oxford OX5 1PF  
> 
> Confidentiality Notice: The contents of this email from Oxford Gene
> Technology are confidential and intended solely for the person to whom
> it is addressed. It may contain privileged and confidential information.
> If you are not the intended recipient you must not read, copy,
> distribute, discuss or take any action in reliance on it. If you have
> received this email in error please advise the sender so that we can
> arrange for proper delivery. Then please delete the message from your
> inbox. Thank you.
> 
> 
> 
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From genjasp at gmail.com  Wed Jan 13 14:14:26 2010
From: genjasp at gmail.com (Alessandro Cipriani)
Date: Wed, 13 Jan 2010 15:14:26 +0100
Subject: [Biojava-dev] Script for cookbook
In-Reply-To: <982845F6-0845-474A-BEBD-C5D336C03F42@eaglegenomics.com>
References: <588D0DD225D05746B5D8CAE1BE971F3F02C64D8C@EUCLID.internal.ogtip.com>
	<982845F6-0845-474A-BEBD-C5D336C03F42@eaglegenomics.com>
Message-ID: <46b9a2151001130614i1d1b057xfdffa8f0051d0b89@mail.gmail.com>

Hi,
i think it is not a good practice:
-to insert a try/catch block into anothet try/catch block.
-to import all lib even  unrequired
-to make all methods public

otherwise it seems to be ok!

