Adds support for SeqXML version 0.4 Fixes some problems in the SeqXML…

… examples

Bio/SeqIO/SeqXmlIO.py

@@ -101,6 +101,8 @@ def __init__(self,handle):
         self._source = None
         self._source_version = None
         self._version = None
+        self._speciesName = None
+        self._ncbiTaxId = None
 
     def _attr_seqXML(self,attr_dict,record):
         """Parse the document metadata."""
@@ -111,6 +113,10 @@ def _attr_seqXML(self,attr_dict,record):
             self._source_version = attr_dict["sourceVersion"]
         if "version" in attr_dict:
             self._version = attr_dict["seqXMLversion"]
+        if "ncbiTaxID" in attr_dict:
+            self._ncbiTaxId = attr_dict["ncbiTaxID"]
+        if "speciesName" in attr_dict:
+            self._speciesName = attr_dict["speciesName"]
 
     def _attr_property(self,attr_dict,record):
         """Parse key value pair properties and store them as annotations."""
@@ -149,7 +155,15 @@ def _attr_entry(self,attr_dict,record):
             record.annotations["source"] = attr_dict["source"]
         elif self._source != None:
             record.annotations["source"] = self._source
-
+
+        #initialize entry with global species definition
+        #the keywords for the species annotation are taken from SwissIO   
+        if self._ncbiTaxId != None:
+            record.annotations["ncbi_taxid"] = self._ncbiTaxId
+        if self._speciesName != None:
+            record.annotations["organism"] = self._speciesName    
+
+
     def _elem_DNAseq(self,node,record):
         """Parse DNA sequence."""
 
@@ -188,7 +202,6 @@ def _attr_DBRef(self,attr_dict,record):
         if "source" not in attr_dict or "id" not in attr_dict:
             raise ValueError("Invalid DB cross reference.")
 
-        #TODO add type 
         if "%s:%s" % (attr_dict["source"],attr_dict["id"]) not in record.dbxrefs:
             record.dbxrefs.append("%s:%s" % (attr_dict["source"],attr_dict["id"]) )
 
@@ -202,29 +215,39 @@ class SeqXmlWriter(SequentialSequenceWriter):
     Bio.Alphapet.DNAAlphabet or Bio.Alphapet.ProteinAlphabet.
     """
 
-    def __init__(self, handle,seqXML_version=None,source=None,source_version=None):
+    def __init__(self, handle,source=None,source_version=None,species=None,ncbiTaxId=None):
         """Create Object and start the xml generator."""
 
         SequentialSequenceWriter.__init__(self, handle)
 
         self.xml_generator = XMLGenerator(handle, "utf-8")
         self.xml_generator.startDocument()
-        self.seqXML_version = seqXML_version
         self.source = source
         self.source_version = source_version
+        self.species = species
+        self.ncbiTaxId = ncbiTaxId
 
     def write_header(self):
         """Write root node with document metadata."""
         SequentialSequenceWriter.write_header(self)
 
         attrs = {"xmlns:xsi":"http://www.w3.org/2001/XMLSchema-instance",
-                 "xsi:noNamespaceSchemaLocation":"http://www.seqxml.org/0.3/seqxml.xsd"}
-        if self.seqXML_version != None:
-            attrs["seqXMLversion"] = self.seqXML_version
+                 "xsi:noNamespaceSchemaLocation":"http://www.seqxml.org/0.4/seqxml.xsd",
+                 "seqXMLversion":"0.4"}
+
         if self.source != None:
             attrs["source"] = self.source
         if self.source_version != None:
             attrs["sourceVersion"] = self.source_ersion
+        if self.species != None:
+            if not isinstance(species,basestring):
+                raise TypeError("species should be of type string")
+            attrs["speciesName"] = self.species
+        if self.ncbiTaxId != None:
+            if not isinstance(self.ncbiTaxId,(basestring,int)):
+                raise TypeError("ncbiTaxID should be of type string or int")
+            attrs["ncbiTaxID"] = self.ncbiTaxId
+
         self.xml_generator.startElement("seqXML", AttributesImpl(attrs))
 
 
@@ -271,10 +294,12 @@ def _write_species(self,record):
             if not isinstance(record.annotations["ncbi_taxid"],(basestring,int)):
                 raise TypeError("ncbiTaxID should be of type string or int")
 
