[Biojava-dev] Fwd: [Biojava-l] file i/o with ArrayList

Wed Feb 11 11:21:23 UTC 2015

Hi Stefan,
I don't want to talk about the design of the system. I know what you mean
because I have already had the need to work on that and, yes, there are
some choices that I would have not taken. But my choice, entering in a
collaborative project, was to mantain the planned design to be sure to add
some extra features without run the risk of getting lost in huge
modifications, minimize the impact of modifications on the API and moreover
to have some kind of "respect" for the work of people before me.
Unless the system works in reasonable time, in my opinion this is the
important thing.

Moreover be aware that there is also a parallel GenbankProxyLoader system
that I'm pretty sure that it is not receiving your patches (catenated
sequence loading). To be checked.

About section keys, unknown tags and collecting them in a list, I partially
agree with you (more no than yes) because the Genbank format is highly
specified and formal, please have a look at the link below. The best think
would have to throw an Exception in unsupported cases but this would
definitely limit the parser usage.
http://www.insdc.org/files/feature_table.html

About reference, authors and dblink, as prevously mentioned, I have no
exceptions to add those properties to AbstractSequence even if I feel they
make poor sense outside your specific use case.

Andreas has the last word on this, however.

My suggestion is just to carefully check your new added tags since it seems
to me that SOURCE_TAG is the same of your DBSOURCE but I know that this
topic is also debated in the others bio* projects so it is not trivial.

Happy biojava-ing,
Paolo

2015-02-11 0:13 GMT+01:00 stefan harjes <stefanharjes at yahoo.de>:

> Hi Paolo,
>
> come on now the reader returns a LinkedHashMap. If it would only read one
> sequence, it could simply return the sequence. Also the actual method call
> contains a integer parameter indicating how many sequences should be
> fetched. In my pull request I patched the reader so that it actually does
> that.
>
> The sectionKey tags I was talking about are actually 'PRIMARY',
> DBREFERENCE' and "DBLINK'. I think it would be better not to ask after
> every single key, but simply collect all 'not known' keys together with
> their values and store them in a list. Then you could just read/write them
> without silently forget about them. Right now if any unknown tag is read,
> it is simply recognized and then dropped, which I do not consider friendly.
>
> Cheers
> Stefan
>
>
>
>
>   Paolo Pavan <paolo.pavan at gmail.com> schrieb am 23:56 Dienstag,
> 10.Februar 2015:
>
>
> Hi Stefan, thank you for the review.
> You are actually surprising me since if I'm not sure that the reader
> parser supports multiple genbank files catenated I tought instead that all
> the info now are full filled in the sequence object.
> There are just few tags that are not imported (KEYWORDS_TAG, SOURCE_TAG,
> REFERENCE_TAG, BASE_COUNT_TAG), the documentation says that this is because
> they are anyway inferrable by different fields. I can also add this is
> because, as in the case of authors and reference tags, there is not such a
> property in the AbstractSequence class and I see poor sense to have it,
> unless you are doing this sort of swapping job. Anyway, it could be
> certainly added.
>
> About writer and its failure in writing the reported accession: even if I
> can't go in deep now, it may well be that it is failing in writing
> InsdcLocations (also known as split locations, for example
> *join(58474..59052,59052..59279)* reported in your genome file) since
> they have been used more sistematically by the last updated genbank reader.
> It may need a quick review along with db_xref qualifiers as well.
>
> In the end about alignment, if you are using NedlemanWunsch or such in the
> alignment package, be sure to load them with the proper
> AmbiguityDNACompoundSet.
>
> Cheers,
> Paolo
>
> 2015-02-10 10:28 GMT+01:00 stefan harjes <stefanharjes at yahoo.de>:
>
> Hi Paolo, biojava-dev
>
> I had a look myself. First I noticed, that GenbankWriter was actually more
> sophisticated than the Reader, as it was able to write more than one
> sequence. I submitted a pull request to patch GenbankReader which enables
> reading more than one genbank sequence from one file. When we speak of full
> Genbank reading capability, there are still at least 5 sectionKeys which
> are just ignored in the reader. I think there should be a way of simply
> storing them in a List and not asking for each one of them, maybe I will
> look there later.
>
> The writer is doing pretty well, but you should try to write
> 'NC_000913.gb' which crashed it in my case (writing nothing/no exception).
>
> I added two more test cases, but I think in order to really test the
> reader/writer capabilities we need a test where several sequences/proteins
> are read, merge into an array and written to stream. Upon reading this
> stream again, we should compare if they are still identical.
>
> Also I noticed, that you can not compare (align) a DNA sequence with non
> ambiguous nucleotide to a sequence with ambiguous nucleotide compounds even
> though a matrix dedicated for that exact comparison exists.
>
> Cheers
> Stefan
>
>
>   Paolo Pavan <paolo.pavan at gmail.com> schrieb am 4:43 Samstag, 7.Februar
> 2015:
>
>
> Hi Stefan,
> I had a look at the GenbankWriter because I could also need it in the
> future. Can you please specify what are the issues you are meeting? Because
> I made few quick tests and everything seemed work to me.
>
> Just in case, if you are reading then writing a Genbank file, are you
> using the last release of biojava 4.0.0 version? This would explain empty
> genbank files in output (If I have understood correctly what you have done).
>
> Paolo
>
> 2015-02-06 11:03 GMT+01:00 stefan harjes <stefanharjes at yahoo.de>:
>
> @Andreas: Yes I understand, thanks anyhow.
>
> @Paolo: I will have another look at GenbankWriter maybe I find some time.
>
> Cheers
> Stefan
>
>
>
>   Andreas Prlic <andreas at sdsc.edu> schrieb am 7:01 Freitag, 6.Februar
> 2015:
>
>
> Hi Stefan,
>
> thanks for your reply. You are trying to use the code base in a way that
> has not been done before. While I share your desire that this should work
> in principle, I think it is also important to point out that we never
> promised that serialization would be a supported feature. We started a
> thread to add better support on this here:
> https://github.com/biojava/biojava/issues/249 .
>
> Regarding your project: It seems it would make sense to split your array
> of sequences into two: DNA sequences and protein sequences. Dealing with
> each of those separately might be easier.
>
> Andreas
>
>
> On Wed, Feb 4, 2015 at 3:42 PM, stefan harjes <stefanharjes at yahoo.de>
> wrote:
>
> Hi Andreas,
>
> yes I took a look at FastaWriterHelper as well as GenbankWriter and they
> only seem to implement writing the name and sequence as fasta. Also they do
> not allow to read/write a mixed array of protein and DNA sequences. I asked
> myself what is the sense of constructing a complicated sequence with
> annotations, features and links, if I can only write fasta?
>
> This lead me to check out why one of the most basic classes of biojava
> like sequence (i.e. AbstractSequence) is not serializable.
> (Isn't it like String for java?)
>
> The first thing I noticed is that for some reason every sequence has a
> proxyloader. As fas as I understand the proxy is implemented in order to
> not load the entire sequence in case it is very big. Sure, then you can
> load sequences which have Gigabase length. But I have never in my 25 years
> of biochemistry actually worked with a single sequence of > 1GB. While
> there are some plant chromosomes which might fit this description, I would
> argue that the vast majority of biological sequences are much smaller and
> thus do not need a proxy for a single sequence. Thus, I would conclude that
> a small subset of ChromosomeSequence might need a proxyreader
> implementation.
> And thus it should be implemented there and not in the most basic class?
>
> The first class which prevents serialization is as you mentioned
> NucleotideCompound. I lack the biojava experience to say what is essential
> in NucleotideCompond and why it does not allow an empty constructor. But I
> saw for example in biojava 3.1 that compounds are allowed to have flexible
> name length, which I have never seen in actual sequence data, where it is
> always 1 or three characters. Is it not a better strategy to keep basic
> classes such as Sequence and Compound more basic in order to allow
> serialization. Implementation of more complex features could then be moved
> to classes which extend the basic classes?
>
> In my humble opinion one could instantiate a compound without a 'base'
> name but once this compound is added to the compound set, I could check
> that it actually has a base name?
>
> I do not want to sound like a know-it-all and do not try to reinvent
> biojava. However to be honest the (unsuccessful) effort in trying to
> serialize an ArrayList<Sequence<?>> either to send it around over TCP/IP,
> to JSON or to disk has been so frustrating and time consuming, that I
> actually consider changing to jython/biopython, biojavaX, or to write my
> own implementation.
>
> Cheers
> Stefan
>
>
>
>
>
>
>   Andreas Prlic <andreas at sdsc.edu> schrieb am 4:32 Donnerstag, 5.Februar
> 2015:
>
>
>
>
> Hi Stefan,
>
> just another quick follow up. You took a look at FastaWriterHelper and it
> was not useful, right? You need to serialize some header information as
> well, or what was the problem with it?
>
>
> http://www.biojava.org/docs/api/org/biojava/nbio/core/sequence/io/FastaWriterHelper.html
>
> Thanks,
>
> Andreas
>
>
> On Wed, Feb 4, 2015 at 7:13 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
> Thanks for pointing this out, Stefan. The problem is that the
> NucleotideCompound class does not have a zero-args constructor. That means
> you need to tweak kryo a bit. Kryo can be configured to use an
> InstantiatorStrategy to handle creating instances of a class.
> https://github.com/EsotericSoftware/kryo/blob/master/README.md
>
> Having said that, we need to improve the API and make something like this
> easier.
>
> Andreas
>
>
>
>
>
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