Regards

Alex


2010/1/13 Richard Holland <holland at eaglegenomics.com>:
> Just a few minor points, otherwise all good:
>
> ?1. Your 'trying EMBL' code just tries Genbank again!
> ?2. Typo in the FileNotFoundException message.
> ?3. Check to see that your ComparableTerm retrieval statements using RichObjectFactory are not already defined as constants in RichSequence.Terms or GenbankFormat.Terms. If they are, use the constants instead as this makes the code clearer.
> ?4. Your system.out line that prints the results has Chr1 hardcoded - should this be a parameter, or read from the file maybe?
>
> cheers,
> Richard
>
> On 13 Jan 2010, at 12:49, Jolyon Holdstock wrote:
>
>> Hi,
>>
>>
>>
>> I was going to add the following script to the annotation section of the
>> cookbook.
>>
>> It takes an EMBL or Genbank file and outputs information about each CDS
>> feature.
>>
>>
>>
>> I just wanted to check this was OK and also is this the most efficient
>> way of doing this?
>>
>>
>>
>> Cheers,
>>
>>
>>
>> Jolyon
>>
>>
>>
>> [CODE]
>>
>> import java.io.*;
>>
>> import java.util.*;
>>
>> import org.biojava.bio.*;
>>
>> import org.biojava.bio.seq.*;
>>
>> import org.biojava.bio.seq.io.*;
>>
>> import org.biojavax.*;
>>
>> import org.biojavax.ontology.*;
>>
>> import org.biojavax.bio.*;
>>
>> import org.biojavax.bio.seq.*;
>>
>>
>>
>> public class ExtractInformation {
>>
>> ?//Create the RichSequence object
>>
>> ?RichSequence richSeq;
>>
>> ?public ExtractInformation(String fileName){
>>
>> ? ?//Load the sequence file
>>
>> ? ?try {
>>
>> ? ? ?richSeq = RichSequence.IOTools.readGenbankDNA(new
>> BufferedReader(new FileReader(fileName)),null).nextRichSequence();
>>
>> ? ?}
>>
>> ? ?catch(FileNotFoundException fnfe){
>>
>> ? ? ?System.out.println("FilwNotFoundException: " + fnfe);
>>
>> ? ?}
>>
>> ? ?catch(BioException bioe1){
>>
>> ? ? ?System.err.println("Not a Genbank sequence trying EMBL");
>>
>> ? ? ?try ?{
>>
>> ? ? ? ?richSeq = RichSequence.IOTools.readGenbankDNA(new
>> BufferedReader(new FileReader(fileName)),null).nextRichSequence();
>>
>> ? ? ?}
>>
>> ? ? ?catch(BioException bioe2){
>>
>> ? ? ? ?System.err.println("Not an EMBL sequence either");
>>
>> ? ? ? ?System.exit(1);
>>
>> ? ? ?}
>>
>> ? ? ?catch(FileNotFoundException fnfe){
>>
>> ? ? ? ?System.out.println("FilwNotFoundException: " + fnfe);
>>
>> ? ? ?}
>>
>> ? ?}
>>
>> ? ?//Filter the sequence on CDS features
>>
>> ? ?FeatureFilter ff = new FeatureFilter.ByType("CDS");
>>
>> ? ?FeatureHolder fh = richSeq.filter(ff);
>>
>>
>>
>> ? ?//Iterate through the CDS features
>>
>> ? ?for (Iterator <RichFeature> i = fh.features(); i.hasNext();){
>>
>> ? ? ?RichFeature rf = i.next();
>>
>>
>>
>> ? ? ?//Get the strand orientation of the feature
>>
>> ? ? ?char featureStrand = rf.getStrand().getToken();
>>
>>
>>
>> ? ? ?//Get the location of the feature
>>
>> ? ? ?String featureLocation = rf.getLocation().toString();
>>
>>
>>
>> ? ? ?//Get the annotation of the feature
>>
>> ? ? ?RichAnnotation ra = (RichAnnotation)rf.getAnnotation();
>>
>>
>>
>> ? ? ?//Create the required ComparableTerms
>>
>> ? ? ?ComparableTerm geneTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");
>>
>> ? ? ?ComparableTerm locusTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("locus_tag");
>>
>> ? ? ?ComparableTerm productTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("product");
>>
>> ? ? ?ComparableTerm synonymTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene_synonym");
>>
>> ? ? ?ComparableTerm proteinIDTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("protein_id");
>>
>>
>>
>> ? ? ?//Create empty strings
>>
>> ? ? ?String gene = "";
>>
>> ? ? ?String locus = "";
>>
>> ? ? ?String product = "";
>>
>> ? ? ?String geneSynonym = "";
>>
>> ? ? ?String proteinID = "";
>>
>>
>>
>> ? ? ?//Iterate through the notes in the annotation
>>
>> ? ? ?for (Iterator <Note> it = ra.getNoteSet().iterator();
>> it.hasNext();){
>>
>> ? ? ? ?Note note = it.next();
>>
>>
>>
>> ? ? ?//Check each note to see if it matches one of the required
>> ComparableTerms
>>
>> ? ? ? ?if(note.getTerm().equals(locusTerm)){
>>
>> ? ? ? ? ?locus = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ? ?if(note.getTerm().equals(productTerm)){
>>
>> ? ? ? ? ?product = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ? ?if(note.getTerm().equals(geneTerm)){
>>
>> ? ? ? ? ?gene = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ? ?if(note.getTerm().equals(synonymTerm)){
>>
>> ? ? ? ? ?geneSynonym = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ? ?if(note.getTerm().equals(proteinIDTerm)){
>>
>> ? ? ? ? ?proteinID = note.getValue().toString();
>>
>> ? ? ? ?}
>>
>> ? ? ?}
>>
>> ? ? ?//Outout the feature information
>>
>> ? ? ?System.out.println(locus + " ?" + gene + " ?" + geneSynonym + " ?"
>> + proteinID + " ?" + product +" ?" + featureStrand +" ?Chr1:" +
>> featureLocation);
>>
>> ? ?}
>>
>> ?}
>>
>>
>>
>> ?public static void main(String args []){
>>
>> ? ?if (args.length != 1){
>>
>> ? ? ?System.out.println("Usage: java ExtractInformation <file in
>> Genbank or EMBL format>");
>>
>> ? ? ?System.exit(1);
>>
>> ? ?}
>>
>> ? ?else {
>>
>> ? ? ?new ExtractInformation(args[0]);
>>
>> ? ?}
>>
>> ?}
>>
>> }
>>
>> [/CODE]
>>
>>
>>
>> Dr. Jolyon Holdstock
>> Senior Computational Biologist,
>>
>> Oxford Gene Technology,
>> Begbroke Science Park,
>> Sandy Lane, Yarnton,
>> Oxford, OX5 1PF, UK.
>>
>> T: +44 (0)1865 856 852
>> F: +44 (0)1865 842 116
>> E: jolyon.holdstock at ogt.co.uk <mailto:nicola.booton-mander at ogt.co.uk>
>>
>> W: www.ogt.co.uk <blocked::http://www.ogt.co.uk/>
>>
>>
>>
>> Looking to outsource your microarray studies? Look no further.
>> Click here to tour our facilities
>> <http://www.ogt.co.uk/highthroughputservices.html>
>>
>> Click here to request a quotation
>> <http://www.ogt.co.uk/htsquotationrequest.asp>
>>
>>
>>
>> Scientific pedigree delivering high quality microarray results to you:
>>
>> * ? ? ? ? Service capacity >1000 samples per week
>>
>> * ? ? ? ? Rigorous QC <http://www.ogt.co.uk/hts_qc.html> ?from sample to
>> result
>>
>> * ? ? ? ? Applications <http://www.ogt.co.uk/hts_apps.html> ?available
>> include aCGH, CNV, methylation studies and miRNA
>>
>>
>>
>> Oxford Gene Technology (Operations) Ltd. Registered in England No:
>> 03845432 Begbroke Science Park Sandy Lane Yarnton Oxford OX5 1PF
>>
>> Confidentiality Notice: The contents of this email from Oxford Gene
>> Technology are confidential and intended solely for the person to whom
>> it is addressed. It may contain privileged and confidential information.
>> If you are not the intended recipient you must not read, copy,
>> distribute, discuss or take any action in reliance on it. If you have
>> received this email in error please advise the sender so that we can
>> arrange for proper delivery. Then please delete the message from your
>> inbox. Thank you.
>>
>>
>>
>>
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



From mahogny at areta.org  Sun Jan 17 17:52:45 2010
From: mahogny at areta.org (Johan Henriksson)
Date: Sun, 17 Jan 2010 18:52:45 +0100
Subject: [Biojava-dev] biojava hackathon
In-Reply-To: <dd8886300912210723r2b22847dq48db52e14fcb1a0a@mail.gmail.com>
References: <dd8886300912210723r2b22847dq48db52e14fcb1a0a@mail.gmail.com>
Message-ID: <dd8886301001170952k2684c4f4xf6e53951b063dbe8@mail.gmail.com>

sorry, I will not be able to attend the hackathon this year for a whole lot
of reasons. in addition, sorry for telling this so late.

I'm looking forward to the next one though; happy hacking to the rest of
you!

/Johan

-- 
-----------------------------------------------------------
Johan Henriksson
PhD student, Karolinska Institutet
http://mahogny.areta.org  http://www.endrov.net


From heuermh at acm.org  Tue Jan 19 04:54:21 2010
From: heuermh at acm.org (Michael Heuer)
Date: Mon, 18 Jan 2010 23:54:21 -0500 (EST)
Subject: [Biojava-dev] hackathon task list, pom refactoring, &c.
In-Reply-To: <E304F7F2-09B7-4C46-92F9-F9CA6E68C5EC@eaglegenomics.com>
Message-ID: <Pine.GSO.4.44.1001182335530.409-100000@shell3.shore.net>

Hello Hackathon participants,

Might we start a task list for the hackathon tomorrow, on the biojava
wiki perhaps?  It would be nice to be able to contribute to the list of
tasks and to claim tasks to work on from off-site.