+            #The local species definition is only written if it differs from the global species definition
+            if record.annotations["organism"] != self.species or record.annotations["ncbi_taxid"] != self.ncbiTaxId:
 
-            attr = { "name" : record.annotations["organism"], "ncbiTaxID" :record.annotations["ncbi_taxid"] }   
-            self.xml_generator.startElement("species",AttributesImpl(attr))
-            self.xml_generator.endElement("species")
+                attr = { "name" : record.annotations["organism"], "ncbiTaxID" :record.annotations["ncbi_taxid"] }   
+                self.xml_generator.startElement("species",AttributesImpl(attr))
+                self.xml_generator.endElement("species")
 
 
     def _write_description(self,record):
@@ -330,16 +355,14 @@ def _write_dbxrefs(self,record):
 
             for dbxref in record.dbxrefs:
 
-                #TODO add type
                 if not isinstance(dbxref,basestring):
-                    raise TypeError("dbxrefs should of type list of string")
+                    raise TypeError("dbxrefs should be of type list of string")
                 if dbxref.find(':') < 1:
                     raise ValueError("dbxrefs should be in the form ['source:id', 'source:id' ]")
 
                 dbsource,dbid = dbxref.split(':',1)
 
-
-                attr = { "type" : "unknown", "source" : dbsource, "id" : dbid }
+                attr = { "source" : dbsource, "id" : dbid }
                 self.xml_generator.startElement("DBRef",AttributesImpl(attr))
                 self.xml_generator.endElement("DBRef")
 
@@ -385,8 +408,10 @@ def _write_properties(self,record):
 
     SeqIO.write(records,stringHandle,"seqxml")
     SeqIO.write(records,sys.stdout,"seqxml")
+    print
 
     stringHandle.seek(0)
     records = list(SeqIO.parse(stringHandle,"seqxml"))
 
     SeqIO.write(records,sys.stdout,"seqxml")
+    print

Tests/SeqXML/corrupt_example1.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<seqXML source="Ensembl" sourceVersion="56" seqXMLversion="0.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.seqxml.org/0.3/seqxml.xsd">
+<seqXML source="Ensembl" sourceVersion="56" seqXMLversion="0.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.seqxml.org/0.4/seqxml.xsd">
     <entry id="ENSMUSG00000076441">
         <species name="Mus musculus"/>
         <description>/NCBI Tax id is missing</description>

Tests/SeqXML/corrupt_example2.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<seqXML source="Ensembl" sourceVersion="56" seqXMLversion="0.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.seqxml.org/0.2/seqxml.xsd">
+<seqXML source="Ensembl" sourceVersion="56" seqXMLversion="0.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.seqxml.org/0.4/seqxml.xsd">
     <entry>
         <species name="Homo sapiens" ncbiTaxID="9606"/>
         <description>id is missing</description>

