[Biojava-l] Biojava-l Digest, Vol 101, Issue 14
Khalil El Mazouari
khalil.elmazouari at gmail.com
Thu Jun 30 17:59:43 UTC 2011
Hi Hedwig
try this:
RichFeature richFeature = RichFeature.Tools.makeEmptyFeature();
RichLocation richLocation = new SimpleRichLocation(
new SimplePosition(start), new SimplePosition(end), rank, RichLocation.Strand.POSITIVE_STRAND);
richFeature.setLocation(richLocation);
richFeature.setType("misc_feat"); // or get it from RichObjectFactory.
richSequence.getFeatureSet().add(richFeature);
Regards,
khalil
On 30 Jun 2011, at 18:00, biojava-l-request at lists.open-bio.org wrote:
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> Today's Topics:
>
> 1. Re: make feature to create embl or genbank file (Hedwig Kurka)
> 2. Re: make feature to create embl or genbank file (Hedwig Kurka)
> 3. Re: make feature to create embl or genbank file (Richard Holland)
> 4. Re: make feature to create embl or genbank file (George Waldon)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 30 Jun 2011 10:31:47 +0200
> From: Hedwig Kurka <kurka at mikro.biologie.tu-muenchen.de>
> Subject: Re: [Biojava-l] make feature to create embl or genbank file
> To: George Waldon <gwaldon at geneinfinity.org>,
> biojava-l at lists.open-bio.org
> Message-ID: <4E0C3473.7070406 at mikro.biologie.tu-muenchen.de>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi George,
>
> Thank you for your answer.
> I have some questions. Maybe very stupid, but I don't know how to get
> RichLocation objects.
> RichLocation loc = (RichLocation) new RangeLocation(start, stop);
> That doesn't work.
> And where does the programm know, that the feature lies on the plus or
> the minus strand?
>
> Regards,
> Hedwig
>
> Am 29.06.2011 17:39, schrieb George Waldon:
>> Hi Hedwig,
>>
>> The problem holds with StrandedFeature. The strandeness of a feature
>> is the transdeness of its location. StrandedFeature should be
>> eliminated from bj1. Use biojavaX instead, something like this, once
>> you have created a RichLocation on the appropriate strand:
>>
>> public Feature.Template getFeatureTemplate(RichSequence
>> parent,RichLocation loc) {
>> RichFeature.Template templ = new RichFeature.Template();
>> RichAnnotation rans = new SimpleRichAnnotation();
>> templ.annotation = rans;
>> templ.sourceTerm = // find an appropriate term
>> templ.typeTerm =
>> RichObjectFactory.getDefaultOntology().getOrCreateTerm("CDS");
>> templ.featureRelationshipSet = new TreeSet();
>> templ.rankedCrossRefs = new TreeSet();
>> templ.location = loc;
>>
>> // add notes if any you'd like
>>
>> return templ;
>> }
>>
>> That should make it into the output file.
>>
>> Regards,
>> George
>>
>>
>> Quoting Hedwig Kurka <kurka at mikro.biologie.tu-muenchen.de>:
>>
>>> Hello all,
>>>
>>> I have a problem concerning creating EMBL or Genbank files.
>>> Below is a fragment of my code and an example of how the EMBL file looks
>>> like.
>>>
>>> String name = "test genome";
>>> String seqString = pFasta.getSequence(1, pFasta.getLength());
>>> Sequence seq = DNATools.createDNASequence(seqString, name);
>>> Alphabet dna = AlphabetManager.alphabetForName("DNA");
>>> RichSequence rs =
>>> Tools.createRichSequence(RichObjectFactory.getDefaultNamespace(), name,
>>> seqString, dna);
>>> Set<Feature> rfeatSet = new HashSet<Feature>();
>>> StrandedFeature.Template t = new StrandedFeature.Template();
>>> for(int i=0; i<annotierten.size(); i++){
>>> int start = (int) Math.abs(anno.get(i).getStart());
>>> int stop = (int) Math.abs(anno.get(i).getStop());
>>> t.type = "CDS";
>>> if(start < stop){
>>> t.location = new RangeLocation(start, stop);
>>> t.strand = StrandedFeature.POSITIVE;
>>> }
>>> if(start > stop){
>>> t.location = new RangeLocation(stop, start);
>>> t.strand = StrandedFeature.NEGATIVE;
>>> }
>>> Feature f = seq.createFeature(t);
>>> RichFeature rf = RichFeature.Tools.enrich(f);
>>> rfeatSet.add(rf);
>>> }
>>> rs.setFeatureSet(rfeatSet);
>>> rs = RichSequence.Tools.enrich(rs);
>>> RichSequence.IOTools.writeEMBL(output, rs,
>>> RichObjectFactory.getDefaultNamespace());
>>>
>>> EMBL file:
>>> FT any 1889536..1890903
>>> FT any 134636..136987
>>> FT any 3727110..3727625
>>> FT any 2812636..2813517
>>> FT any 580648..581643
>>> FT any 2330962..2331921
>>> FT any 1012371..1013513
>>> FT any 1260854..1261720
>>> FT any 1602858..1603706
>>> FT any 4108079..4108999
>>> FT any 346637..347731
>>> FT any 4073395..4074549
>>>
>>> I wonder where the information of plus and minus strand is, why is there
>>> "any" in the file and not "CDS" and so on.
>>>
>>> As tutorial I found that:
>>> http://www.biojava.org/wiki/BioJava:Cookbook:Locations:Feature. Is there
>>> another one?
>>>
>>> Thank you for your help!
