biointerchange 0.1.0 → 0.1.2

data/supplemental/java/biointerchange/src/test/java/org/biointerchange/AppTest.java

@@ -0,0 +1,38 @@
+package org.biointerchange;
+
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+/**
+ * Unit test for simple App.
+ */
+public class AppTest 
+    extends TestCase
+{
+    /**
+     * Create the test case
+     *
+     * @param testName name of the test case
+     */
+    public AppTest( String testName )
+    {
+        super( testName );
+    }
+
+    /**
+     * @return the suite of tests being tested
+     */
+    public static Test suite()
+    {
+        return new TestSuite( AppTest.class );
+    }
+
+    /**
+     * Rigourous Test :-)
+     */
+    public void testApp()
+    {
+        assertTrue( true );
+    }
+}

data/supplemental/python/biointerchange/__init__.py

@@ -0,0 +1,4 @@
+from gff3o import *
+from gvf1o import *
+from sio import *
+

data/supplemental/python/biointerchange/gff3o.py

@@ -0,0 +1,581 @@
+import rdflib
+
+from rdflib import Namespace
+
+__namespace_GFF3O = Namespace('http://www.biointerchange.org/gff3o#')
+
+def _namespace_GFF3O(accession):
+    return __namespace_GFF3O[accession]
+
+class GFF3O:
+
+    @classmethod
+    def strand(cls):
+        """Either:
+            Strand of the feature.
+            (cls, GFF3_0010)
+        Or:
+            Strand of a target -- if applicable.
+            (GFF3_0045)
+        """
+        return [ _namespace_GFF3O('GFF3_0010'), _namespace_GFF3O('GFF3_0045') ]
+
+    @classmethod
+    def attributes(cls):
+        """Tag name/value pair attributes of a feature that are not covered by object-/data-properties of the ontology. Tags that are represented as object-/data-properties are: ID, Name, Alias, Parent, Target, Gap, Derives_from, Dbxref, Ontology_term, Ontology_term, or Is_circular
+        (cls, GFF3_0012)
+        """
+        return _namespace_GFF3O('GFF3_0012')
+
+    @classmethod
+    def parent(cls):
+        """Link out to the parent feature.
+        (cls, GFF3_0014)
+        """
+        return _namespace_GFF3O('GFF3_0014')
+
+    @classmethod
+    def contains(cls):
+        """Relationship that describes which features belong to a feature set.
+        (cls, GFF3_0015)
+        """
+        return _namespace_GFF3O('GFF3_0015')
+
+    @classmethod
+    def region(cls):
+        """Either:
+            FALDO "Region" instance replacement for a feature's start, stop, strand properties.
+            (cls, GFF3_0021)
+        Or:
+            FALDO "Region" instance replacement for a target's start, stop, strand  properties.
+            (GFF3_0050)
+        """
+        return [ _namespace_GFF3O('GFF3_0021'), _namespace_GFF3O('GFF3_0050') ]
+
+    @classmethod
+    def species(cls):
+        """NCBI Taxonomy Ontology "NCBITaxon_1" (cls, or sub-classes) instance that denotes the species for a feature set.
+        (GFF3_0023)
+        """
+        return _namespace_GFF3O('GFF3_0023')
+
+    @classmethod
+    def set_properties(cls):
+        """Either:
+            Properties that are directly associated with Set class instances.
+            (cls, GFF3_0025)
+        Or:
+            Properties that are directly associated with Set class instances.
+            (GFF3_0027)
+        """
+        return [ _namespace_GFF3O('GFF3_0025'), _namespace_GFF3O('GFF3_0027') ]
+
+    @classmethod
+    def feature_properties(cls):
+        """Either:
+            Properties that are directly associated with Feature class instances.
+            (cls, GFF3_0026)
+        Or:
+            Properties that are directly associated with Feature class instances.