Today I refactored and cleaned up all the maven poms.  Build and test
works for me on linux, win, and mac with commandline maven.  Eclipse via
m2eclipse is good for almost everything, but has trouble firing off the
maven-jaxb2-plugin code generation step.

If you want to give it a try, version maven 3.0.6-alpha is a lot
more picky about reproducable builds than earlier versions, and
complained a ton when I first started.  Now the only warning is the
deprecated maven1 repo link at java.net.

I have set up cia.vc to post svn commit notification via IRC to #biojava
on irc.freenode.net.  I'll also be on there most of the day tomorrow, or
available on google chat.

Ah, with the blogs and the twitter and stuff, I can't keep up.  ;)

   michael



From heuermh at acm.org  Tue Jan 19 05:02:28 2010
From: heuermh at acm.org (Michael Heuer)
Date: Tue, 19 Jan 2010 00:02:28 -0500 (EST)
Subject: [Biojava-dev] [Biojava-l] BioJava Hackathon - Day 1
In-Reply-To: <95988839-75A3-4087-8071-5A19BEECDD04@eaglegenomics.com>
Message-ID: <Pine.GSO.4.44.1001182354410.409-100000@shell3.shore.net>

On Mon, 18 Jan 2010, Richard Holland wrote:

> ...
>
> Also by making the new SymbolList implement the standard List
> interface from Collections, it can be used in nice Java shortcuts such
> as the new foreach loops, and standard iterators can be used (instead of
> the current SymbolListIterator method). Collections API can also be used
> then to do things like subsets or reverses.

Is this a good idea?  It might preclude some efficient implementation
strategies, such as ParallelArray from JSR166

http://gee.cs.oswego.edu/dl/jsr166/dist/extra166ydocs/extra166y/ParallelArray.html

Would Iterable be sufficient enough?

Also, List indexing is not compatible with typical sequence feature
indexing.

   michael



From holland at eaglegenomics.com  Tue Jan 19 05:45:14 2010
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 19 Jan 2010 05:45:14 +0000
Subject: [Biojava-dev] [Biojava-l] BioJava Hackathon - Day 1
In-Reply-To: <Pine.GSO.4.44.1001182354410.409-100000@shell3.shore.net>
References: <Pine.GSO.4.44.1001182354410.409-100000@shell3.shore.net>
Message-ID: <56B4AA4E-FF88-4D4E-BD95-49B76194FA82@eaglegenomics.com>

Good point - Iterable would probably be fine.

On 19 Jan 2010, at 05:02, Michael Heuer wrote:

> On Mon, 18 Jan 2010, Richard Holland wrote:
> 
>> ...
>> 
>> Also by making the new SymbolList implement the standard List
>> interface from Collections, it can be used in nice Java shortcuts such
>> as the new foreach loops, and standard iterators can be used (instead of
>> the current SymbolListIterator method). Collections API can also be used
>> then to do things like subsets or reverses.
> 
> Is this a good idea?  It might preclude some efficient implementation
> strategies, such as ParallelArray from JSR166
> 
> http://gee.cs.oswego.edu/dl/jsr166/dist/extra166ydocs/extra166y/ParallelArray.html
> 
> Would Iterable be sufficient enough?
> 
> Also, List indexing is not compatible with typical sequence feature
> indexing.
> 
>   michael
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/




From ayates at ebi.ac.uk  Tue Jan 19 08:50:49 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 19 Jan 2010 08:50:49 +0000
Subject: [Biojava-dev] [Biojava-l] BioJava Hackathon - Day 1
In-Reply-To: <56B4AA4E-FF88-4D4E-BD95-49B76194FA82@eaglegenomics.com>
References: <Pine.GSO.4.44.1001182354410.409-100000@shell3.shore.net>
	<56B4AA4E-FF88-4D4E-BD95-49B76194FA82@eaglegenomics.com>
Message-ID: <25714175-4B75-4D30-AA42-E0176060DCAB@ebi.ac.uk>

This somewhat targets what this new version should be about; making  
the most of Java5+ features (Iterable & generics being the first  
things that spring to mind).


On 19 Jan 2010, at 05:45, Richard Holland wrote:

> Good point - Iterable would probably be fine.
>
> On 19 Jan 2010, at 05:02, Michael Heuer wrote:
>
>> On Mon, 18 Jan 2010, Richard Holland wrote:
>>
>>> ...
>>>
>>> Also by making the new SymbolList implement the standard List
>>> interface from Collections, it can be used in nice Java shortcuts  
>>> such
>>> as the new foreach loops, and standard iterators can be used  
>>> (instead of
>>> the current SymbolListIterator method). Collections API can also  
>>> be used
>>> then to do things like subsets or reverses.
>>
>> Is this a good idea?  It might preclude some efficient implementation
>> strategies, such as ParallelArray from JSR166
>>
>> http://gee.cs.oswego.edu/dl/jsr166/dist/extra166ydocs/extra166y/ParallelArray.html
>>
>> Would Iterable be sufficient enough?
>>
>> Also, List indexing is not compatible with typical sequence feature
>> indexing.
>>
>>  michael
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev



From andy.law at roslin.ed.ac.uk  Tue Jan 19 09:23:26 2010
From: andy.law at roslin.ed.ac.uk (Andy Law (RI))
Date: Tue, 19 Jan 2010 09:23:26 +0000
Subject: [Biojava-dev] hackathon task list, pom refactoring, &c.
In-Reply-To: <Pine.GSO.4.44.1001182335530.409-100000@shell3.shore.net>
References: <Pine.GSO.4.44.1001182335530.409-100000@shell3.shore.net>
Message-ID: <6B943C9E-98E1-4788-8860-2B6AC266421C@roslin.ed.ac.uk>


On 19 Jan 2010, at 04:54, Michael Heuer wrote:


>
> I have set up cia.vc to post svn commit notification via IRC to  
> #biojava
> on irc.freenode.net.  I'll also be on there most of the day  
> tomorrow, or
> available on google chat.
>
> Ah, with the blogs and the twitter and stuff, I can't keep up.  ;)


Sheesh! What was ever wrong with posting occasional notes via email?