>>>
>>> And any help is appreciated,
>>>
>>> Hedwig
>>>
>>> _______________________________________________
>>> Biojava-l mailing list - Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>>
>>
>>
>>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 30 Jun 2011 11:02:49 +0200
> From: Hedwig Kurka <kurka at mikro.biologie.tu-muenchen.de>
> Subject: Re: [Biojava-l] make feature to create embl or genbank file
> To: Richard Holland <holland at eaglegenomics.com>,
> biojava-l at lists.open-bio.org
> Message-ID: <4E0C3BB9.2030601 at mikro.biologie.tu-muenchen.de>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I already built the set<RichFeature> and populated it.
> Now I want to give it the RichSequence. But when I do that in that line:
>
> rs.setRichFeatureSet(rfeatSet);
>
> It says, that it needs a Set<Feature>
>
> Regards,
> Hedwig
>
>> I'm not sure what you're trying to do - if you want to build a Set, you can just use the standard Java Collections API to create and populate a Set?
>>
>> cheers,
>> Richard
>>
>> On 30 Jun 2011, at 09:12, Hedwig Kurka wrote:
>>
>>
>>> Hi Richard,
>>>
>>> Thank you for your answer.
>>> If I create RichFeature objects, then I have to do conversions in that line:
>>> RichFeature f = (RichFeature) seq.createFeature(t);
>>> and then I have in that line:
>>> rs.setRichFeatureSet(rfeatSet);
>>> the problem, that I have a Set<RichFeature> and not Set<Feature>, but I
>>> didn't find a method builds a Set containing RichFeature objects on a
>>> RichSequence. Is there one?
>>>
>>>
>>>
>>>> The conversion from Feature to RichFeature does its best but is not
>>>> ideal. As you already have a RichSequence object to work with then you
>>>> would be better creating native RichFeature objects instead of doing
>>>> conversions.
>>>>
>>>> Richard Holland
>>>> Eagle Genomics Ltd
>>>> Sent from my HTC
>>>>
>>>>
>>>>
>>>>
>>>
>> --
>> 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/
>>
>>
>>
>>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 30 Jun 2011 10:36:12 +0100
> From: Richard Holland <holland at eaglegenomics.com>
> Subject: Re: [Biojava-l] make feature to create embl or genbank file
> To: Hedwig Kurka <kurka at mikro.biologie.tu-muenchen.de>
> Cc: biojava-l at lists.open-bio.org
> Message-ID: <285A2F4C-9C8E-4300-A48B-E31E95601570 at eaglegenomics.com>
> Content-Type: text/plain; charset=us-ascii
>
> There is a coding problem in ThinRichSequence (from which SimpleRichSequence and others extend) that allow only Set<Feature> as input, but require the Feature objects to actually be RichFeature objects. This was for a number of reasons that probably seemed good at the time but I have now forgotten what they were. The workaround is to declare your set as a Set<Feature> but populate it with RichFeature objects (as RichFeature extends Feature and so the Set will still accept them).
>
> The code is being phased out in favour of the new BJ3 model so it is unlikely to be fixed, but hopefully this workaround solves your particular case.
>
> cheers,
> Richard
>
> On 30 Jun 2011, at 10:02, Hedwig Kurka wrote:
>
>> I already built the set<RichFeature> and populated it.
>> Now I want to give it the RichSequence. But when I do that in that line:
>>
>> rs.setRichFeatureSet(rfeatSet);
>>
>> It says, that it needs a Set<Feature>
>>
>> Regards,
>> Hedwig
>>
>>> I'm not sure what you're trying to do - if you want to build a Set, you can just use the standard Java Collections API to create and populate a Set?
>>>
>>> cheers,
>>> Richard
>>>
>>> On 30 Jun 2011, at 09:12, Hedwig Kurka wrote:
>>>
>>>
>>>> Hi Richard,
>>>>
>>>> Thank you for your answer.
>>>> If I create RichFeature objects, then I have to do conversions in that line:
>>>> RichFeature f = (RichFeature) seq.createFeature(t);
>>>> and then I have in that line:
>>>> rs.setRichFeatureSet(rfeatSet);
>>>> the problem, that I have a Set<RichFeature> and not Set<Feature>, but I
>>>> didn't find a method builds a Set containing RichFeature objects on a
>>>> RichSequence. Is there one?
>>>>
>>>>
>>>>
>>>>> The conversion from Feature to RichFeature does its best but is not
>>>>> ideal. As you already have a RichSequence object to work with then you
>>>>> would be better creating native RichFeature objects instead of doing
>>>>> conversions.
>>>>>
>>>>> Richard Holland
>>>>> Eagle Genomics Ltd
>>>>> Sent from my HTC
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>> --
>>> 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/
>>>
>>>
>>>
>>>
>>
>
> --
> 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/
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 30 Jun 2011 10:24:23 -0500
> From: George Waldon <gwaldon at geneinfinity.org>
> Subject: Re: [Biojava-l] make feature to create embl or genbank file
> To: Hedwig Kurka <kurka at mikro.biologie.tu-muenchen.de>
> Cc: "biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>
> Message-ID: <20110630102423.185442z4cl0wn7eo at gator1273.hostgator.com>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> No stupid question here, only bad answer. Hope this one is good:
>
> http://www.biojava.org/wiki/BioJava:BioJavaXDocs#Working_with_RichLocation_objects.
>
> - George
>
> Quoting Hedwig Kurka <kurka at mikro.biologie.tu-muenchen.de>:
>
>> Hi George,
>>
>> Thank you for your answer.
>> I have some questions. Maybe very stupid, but I don't know how to get
>> RichLocation objects.
>> RichLocation loc = (RichLocation) new RangeLocation(start, stop);
>> That doesn't work.
>
>
>
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
> End of Biojava-l Digest, Vol 101, Issue 14
> ******************************************
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