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ontology repacking and exporting - relates to #34 #44

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ontology repacking and exporting - relates to #34 #44

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Commits on Apr 28, 2020

  1. do the data repack into the ontology containers with further RDF 'tur… 

    …tle' format dump
    @dimatr
    dimatr committed Apr 28, 2020
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Commits on Apr 30, 2020

  1. Merge remote-tracking branch 'remotes/origin/master' into ontology 

    # Conflicts:
#	matrixcomponent/PangenomeSchematic.py
    @dimatr
    dimatr committed Apr 30, 2020
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  2. further ontology fixes: real path names; better forward* and reverse*… 

    … edges definition for Component and Bin containers; Links are a part of ZoomLevel component
    @dimatr
    dimatr committed Apr 30, 2020
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Commits on May 11, 2020

  1. - do not forget to store the path_id 

    - use faldo.ExactPosition when appropriate
    @dimatr
    dimatr committed May 11, 2020
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Commits on May 12, 2020

  1. - explicit faldo:ExactPosition containers 

    - every Link has linkRank numbered after the pair sort (component.id, [component.departures])
    @dimatr
    dimatr committed May 12, 2020
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Commits on Jun 16, 2020

  1. Merge branch 'master' into ontology 

    # Conflicts:
#	matrixcomponent/JSONparser.py
#	matrixcomponent/PangenomeSchematic.py
#	matrixcomponent/matrix.py
#	segmentation.py
    @dimatr
    dimatr committed Jun 16, 2020
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  2. write faldo:ForwardStrandPosition, faldo:position and faldo:reference… 

    … in each Position. Add Path write out
    @dimatr
    dimatr committed Jun 16, 2020
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  3. create ontology folder when needed

    @dimatr
    dimatr committed Jun 16, 2020
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  4. proper name and strand directions

    @dimatr
    dimatr committed Jun 16, 2020
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  5. directions

    @dimatr
    dimatr committed Jun 16, 2020
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Commits on Jun 17, 2020

  1. fix bin_edge in .ttl output; but might be slow

    @subwaystation
    subwaystation committed Jun 17, 2020
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Commits on Jun 18, 2020

  1. recycle temp objects, do not create new ones

    @dimatr
    dimatr committed Jun 18, 2020
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  2. positionPercent and inversionPercent are printed as doubles

    @dimatr
    dimatr committed Jun 18, 2020
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Commits on Jun 22, 2020

  1. fix orientation

    @subwaystation
    subwaystation committed Jun 22, 2020
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Commits on Jun 24, 2020

  1. add base IRI

    @subwaystation
    subwaystation committed Jun 24, 2020
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  2. added example SPARQL queries

    @subwaystation
    subwaystation committed Jun 24, 2020
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Commits on Jun 26, 2020

  1. Link -> ZoomLevel, replace pg with vg, add 'path/'

    @subwaystation
    subwaystation committed Jun 26, 2020
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  2. Actually emit the position percentage instead of the coverage of a bin.

    @subwaystation
    subwaystation committed Jun 26, 2020
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Commits on Jul 4, 2020

  1. a big update: 

    * parallel write out of the gzip compressed ontology files - no memory leaks due to the utilization of separate processes!
* use the N-triples format to be 10x quicker than the Turtle (see format='nt' in PangenomeSchematic.py)
* be gentle with the string variables, do not use "a"+"b" but rather "{0}{1}".format(a,b). This does not create small temporary object and leads to a lower memory fragmentation/leak
* the RDF output folder is named *-rdf
    @dimatr
    dimatr committed Jul 4, 2020
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Commits on Jul 18, 2020

  1. Update requirements.txt

    @6br
    6br committed Jul 18, 2020
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Commits on Jul 26, 2020

  1. Add 'path/' on cells

    @6br
    6br committed Jul 26, 2020
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  2. Add assertion

    @6br
    6br committed Jul 26, 2020
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  3. Add assertion

    @6br
    6br committed Jul 26, 2020
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  4. Add logger info

    @6br
    6br committed Jul 26, 2020
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  5. Register logger

    @6br
    6br committed Jul 26, 2020
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  6. Merge branch 'ontology' of https://github.com/graph-genome/component_… 

    …segmentation into ontology
    @6br
    6br committed Jul 26, 2020
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  7. Register logger

    @6br
    6br committed Jul 26, 2020
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  8. Register logger

    @6br
    6br committed Jul 26, 2020
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  9. Add bin logger

    @6br
    6br committed Jul 26, 2020
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  10. Disable parallel on rdf writer

    @6br
    6br committed Jul 26, 2020
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