Add better support for serializing collections of Sequences #249

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1. emckee2006 commented on Feb 4, 2015

   

   emckee2006

   on Feb 4, 2015

   Contributor

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   Genbank is an alternative as well, and might save more metadata about the
   sequences.
   On Feb 4, 2015 10:33 AM, "Andreas Prlic" notifications@github.com wrote:

   We don't have an easy way of serializing/deserializing a collection of
   sequences. This does not work:

   http://mailman.open-bio.org/pipermail/biojava-l/2015-February/011357.html

   Alternative workarounds could be:

   • Tweak Kryo for some nonstandard InstantiatorStrategy
   • Use BioJava's built in FASTA writer helper (but it might not
     serialize some header information)

   —
   Reply to this email directly or view it on GitHub
   #249.
2. heuermh commented on Feb 4, 2015

   

   heuermh

   on Feb 4, 2015

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   To add to the suggestions already made:

   • Use default java serialization (even if not the best format, this should be made to work)
   • Add annotations to support JSON (and other formats) mapping via e.g. Jackson, Gson
   • Add annotations to support Apache Thrift format mapping via e.g. Swift swift-codec
   • Persist to the BioSQL relational database schema; note however that support for it in biojava-legacy has suffered some bit rot
   • Serialize/deserialize to OWL/RDF or similar Linked Data formats; e.g. http://www.uniprot.org/core/, https://github.com/JervenBolleman/FALDO, http://www.obofoundry.org/cgi-bin/detail.cgi?id=sequence, etc.
   • Convert to Big Data Genomics schemas (bdg-formats) in Apache Avro format; used in ADAM among other things
   • Convert to Global Alliance for Genomics and Health (GA4GH) schemas in Apache Avro format; generic sequence with features is not supported by this model, only genomic reference sequences and (WIP) assemblies of genomic reference sequences
   • Persist using Google Genomics APIs; again a generic sequence with features is not supported by this model, only genomic reference sequences
3. andreasprlic

   added this to the BioJava 4.1.0 milestone on Feb 4, 2015
4. andreasprlic

   added

   new featureNew method or data structureNew method or data structure

   on Feb 4, 2015
5. andreasprlic

   modified the milestones: BioJava 4.2.0, BioJava 4.1.0 on Jun 25, 2015
6. andreasprlic

   modified the milestones: BioJava 5.0.0, BioJava 4.2.0 on Mar 1, 2016
7. andreasprlic

   modified the milestones: BioJava 6.0This milestone has been deleted, BioJava 5.0.0 on Sep 14, 2016
8. josemduarte

   modified the milestones: BioJava 6.0.0, 6.1.0 on Oct 29, 2021