+            (GFF3_0028)
+        """
+        return [ _namespace_GFF3O('GFF3_0026'), _namespace_GFF3O('GFF3_0028') ]
+
+    @classmethod
+    def dbxref(cls):
+        """A database cross-reference to associate a sequence alteration to its  representation in another database.
+        (cls, GFF3_0034)
+        """
+        return _namespace_GFF3O('GFF3_0034')
+
+    @classmethod
+    def ontology_term(cls):
+        """A cross-reference to an ontology term that is associated with a feature.
+        (cls, GFF3_0035)
+        """
+        return _namespace_GFF3O('GFF3_0035')
+
+    @classmethod
+    def target(cls):
+        """Identifies the target that the features aligns to.
+        (cls, GFF3_0039)
+        """
+        return _namespace_GFF3O('GFF3_0039')
+
+    @classmethod
+    def target_properties(cls):
+        """Either:
+            Properties that are directly associated with Target class instances.
+            (cls, GFF3_0044)
+        Or:
+            Properties that are directly associated with Target class instances.
+            (GFF3_0040)
+        """
+        return [ _namespace_GFF3O('GFF3_0044'), _namespace_GFF3O('GFF3_0040') ]
+
+    @classmethod
+    def strand(cls):
+        """Either:
+            Strand of the feature.
+            (cls, GFF3_0010)
+        Or:
+            Strand of a target -- if applicable.
+            (GFF3_0045)
+        """
+        return [ _namespace_GFF3O('GFF3_0010'), _namespace_GFF3O('GFF3_0045') ]
+
+    @classmethod
+    def derives_from(cls):
+        """Describes a temporal relationship between two features, where the object denotes the subjects origin.
+        (cls, GFF3_0047)
+        """
+        return _namespace_GFF3O('GFF3_0047')
+
+    @classmethod
+    def region(cls):
+        """Either:
+            FALDO "Region" instance replacement for a feature's start, stop, strand properties.
+            (cls, GFF3_0021)
+        Or:
+            FALDO "Region" instance replacement for a target's start, stop, strand  properties.
+            (GFF3_0050)
+        """
+        return [ _namespace_GFF3O('GFF3_0021'), _namespace_GFF3O('GFF3_0050') ]
+
+    @classmethod
+    def seqid(cls):
+        """ID of the landmark that establishes the coordinate system for the current feature.
+        (cls, GFF3_0004)
+        """
+        return _namespace_GFF3O('GFF3_0004')
+
+    @classmethod
+    def source(cls):
+        """A free text qualifier that describes the algorithm or operating procedure that generated this feature.  For example, the name of the software that generated this feature or a database name.
+        (cls, GFF3_0005)
+        """
+        return _namespace_GFF3O('GFF3_0005')
+
+    @classmethod
+    def type(cls):
+        """Type of the feature, which is either a term from the "lite" version of the Sequence Ontology (cls, SOFA), a term from the full Sequence Ontology (SO) that is a child of sequence_feature (SO:0000110), or a SOFA or SO accession number.
+        (GFF3_0006)
+        """
+        return _namespace_GFF3O('GFF3_0006')
+
+    @classmethod
+    def start(cls):
+        """Either:
+            Start coordinate of the feature on the seqid landmark.
+            (cls, GFF3_0007)
+        Or:
+            Start coordinate of the target.
+            (GFF3_0042)
+        """
+        return [ _namespace_GFF3O('GFF3_0007'), _namespace_GFF3O('GFF3_0042') ]
+
+    @classmethod
+    def end(cls):
+        """Either:
+            End coordinate of the feature on the seqid landmark.
+            (cls, GFF3_0008)
+        Or:
+            End coordinate of the target.
+            (GFF3_0043)
+        """
+        return [ _namespace_GFF3O('GFF3_0008'), _namespace_GFF3O('GFF3_0043') ]
+
+    @classmethod
+    def score(cls):
+        """Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
+        (cls, GFF3_0009)
+        """
+        return _namespace_GFF3O('GFF3_0009')
+
+    @classmethod
+    def phase(cls):
+        """Phase for "CDS" features. It indicates where the feature begins with reference to the reading frame. For forward strand features, phase is counted from the start field, whilst for reverse strand features, phase is counted from the end field.