Tests/SeqXML/dna_example.xml

@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<seqXML source="Ensembl" sourceVersion="56" seqXMLversion="0.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.seqxml.org/0.3/seqxml.xsd">
+<seqXML source="Ensembl" sourceVersion="56" seqXMLversion="0.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.seqxml.org/0.4/seqxml.xsd">
     <entry id="ENSMUSG00000076441">
         <species name="Mus musculus" ncbiTaxID="10090"/>
         <description>argininosuccinate synthetase 1 Gene [Source:MGI (curated);Acc:Ass1-001]</description>
         <DNAseq>CTTTGATTCACCATTTACTGGGAGCCCACGGCGATCTGGGCAGGTGCCAGGCCAGGACGTTAAAATGGCATCCCCAGCCATCCTTGGCCAACTCGTTTGCATTTTCTTGTGAACCCTTAGCTCTGGCTTGTGGGCTAGCATCAGGGAAAGCAAGAGCCTCTGAGGGGCAGATGCTTCAGTCTTTAAATCGAGTGGGGCTACACAGCCTCTGAACCTAAGCAATTTGCATCTTCACTCCCGCCTTGCAGCGCTTTCAAGGGTTCTTGCAAGACAGCTGCGATCAGCCTTGCTAGTCACGCGGGTTCCAACCTCTGCCGCCCTCCCAGGCGCCACCAGCGGGTCAGGATCAGGGGACCTAAATTGCAAGAGCCCACGCCCGTGCGCCCCCGGGAGGTGGTGCGGGCGCCAAGGGAAGAGGGAGGGGCCAGCGGGAGAGAGCGCGGGGCCACGCCCACCCGCAGGTGGCCTCGAGCCCTGAGAGGCTCGGAGCGGGGGCCGGGCCCGAGGGCGGGGCCTTTCTCGCGCCCGTCCCCACGTGTCCCAGGTTCCTGCCCCCCCCAGGCCCTGTGCTTATAACCCTGGATGCGCGCCTCTCTCAGCCCTGCTCCGCCGTCTGCCACTGCCGCCTGGGCTCACTGGTAAGAAGTTCCGGGCCCTTCTTGGTCCCCACTCTCTATCCAGGGTCTCATGACCAAGGAATCCCAGAGGGAGCGAGCAGCTGCAGGGGGTGGGCTCAGGGCAGCCCCCGAGTGACCGCGCAGTTAGTGGAAGGAAGGAGGCTGATGTCCGGGGCGCTGTGACGCACACGTTCCTCCTGCCTAGGGAACCCATGTAGGAGAACGGGTCCCAAGGTCTCCGGAGCAGGAGGACTATGGAGGTCCCCCTCTGGTTTTTCACGATCCTCTGTGTGCTGCGAAGGCTCCAAGTAGAGTCCCGGAGAGTCCAGAGGGTTGGGGGCTTCCGAATCCCTCTCCCTGGATCAGATTCGCCGATCTATGTTCAGGCTTGTTTCTCAAAGTAAGCAAAAGGTCCAGCCCCTCTTTGCCCTTAGGGGCTTGGGCGTGTGCCTTTCTCCTGAGTGTGACAGTACCCTGCTCTGGTGGACACGCGAACCCTGCCTACCCGTCCCGGGTCCTTCCTAGGCTGTGACTGGTTTCTCTTCTCCGTAGGGTGCAATGCCAGGCTCAGTCTGGGTGGGGCTTCTAGACAGGTTTCCTGCTAGCTGGCTGGCTCTTTGGGAGGAGCCCCTTCGCAGGAAATGTCTGTTTCTGGCTTGTTAACGGCTTGGGCCCTTCTCTGGAAGGCAGGCTAACCGAGAAATCGAGGGAAATCTTCTCCAGGAGAACTAACCGCGCTCTCAGTATTCCCCTCTGTGAAGTGGGTCTGTCAGGCTGTCTGCAAGTGCAGCTGGCAGGAGCAGACCTGCCCTTTCCCCAGGGGTAGAGTAGGAAAACCCTTCCTTTGATCCCTCGCTTTGCGGCTCCTCCACCTGGCAGGTGACCCCTGACGTCAGCCTCCCAGCTCCAGGGCTGCCAGCCTTGTGCCTGGACTCAGAACTCTTGCTGTCCAAGAGTTCAAGTTCAGTGAGCTGTTTTGAGAACTGTGGCCAGGGTCTGCCCACTTGCTCACTGGGTCTGGGATGAAGACCTGAAAAGACAGGGTCCCGTCCCCCCCCCCCCCCCGCAACCCTCCCCAGCCACCTACTCCCCCACTCCTCCACCCCCTCCCCCGCCCCAGACAAGGCTTTCAGAAGGAAGAAGACAGTGGAGAAACCTAAGAGCTGGGCTGGGCAGAGACTGGAATAGCCTCCATTTCAAACTCCCCCTACCCTCTCCCCCTCCCACCATAAACCAGCCAAGTCTGGGAGCATTGGAAGGGCCTCAGGGCTGCCCAAGGAATTCTGACTTTACCCAGTGCCCATGGAGTCCATAAATGAAGGGCAACTTCTGTCCACTACCCACCTCCTCCACGCACATAGTAGGACAGAACAGCTCTTAGCACCCTTGGTCAAGTGTGCCCCTCACCCCAGCTGCCTGCCTGCTCTGAGCTGAGGAAGTCAGACACTCCAGGAGCCTTGGGGTGGAGCCACGCCCCGGCCCACCTGCTGCATTTTCTCAGGGCCCATCTCATTGACCTTGGACGCCCCTAGGTCAGCCAGATCCCTCCACCAGGCTGTGAACACACTGCTTCTGGAGTGAGTGCCTTCCTTGCGGGCAGCCCTGCAGGAAGAGATACCTTGCTGAACTCTGGGTCTGAGGCATCGGTTTTCACTGAAGGTTTTGGGCAGAGTTCACTTCCCAGGACCTGGCTCCCTGTTCTTTTGAGGCTGGTTCCTCCCTAGACCTGGAAAATGGCTGGGCACCCAGAGCCTCAGTTGGTAGCATTAATGAGTGGACTGGTGTGTTCTTCTAGTGTTACTGGAGCTGTTAGCATCAGAGCACGGGCTCTGGCTGTCCCTGA</DNAseq>
-        <alternativeID source="UCSC" id="uc008jdu.1"/>
+        <DBRef source="UCSC" id="uc008jdu.1"/>
     </entry>
     <entry id="fake1">
         <species name="Mus musculus" ncbiTaxID="10090"/>