Later,

Andy
--------
Yada, yada, yada...
The University of Edinburgh is a charitable body, registered in  
Scotland, with registration number SC005336
Disclaimer: This e-mail and any attachments are confidential and  
intended solely for the use of the recipient(s) to whom they are  
addressed. If you have received it in error, please destroy all copies  
and inform the sender.





From jw12 at sanger.ac.uk  Tue Jan 19 10:41:12 2010
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Tue, 19 Jan 2010 10:41:12 +0000
Subject: [Biojava-dev] DAS Workshop Registrations now Open (workshop date
	7-9 April 2010)
Message-ID: <9EDF4E46-15F8-434E-B557-2DE5906C4182@sanger.ac.uk>

If you don't know about DAS and wish to know how to distribute your  
latest biological annotation to the world then the upcoming DAS  
workshop maybe for you.
If you know about DAS and are maybe a DAS client developer then the  
upcoming DAS workshop is for you (as you will need to know about the  
upcoming DAS 1.6 Specification and how it may affect your software).

For information on the workshop and registration please go to:

http://www.ebi.ac.uk/training/handson/DAS_070410.html



Jonathan Warren
Senior Developer and DAS coordinator
jw12 at sanger.ac.uk








-- 
 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 heuermh at acm.org  Wed Jan 20 00:52:29 2010
From: heuermh at acm.org (Michael Heuer)
Date: Tue, 19 Jan 2010 19:52:29 -0500 (EST)
Subject: [Biojava-dev] sequence-core tests currently do not compile
In-Reply-To: <6B943C9E-98E1-4788-8860-2B6AC266421C@roslin.ed.ac.uk>
Message-ID: <Pine.GSO.4.44.1001191950560.15376-100000@shell3.shore.net>


Module sequence-core tests currently do not compile

[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-compiler-plugin:2.0.2:testCompile
(default-testCompile) on project sequence-co
re: Compilation failure: Compilation failure:
C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[8,7]
class DNATests
is public, should be declared in a file named DNATests.java

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[45,9]
cannot find sy
mbol
symbol  : class Sequence
location: class org.biojava3.core.DNATests

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[45,28]
cannot find s
ymbol
symbol  : class DNACompound
location: class org.biojava3.core.DNATests

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[40,17]
cannot find s
ymbol
symbol  : class BadSequence
location: class org.biojava3.core.DNATests

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[12,15]
getSeq(java.l
ang.String) in org.biojava3.core.DNATests cannot be applied to ()

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[18,15]
getSeq(java.l
ang.String) in org.biojava3.core.DNATests cannot be applied to ()

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[24,15]
getSeq(java.l
ang.String) in org.biojava3.core.DNATests cannot be applied to ()

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[37,16]
cannot find s
ymbol
symbol  : variable toString
location: class java.lang.String

C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence-core\src\test\java\org\biojava3\core\DnaTests.java:[47,15]
cannot find s
ymbol
symbol  : class DNASequence
location: class org.biojava3.core.DNATests



From ayates at ebi.ac.uk  Wed Jan 20 09:55:31 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Wed, 20 Jan 2010 09:55:31 +0000
Subject: [Biojava-dev] sequence-core tests currently do not compile
In-Reply-To: <Pine.GSO.4.44.1001191950560.15376-100000@shell3.shore.net>
References: <Pine.GSO.4.44.1001191950560.15376-100000@shell3.shore.net>
Message-ID: <9981AAC1-1197-4DF7-B347-5ADE4E0C03C0@ebi.ac.uk>

Hmmm interesting. That should have all been commented out I thought. I  
will fix & commit back
On 20 Jan 2010, at 00:52, Michael Heuer wrote:

>
> Module sequence-core tests currently do not compile
>
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-compiler-plugin:2.0.2:testCompile
> (default-testCompile) on project sequence-co
> re: Compilation failure: Compilation failure:
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[8,7]
> class DNATests
> is public, should be declared in a file named DNATests.java
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[45,9]
> cannot find sy
> mbol
> symbol  : class Sequence
> location: class org.biojava3.core.DNATests
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[45,28]
> cannot find s
> ymbol
> symbol  : class DNACompound
> location: class org.biojava3.core.DNATests
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[40,17]
> cannot find s
> ymbol
> symbol  : class BadSequence
> location: class org.biojava3.core.DNATests
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[12,15]
> getSeq(java.l
> ang.String) in org.biojava3.core.DNATests cannot be applied to ()
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[18,15]
> getSeq(java.l
> ang.String) in org.biojava3.core.DNATests cannot be applied to ()
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[24,15]
> getSeq(java.l
> ang.String) in org.biojava3.core.DNATests cannot be applied to ()
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[37,16]
> cannot find s
> ymbol
> symbol  : variable toString
> location: class java.lang.String
>
> C:\cygwin\home\heuermh\working\biojava-live-trunk\sequence\sequence- 
> core\src\test\java\org\biojava3\core\DnaTests.java:[47,15]
> cannot find s
> ymbol
> symbol  : class DNASequence
> location: class org.biojava3.core.DNATests
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev



From HWillis at scripps.edu  Tue Jan 26 18:09:36 2010
From: HWillis at scripps.edu (Scooter Willis)
Date: Tue, 26 Jan 2010 13:09:36 -0500
Subject: [Biojava-dev] Code Update
Message-ID: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>


I checked in updates with test cases for Fasta fileparsing where the main focus is on the fasta header.  The test cases are based on the wikipedia examples so results will vary with actual files. It is very easy now to do a custom header parser so we have lots of flexibility.  I also started the code for the file pointer sequence proxy where the key usage is creating a sequence with the header and storing a reference to the file and offset in the file for the start of the sequence. When a method is called related to getting a sequence/subsequence the init() method is called to load the sequence data via RandomAccessFile with a seek to the offset. It turns out that none of the java io classes will actually return an offset index of the actual bytes read. This also gets complicated with the readline() methods where the CR and/or LF is stripped off when the string is returned so you can't keep track of it externally. I copied the BufferedReader.java class to BufferedReaderBytesRead.java and keep track of the file pointer internally. This code still needs to be tested. This should be a great way to load large date sets with minimal memory. To complete this approach I will probably do a collection that is proxy aware that can go through and free up storage by returning a sequence to its proxy state.

I will work this week on getting some wiki pages created to give examples on using the header parsing interface and proxy sequences. How do we want to organize wiki pages related to biojava3 work? 

Thanks

Scooter


From andreas at sdsc.edu  Tue Jan 26 18:45:59 2010
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 26 Jan 2010 10:45:59 -0800
Subject: [Biojava-dev] Code Update
In-Reply-To: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
References: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
Message-ID: <59a41c431001261045g301d8a48hbd55999cafa5601c@mail.gmail.com>

the cookbook approach seems to work quite well. You could start a new
"Chapter" in the book and make it clear that this will be only
available once biojava 3 has been released (or via SVN checkout)

Andreas

On Tue, Jan 26, 2010 at 10:09 AM, Scooter Willis <HWillis at scripps.edu> wrote:
>
> I checked in updates with test cases for Fasta fileparsing where the main focus is on the fasta header. ?The test cases are based on the wikipedia examples so results will vary with actual files. It is very easy now to do a custom header parser so we have lots of flexibility. ?I also started the code for the file pointer sequence proxy where the key usage is creating a sequence with the header and storing a reference to the file and offset in the file for the start of the sequence. When a method is called related to getting a sequence/subsequence the init() method is called to load the sequence data via RandomAccessFile with a seek to the offset. It turns out that none of the java io classes will actually return an offset index of the actual bytes read. This also gets complicated with the readline() methods where the CR and/or LF is stripped off when the string is returned so you can't keep track of it externally. I copied the BufferedReader.java class to BufferedReaderBytes!
> ?Read.java and keep track of the file pointer internally. This code still needs to be tested. This should be a great way to load large date sets with minimal memory. To complete this approach I will probably do a collection that is proxy aware that can go through and free up storage by returning a sequence to its proxy state.
>
> I will work this week on getting some wiki pages created to give examples on using the header parsing interface and proxy sequences. How do we want to organize wiki pages related to biojava3 work?
>
> Thanks
>
> Scooter
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



From ayates at ebi.ac.uk  Tue Jan 26 19:58:43 2010
From: ayates at ebi.ac.uk (Andy Yates)
Date: Tue, 26 Jan 2010 19:58:43 +0000
Subject: [Biojava-dev] Code Update
In-Reply-To: <59a41c431001261045g301d8a48hbd55999cafa5601c@mail.gmail.com>
References: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
	<59a41c431001261045g301d8a48hbd55999cafa5601c@mail.gmail.com>
Message-ID: <7075E1DA-E19E-4AB0-A6DC-DF2A62D7DDE8@ebi.ac.uk>

Talking about code updates I've got DNA -> RNA -> Peptide working  
quite well. It's about a day or two of tinkering away from being  in a  
sensible state. There's also some utilities I've gone & created;  
they've gone into org.biojava3.core.util ... anyone got any better  
suggestions as to where they should live?

Andy

On 26 Jan 2010, at 18:45, Andreas Prlic wrote:

> the cookbook approach seems to work quite well. You could start a new
> "Chapter" in the book and make it clear that this will be only
> available once biojava 3 has been released (or via SVN checkout)
>
> Andreas
>
> On Tue, Jan 26, 2010 at 10:09 AM, Scooter Willis  
> <HWillis at scripps.edu> wrote:
>>
>> I checked in updates with test cases for Fasta fileparsing where  
>> the main focus is on the fasta header.  The test cases are based on  
>> the wikipedia examples so results will vary with actual files. It  
>> is very easy now to do a custom header parser so we have lots of  
>> flexibility.  I also started the code for the file pointer sequence  
>> proxy where the key usage is creating a sequence with the header  
>> and storing a reference to the file and offset in the file for the  
>> start of the sequence. When a method is called related to getting a  
>> sequence/subsequence the init() method is called to load the  
>> sequence data via RandomAccessFile with a seek to the offset. It  
>> turns out that none of the java io classes will actually return an  
>> offset index of the actual bytes read. This also gets complicated  
>> with the readline() methods where the CR and/or LF is stripped off  
>> when the string is returned so you can't keep track of it  
>> externally. I copied the BufferedReader.java class to  
>> BufferedReaderBytes!
>>  Read.java and keep track of the file pointer internally. This code  
>> still needs to be tested. This should be a great way to load large  
>> date sets with minimal memory. To complete this approach I will  
>> probably do a collection that is proxy aware that can go through  
>> and free up storage by returning a sequence to its proxy state.
>>
>> I will work this week on getting some wiki pages created to give  
>> examples on using the header parsing interface and proxy sequences.  
>> How do we want to organize wiki pages related to biojava3 work?
>>
>> Thanks
>>
>> Scooter
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev



From HWillis at scripps.edu  Tue Jan 26 20:17:47 2010
From: HWillis at scripps.edu (Scooter Willis)
Date: Tue, 26 Jan 2010 15:17:47 -0500
Subject: [Biojava-dev] Code Update
In-Reply-To: <7075E1DA-E19E-4AB0-A6DC-DF2A62D7DDE8@ebi.ac.uk>
References: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
	<59a41c431001261045g301d8a48hbd55999cafa5601c@mail.gmail.com>
	<7075E1DA-E19E-4AB0-A6DC-DF2A62D7DDE8@ebi.ac.uk>
Message-ID: <56D4673E-EB91-43BA-BE0F-99BCD202752A@scripps.edu>

Andy

Let me know when you have that in a healthy state and I will work on the gtf/gff3 parser->create gene->transcript->(exon)->to protein code.

Scooter

On Jan 26, 2010, at 2:58 PM, Andy Yates wrote:

> Talking about code updates I've got DNA -> RNA -> Peptide working  
> quite well. It's about a day or two of tinkering away from being  in a  
> sensible state. There's also some utilities I've gone & created;  
> they've gone into org.biojava3.core.util ... anyone got any better  
> suggestions as to where they should live?
> 
> Andy
> 
> On 26 Jan 2010, at 18:45, Andreas Prlic wrote:
> 
>> the cookbook approach seems to work quite well. You could start a new
>> "Chapter" in the book and make it clear that this will be only
>> available once biojava 3 has been released (or via SVN checkout)
>> 
>> Andreas
>> 
>> On Tue, Jan 26, 2010 at 10:09 AM, Scooter Willis  
>> <HWillis at scripps.edu> wrote:
>>> 
>>> I checked in updates with test cases for Fasta fileparsing where  
>>> the main focus is on the fasta header.  The test cases are based on  
>>> the wikipedia examples so results will vary with actual files. It  
>>> is very easy now to do a custom header parser so we have lots of  
>>> flexibility.  I also started the code for the file pointer sequence  
>>> proxy where the key usage is creating a sequence with the header  
>>> and storing a reference to the file and offset in the file for the  
>>> start of the sequence. When a method is called related to getting a  
>>> sequence/subsequence the init() method is called to load the  
>>> sequence data via RandomAccessFile with a seek to the offset. It  
>>> turns out that none of the java io classes will actually return an  
>>> offset index of the actual bytes read. This also gets complicated  
>>> with the readline() methods where the CR and/or LF is stripped off  
>>> when the string is returned so you can't keep track of it  
>>> externally. I copied the BufferedReader.java class to  
>>> BufferedReaderBytes!
>>> Read.java and keep track of the file pointer internally. This code  
>>> still needs to be tested. This should be a great way to load large  
>>> date sets with minimal memory. To complete this approach I will  
>>> probably do a collection that is proxy aware that can go through  
>>> and free up storage by returning a sequence to its proxy state.
>>> 
>>> I will work this week on getting some wiki pages created to give  
>>> examples on using the header parsing interface and proxy sequences.  
>>> How do we want to organize wiki pages related to biojava3 work?
>>> 
>>> Thanks
>>> 
>>> Scooter
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>> 
>> 
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 




From jacobsen at ebi.ac.uk  Wed Jan 27 11:32:31 2010
From: jacobsen at ebi.ac.uk (Jules Jacobsen)
Date: Wed, 27 Jan 2010 11:32:31 +0000
Subject: [Biojava-dev] Code Update
In-Reply-To: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
References: <5DC3EABB-E571-4D23-BDA7-D74A0CCAD804@scripps.edu>
Message-ID: <4B60244F.2070603@ebi.ac.uk>

Cool - I've a sudden need for a SELEX reader/parser so will try and 
knock one of those together in the immediate future - might lift some 
code from Jalview for this purpose and see how the new 
MultipleSequenceAlignment class behaves in real life.

Plus I've just tweaked the FastaReader and FastaWriter to be setup-neutral.

Jules

On 26/01/2010 18:09, Scooter Willis wrote:
> I checked in updates with test cases for Fasta fileparsing where the main focus is on the fasta header.  The test cases are based on the wikipedia examples so results will vary with actual files. It is very easy now to do a custom header parser so we have lots of flexibility.  I also started the code for the file pointer sequence proxy where the key usage is creating a sequence with the header and storing a reference to the file and offset in the file for the start of the sequence. When a method is called related to getting a sequence/subsequence the init() method is called to load the sequence data via RandomAccessFile with a seek to the offset. It turns out that none of the java io classes will actually return an offset index of the actual bytes read. This also gets complicated with the readline() methods where the CR and/or LF is stripped off when the string is returned so you can't keep track of it externally. I copied the BufferedReader.java class to BufferedReaderBytes!
>   Read.java and keep track of the file pointer internally. This code still needs to be tested. This should be a great way to load large date sets with minimal memory. To complete this approach I will probably do a collection that is proxy aware that can go through and free up storage by returning a sequence to its proxy state.
>
> I will work this week on getting some wiki pages created to give examples on using the header parsing interface and proxy sequences. How do we want to organize wiki pages related to biojava3 work?
>
> Thanks
>
> Scooter
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>    