+        (cls, GFF3_0011)
+        """
+        return _namespace_GFF3O('GFF3_0011')
+
+    @classmethod
+    def tag(cls):
+        """Tag name of a feature attribute.
+        (cls, GFF3_0013)
+        """
+        return _namespace_GFF3O('GFF3_0013')
+
+    @classmethod
+    def version(cls):
+        """Version of the GFF3 specification that defines the feature set contents.
+        (cls, GFF3_0022)
+        """
+        return _namespace_GFF3O('GFF3_0022')
+
+    @classmethod
+    def build(cls):
+        """Name of a genome assembly build that denotes the provenance of features in a feature set. For example, 'NCBI 36' or 'FlyBase r4.1'.
+        (cls, GFF3_0024)
+        """
+        return _namespace_GFF3O('GFF3_0024')
+
+    @classmethod
+    def set_properties(cls):
+        """Either:
+            Properties that are directly associated with Set class instances.
+            (cls, GFF3_0025)
+        Or:
+            Properties that are directly associated with Set class instances.
+            (GFF3_0027)
+        """
+        return [ _namespace_GFF3O('GFF3_0025'), _namespace_GFF3O('GFF3_0027') ]
+
+    @classmethod
+    def feature_properties(cls):
+        """Either:
+            Properties that are directly associated with Feature class instances.
+            (cls, GFF3_0026)
+        Or:
+            Properties that are directly associated with Feature class instances.
+            (GFF3_0028)
+        """
+        return [ _namespace_GFF3O('GFF3_0026'), _namespace_GFF3O('GFF3_0028') ]
+
+    @classmethod
+    def attribute_properties(cls):
+        """Properties that are directly associated with Attribute class instances.
+        (cls, GFF3_0029)
+        """
+        return _namespace_GFF3O('GFF3_0029')
+
+    @classmethod
+    def dbxref_properties(cls):
+        """Properties that are directly associated with DBXRef class instances.
+        (cls, GFF3_0031)
+        """
+        return _namespace_GFF3O('GFF3_0031')
+
+    @classmethod
+    def name(cls):
+        """Either:
+            Name of an external database. For example, "dbSNP" or "OMIM".
+            (cls, GFF3_0032)
+        Or:
+            Name of a feature, which can be used for display purposes. The name is not a unique property among features.
+            (GFF3_0036)
+        """
+        return [ _namespace_GFF3O('GFF3_0032'), _namespace_GFF3O('GFF3_0036') ]
+
+    @classmethod
+    def xref(cls):
+        """External database identifier. For example, for dbSNP, this identifier could be "rs3131969".
+        (cls, GFF3_0033)
+        """
+        return _namespace_GFF3O('GFF3_0033')
+
+    @classmethod
+    def name(cls):
+        """Either:
+            Name of an external database. For example, "dbSNP" or "OMIM".
+            (cls, GFF3_0032)
+        Or:
+            Name of a feature, which can be used for display purposes. The name is not a unique property among features.
+            (GFF3_0036)
+        """
+        return [ _namespace_GFF3O('GFF3_0032'), _namespace_GFF3O('GFF3_0036') ]
+
+    @classmethod
+    def alias(cls):
+        """An alternative name for a feature. This can be another descriptive name of a feature, such as a locus name or accession number.
+        (cls, GFF3_0037)
+        """
+        return _namespace_GFF3O('GFF3_0037')
+
+    @classmethod
+    def target_properties(cls):
+        """Either:
+            Properties that are directly associated with Target class instances.
+            (cls, GFF3_0044)
+        Or:
+            Properties that are directly associated with Target class instances.
+            (GFF3_0040)
+        """
+        return [ _namespace_GFF3O('GFF3_0044'), _namespace_GFF3O('GFF3_0040') ]
+
+    @classmethod
+    def target_id(cls):
+        """ID or accession of the target alignment.
+        (cls, GFF3_0041)
+        """
+        return _namespace_GFF3O('GFF3_0041')
+
+    @classmethod
+    def start(cls):
+        """Either:
+            Start coordinate of the feature on the seqid landmark.
+            (cls, GFF3_0007)
+        Or:
+            Start coordinate of the target.
+            (GFF3_0042)
+        """
+        return [ _namespace_GFF3O('GFF3_0007'), _namespace_GFF3O('GFF3_0042') ]
+
+    @classmethod
+    def end(cls):
+        """Either:
+            End coordinate of the feature on the seqid landmark.
+            (cls, GFF3_0008)
+        Or:
+            End coordinate of the target.
+            (GFF3_0043)
+        """
+        return [ _namespace_GFF3O('GFF3_0008'), _namespace_GFF3O('GFF3_0043') ]
+
+    @classmethod
+    def gap(cls):
+        """Gap describing the feature/target alignment if the sequences are not collinear. The formal description of this property has been lost due to a dead link in the GFF3 specification.
+        (cls, GFF3_0046)
+        """
+        return _namespace_GFF3O('GFF3_0046')
+
+    @classmethod
+    def note(cls):
+        """A free text note.
+        (cls, GFF3_0048)
+        """
+        return _namespace_GFF3O('GFF3_0048')
+
+    @classmethod
+    def is_circular(cls):
+        """Describes whether a feature is circular or not.
+        (cls, GFF3_0049)
+        """
+        return _namespace_GFF3O('GFF3_0049')
+
+    @classmethod
+    def Set(cls):
+        """Set of genomic sequence features, whose identifiers are unique within the set.
+        (cls, GFF3_0001)
+        """
+        return _namespace_GFF3O('GFF3_0001')
+
+    @classmethod
+    def Feature(cls):
+        """A genomic sequence feature.
+        (cls, GFF3_0002)
+        """
+        return _namespace_GFF3O('GFF3_0002')
+
+    @classmethod
+    def Attribute(cls):
+        """Describes additional feature attributes besides ID, Name, Alias, Parent, Target, Gap, Derives_from, Dbxref, Ontology_term, Ontology_term, or Is_circular.
+        (cls, GFF3_0003)
+        """
+        return _namespace_GFF3O('GFF3_0003')
+
+    @classmethod
+    def Strand(cls):
+        """Class describing a genomic strand. Instances of the class (cls, individuals) are used to denote forward-/reverse-strands, etc.
+        (GFF3_0016)
+        """
+        return _namespace_GFF3O('GFF3_0016')
+
+    @classmethod
+    def DBXRef(cls):
+        """A class describing relationships between features and external databases.
+        (cls, GFF3_0030)
+        """
+        return _namespace_GFF3O('GFF3_0030')
+
+    @classmethod
+    def Target(cls):
+        """Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
+        (cls, GFF3_0038)
+        """
+        return _namespace_GFF3O('GFF3_0038')
+
+    @classmethod
+    def Positive(cls):
+        """Location on the positive (cls, forward) strand.
+        (GFF3_0017)
+        """
+        return _namespace_GFF3O('GFF3_0017')
+
+    @classmethod
+    def Negative(cls):
+        """Location on the negative (cls, reverse) strand.
+        (GFF3_0018)
+        """
+        return _namespace_GFF3O('GFF3_0018')
+
+    @classmethod
+    def UnknownStrand(cls):
+        """Strand was not determined, which leaves it open whether the location is on the positive (cls, forward) or negative (reverse) strand.
+        (GFF3_0019)
+        """
+        return _namespace_GFF3O('GFF3_0019')
+
+    @classmethod
+    def NotStranded(cls):
+        """Strand is not applicable.