From chapmanb at 50mail.com  Thu Jan 28 20:35:05 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Thu, 28 Jan 2010 15:35:05 -0500
Subject: [Biojava-dev] OpenBio solution challenge: Project updates at BOSC
	2010
Message-ID: <20100128203505.GG40046@sobchak.mgh.harvard.edu>

Hello all;
The BOSC 2010 organizing committee is hard at work getting prepared for this
July's meeting in Boston:

http://www.open-bio.org/wiki/BOSC_2010

One of the items we've traditionally had at the conference is a project 
update from each of the OpenBio affiliated groups. This year, we're thinking
about organizing these talks around a central theme: the OpenBio solution
challenge. We start with a biological question of general interest, and each
of the project talks would focus around how you would solve that problem 
using your toolkit and programming language.

This is meant to provide a challenge for OpenBio contributors, a nice tutorial
style overview of various projects and approaches for other programmers, and a
fun opportunity to compete and learn from other projects. Conference attendees
will vote on their favorite solution, with the winner receiving fame and
fortune (warning: fortune not guaranteed).

For this to be successful, it of course requires interest and enthusiasm from
y'all fine folks involved with the projects. Specifically:

- Is there interest from your group in participating in the challenge? You'll
  want at least a few people to work on it, and someone to give a presentation 
  at BOSC.

- Do you have suggestions on a good theme or specific biological problem to
  tackle? We'll hope to pick something in a sweet spot that is challenging 
  enough to be of interest, yet reasonable for presentation and preparation.

Let's discuss ideas and get this together. Since the schedule for BOSC is
developing rapidly, please give us an idea if you're interested by
February 12th, and copy responses to the BOSC mailing list as a central 
place for discussion.

bosc at open-bio.org

Thanks,
Brad, Michael, and the BOSC organizing committee


From markw at illuminae.com  Thu Jan 28 21:17:44 2010
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 28 Jan 2010 13:17:44 -0800
Subject: [Biojava-dev] [MOBY-dev] OpenBio solution challenge: Project
 updates at BOSC 2010
In-Reply-To: <20100128203505.GG40046@sobchak.mgh.harvard.edu>
References: <20100128203505.GG40046@sobchak.mgh.harvard.edu>
Message-ID: <op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>


Brad, this sounds exciting!

One thing strikes me, though - by asking for the sub-projects to propose
the "grand challenge" themselves the one thing you can guarantee is that
the "grand challenge" is solvable (or more likely, already solved!)

Other "grand challenge" kinds of meetings have an independent third party
pose the problem that has to be solved, and then all groups work toward a
solution and compare their results.  This would, IMO, be more revealing of
the "state of the art" in each Open-Bio project, and point out where the
weaknesses are that we should be focusing on...  Someone (for example,
you!) could act as the moderator to ensure that the "grand challenge" was
at least a reasonable one, within the scope of what an Open-Bio project
*should* be able to solve...

Just my CAD $0.02

Mark



On Thu, 28 Jan 2010 12:35:05 -0800, Brad Chapman <chapmanb at 50mail.com>  
wrote:

> Hello all;
> The BOSC 2010 organizing committee is hard at work getting prepared for  
> this
> July's meeting in Boston:
>
> http://www.open-bio.org/wiki/BOSC_2010
>
> One of the items we've traditionally had at the conference is a project
> update from each of the OpenBio affiliated groups. This year, we're  
> thinking
> about organizing these talks around a central theme: the OpenBio solution
> challenge. We start with a biological question of general interest, and  
> each
> of the project talks would focus around how you would solve that problem
> using your toolkit and programming language.
>
> This is meant to provide a challenge for OpenBio contributors, a nice  
> tutorial
> style overview of various projects and approaches for other programmers,  
> and a
> fun opportunity to compete and learn from other projects. Conference  
> attendees
> will vote on their favorite solution, with the winner receiving fame and
> fortune (warning: fortune not guaranteed).
>
> For this to be successful, it of course requires interest and enthusiasm  
> from
> y'all fine folks involved with the projects. Specifically:
>
> - Is there interest from your group in participating in the challenge?  
> You'll
>   want at least a few people to work on it, and someone to give a  
> presentation
>   at BOSC.
>
> - Do you have suggestions on a good theme or specific biological problem  
> to
>   tackle? We'll hope to pick something in a sweet spot that is  
> challenging
>   enough to be of interest, yet reasonable for presentation and  
> preparation.
>
> Let's discuss ideas and get this together. Since the schedule for BOSC is
> developing rapidly, please give us an idea if you're interested by
> February 12th, and copy responses to the BOSC mailing list as a central
> place for discussion.
>
> bosc at open-bio.org
>
> Thanks,
> Brad, Michael, and the BOSC organizing committee
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada


From HWillis at scripps.edu  Fri Jan 29 01:03:10 2010
From: HWillis at scripps.edu (Scooter Willis)
Date: Thu, 28 Jan 2010 20:03:10 -0500
Subject: [Biojava-dev] [MOBY-dev] OpenBio solution challenge: Project
 updates at BOSC 2010
In-Reply-To: <op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>
References: <20100128203505.GG40046@sobchak.mgh.harvard.edu>
	<op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <716E205A-5196-409F-A7BC-EF0F52AA997A@scripps.edu>

Brad

I agree with Mark that a particular problem may be biased towards a toolkit/language. Another approach would be to list a collection of problems and each group would then pick a problem to present. Could be a little more interesting to the audience as you are exposed to different problems and the various strengths of each toolkit. This could also help guide future development in the other toolkits as you would benefit from learning about the api and/or programming language. Each group would register a problem that they are going to present. From the group of problems not picked that becomes the surprise challenge where each group has 24 hours to either put together a presentation or an actual solution.