+        (cls, GFF3_0020)
+        """
+        return _namespace_GFF3O('GFF3_0020')
+
+    @classmethod
+    def is_object_property(cls, uri):
+        """Determines whether the given URI is an object property.
+        
+        uri -- URI that is tested for being an object property
+        """
+        if uri == _namespace_GFF3O('GFF3_0010'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0012'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0014'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0015'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0021'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0023'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0025'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0026'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0034'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0035'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0039'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0044'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0045'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0047'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0050'):
+            return True
+        return False
+
+    @classmethod
+    def is_datatype_property(cls, uri):
+        """Determines whether the given URI is a datatype property.
+        
+        uri -- URI that is tested for being a datatype property
+        """
+        if uri == _namespace_GFF3O('GFF3_0004'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0005'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0006'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0007'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0008'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0009'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0011'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0013'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0022'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0024'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0027'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0028'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0029'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0031'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0032'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0033'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0036'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0037'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0040'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0041'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0042'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0043'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0046'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0048'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0049'):
+            return True
+        return False
+
+    @classmethod
+    def is_class(cls, uri):
+        """Determines whether the given URI is a class.
+        
+        uri -- URI that is tested for being a class
+        """
+        if uri == _namespace_GFF3O('GFF3_0001'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0002'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0003'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0016'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0030'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0038'):
+            return True
+        return False
+
+    @classmethod
+    def is_named_individual(cls, uri):
+        """Determines whether the given URI is a named individual.
+        
+        uri -- URI that is tested for being a named individual
+        """
+        if uri == _namespace_GFF3O('GFF3_0017'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0018'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0019'):
+            return True
+        if uri == _namespace_GFF3O('GFF3_0020'):
+            return True
+        return False
+
+    @classmethod
+    def with_parent(cls, uris, parent):
+        """Returns only those URIs that fall under a designated parent URI.
+        
+        uris -- Set of URIs that are tested whether they have the given parent URI.
+        parent -- Parent URI.
+        """
+        return filter(lambda uri: cls.has_parent(uri, parent), uris)
+
+    @classmethod
+    def has_parent(cls, uri, parent):
+        """Recursively tries to determine the parent for a given URI.
+        
+        uri -- URI that is tested for whether it has the given parent URI.
+        parent -- Parent URI.
+        """
+        if cls.__parent_properties.has_key(uri):
+            if cls.__parent_properties[uri] == parent:
+                return True
+            return cls.has_parent(cls.__parent_properties[uri], parent)
+        return False
+
+    __parent_properties = { _namespace_GFF3O('GFF3_0010') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0012') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0014') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0015') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0021') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0023') : _namespace_GFF3O('GFF3_0025') , _namespace_GFF3O('GFF3_0034') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0035') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0039') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0045') : _namespace_GFF3O('GFF3_0044') , _namespace_GFF3O('GFF3_0047') : _namespace_GFF3O('GFF3_0026') , _namespace_GFF3O('GFF3_0050') : _namespace_GFF3O('GFF3_0044') , _namespace_GFF3O('GFF3_0004') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0005') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0006') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0007') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0008') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0009') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0011') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0013') : _namespace_GFF3O('GFF3_0029') , _namespace_GFF3O('GFF3_0022') : _namespace_GFF3O('GFF3_0027') , _namespace_GFF3O('GFF3_0024') : _namespace_GFF3O('GFF3_0027') , _namespace_GFF3O('GFF3_0032') : _namespace_GFF3O('GFF3_0031') , _namespace_GFF3O('GFF3_0033') : _namespace_GFF3O('GFF3_0031') , _namespace_GFF3O('GFF3_0036') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0037') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0041') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0042') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0043') : _namespace_GFF3O('GFF3_0040') , _namespace_GFF3O('GFF3_0046') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0048') : _namespace_GFF3O('GFF3_0028') , _namespace_GFF3O('GFF3_0049') : _namespace_GFF3O('GFF3_0028') }
+