Scooter



On Jan 28, 2010, at 4:17 PM, Mark Wilkinson wrote:

> 
> Brad, this sounds exciting!
> 
> One thing strikes me, though - by asking for the sub-projects to propose
> the "grand challenge" themselves the one thing you can guarantee is that
> the "grand challenge" is solvable (or more likely, already solved!)
> 
> Other "grand challenge" kinds of meetings have an independent third party
> pose the problem that has to be solved, and then all groups work toward a
> solution and compare their results.  This would, IMO, be more revealing of
> the "state of the art" in each Open-Bio project, and point out where the
> weaknesses are that we should be focusing on...  Someone (for example,
> you!) could act as the moderator to ensure that the "grand challenge" was
> at least a reasonable one, within the scope of what an Open-Bio project
> *should* be able to solve...
> 
> Just my CAD $0.02
> 
> Mark
> 
> 
> 
> On Thu, 28 Jan 2010 12:35:05 -0800, Brad Chapman <chapmanb at 50mail.com>  
> wrote:
> 
>> Hello all;
>> The BOSC 2010 organizing committee is hard at work getting prepared for  
>> this
>> July's meeting in Boston:
>> 
>> http://www.open-bio.org/wiki/BOSC_2010
>> 
>> One of the items we've traditionally had at the conference is a project
>> update from each of the OpenBio affiliated groups. This year, we're  
>> thinking
>> about organizing these talks around a central theme: the OpenBio solution
>> challenge. We start with a biological question of general interest, and  
>> each
>> of the project talks would focus around how you would solve that problem
>> using your toolkit and programming language.
>> 
>> This is meant to provide a challenge for OpenBio contributors, a nice  
>> tutorial
>> style overview of various projects and approaches for other programmers,  
>> and a
>> fun opportunity to compete and learn from other projects. Conference  
>> attendees
>> will vote on their favorite solution, with the winner receiving fame and
>> fortune (warning: fortune not guaranteed).
>> 
>> For this to be successful, it of course requires interest and enthusiasm  
>> from
>> y'all fine folks involved with the projects. Specifically:
>> 
>> - Is there interest from your group in participating in the challenge?  
>> You'll
>>  want at least a few people to work on it, and someone to give a  
>> presentation
>>  at BOSC.
>> 
>> - Do you have suggestions on a good theme or specific biological problem  
>> to
>>  tackle? We'll hope to pick something in a sweet spot that is  
>> challenging
>>  enough to be of interest, yet reasonable for presentation and  
>> preparation.
>> 
>> Let's discuss ideas and get this together. Since the schedule for BOSC is
>> developing rapidly, please give us an idea if you're interested by
>> February 12th, and copy responses to the BOSC mailing list as a central
>> place for discussion.
>> 
>> bosc at open-bio.org
>> 
>> Thanks,
>> Brad, Michael, and the BOSC organizing committee
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 
> 
> -- 
> Mark D Wilkinson, PI Bioinformatics
> Assistant Professor, Medical Genetics
> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
> Providence Heart + Lung Institute
> University of British Columbia - St. Paul's Hospital
> Vancouver, BC, Canada
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev




From biopython at maubp.freeserve.co.uk  Fri Jan 29 10:36:40 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Fri, 29 Jan 2010 10:36:40 +0000
Subject: [Biojava-dev] [Bioperl-l] [MOBY-dev] OpenBio solution
	challenge: Project updates at BOSC 2010
In-Reply-To: <op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>
References: <20100128203505.GG40046@sobchak.mgh.harvard.edu>
	<op.u69hfujinbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <320fb6e01001290236l1ad02515w403a19f94dbb6d15@mail.gmail.com>

Hi all,

This is a great topic but should be continue it on just the one mailing list?
Is there a suitable BOSC list, or how about the general Open Bio list?

On Thu, Jan 28, 2010 at 9:17 PM, Mark Wilkinson <markw at illuminae.com> wrote:
>
> Brad, this sounds exciting!
>
> One thing strikes me, though - by asking for the sub-projects to propose
> the "grand challenge" themselves the one thing you can guarantee is that
> the "grand challenge" is solvable (or more likely, already solved!)
>
> Other "grand challenge" kinds of meetings have an independent third party
> pose the problem that has to be solved, and then all groups work toward a
> solution and compare their results. ?This would, IMO, be more revealing of
> the "state of the art" in each Open-Bio project, and point out where the
> weaknesses are that we should be focusing on... ?Someone (for example,
> you!) could act as the moderator to ensure that the "grand challenge" was
> at least a reasonable one, within the scope of what an Open-Bio project
> *should* be able to solve...
>
> Just my CAD $0.02
>
> Mark

One possible problem with having Brad act as moderator is his ties to
Biopython (plus it would be a shame if we'd be one man down for trying
to solve the challenges - grin). Having a project representative "sign off"
on the challenge might work - or simply the whole of the BOSC committee
which is quite balanced. Alternatively some kind of panel of challenges does
seem a good way to reduce individual project bias (as suggest by Scooter),
but there will still need to be a judging committee.

I'm curious what kind of challenges the BOSC committee had in mind -
would something like taking a newly sequence bacteria and producing
an automated annotation as a GenBank, EMBL, or GFF  file be too
ambitious for example? There are already several major projects
to do this e.g. RAST http://rast.nmpdr.org/

Peter
(@Biopython)