Tests/SeqXML/protein_example.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<seqXML source="Ensembl" sourceVersion="56" seqXMLversion="0.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.seqxml.org/0.3/seqxml.xsd">
+<seqXML source="Ensembl" sourceVersion="56" seqXMLversion="0.4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.seqxml.org/0.4/seqxml.xsd">
     <entry id="ENSMUSP00000099904">
         <species name="Mus musculus" ncbiTaxID="10090"/>
         <description>argininosuccinate synthetase 1 Gene [Source:MGI (curated);Acc:Ass1-001]</description>
@@ -18,11 +18,11 @@
         <species name="Homo sapiens" ncbiTaxID="9606"/>
         <description>duplicated property/alternativeID</description>
         <AAseq>GAKKVFIEDVSKEFVEEFIWPAVQSSALYE</AAseq>
+        <DBRef source="someDB" id="G001"/>
+        <DBRef source="someDB" id="G002"/>
         <property name="test" value="1"/>
         <property name="test" value="2"/>
         <property name="test" value="3"/>
-        <DBRef source="someDB" id="G001"/>
-        <DBRef source="someDB" id="G002"/>
     </entry>
     <entry id="minimal">
         <AAseq>S</AAseq>

Tests/test_SeqIO_SeqXML.py

@@ -13,6 +13,7 @@
     "dna" : ["SeqXML/dna_example.xml",4,None],
     "rna" : ["SeqXML/rna_example.xml",5,None],
     "protein" : ["SeqXML/protein_example.xml",5,None],
+    "globalSpecies" : ["SeqXML/global_species_example.xml",2,None],
 }
 
 corrupt_files = {"corrupt1" : ["SeqXML/corrupt_example1.xml",None],
@@ -92,8 +93,8 @@ def test_duplicated_property(self):
 
         self.assertEqual(self.records["protein"][2].annotations["test"],[u"1",u"2",u"3"])
 
-    def test_duplicated_alternativeID(self):
-        """Read multiple alternative identifier form single source"""
+    def test_duplicated_dbxref(self):
+        """Read multiple cross references to a single source"""
 
         self.assertEqual(self.records["protein"][2].dbxrefs,[u"someDB:G001",u"someDB:G002"])
 
@@ -107,14 +108,22 @@ def test_read_minial_required(self):
         self.assertEqual(self.records["rna"][3].dbxrefs,minimalRecord.dbxrefs)
         self.assertEqual(self.records["protein"][3].description,minimalRecord.description)
 
-    def test_species(self):
+    def test_local_species(self):
 
         self.assertEqual(self.records["rna"][1].annotations["organism"],"Mus musculus")
         self.assertEqual(self.records["rna"][1].annotations["ncbi_taxid"],"10090")
 
         self.assertEqual(self.records["rna"][0].annotations["organism"],"Gallus gallus")
         self.assertEqual(self.records["rna"][0].annotations["ncbi_taxid"],"9031")
 
+    def test_global_species(self):
+
+        self.assertEqual(self.records["globalSpecies"][0].annotations["organism"],"Mus musculus")
+        self.assertEqual(self.records["globalSpecies"][0].annotations["ncbi_taxid"],"10090")
+
+        self.assertEqual(self.records["globalSpecies"][1].annotations["organism"],"Homo sapiens")
+        self.assertEqual(self.records["globalSpecies"][1].annotations["ncbi_taxid"],"9606")
+
 
     def test_local_source_definition(self):
 
@@ -148,6 +157,11 @@ def test_read_write_protein(self):
         read1_records = list(SeqIO.parse(test_files["protein"][2],"seqxml"))
         self._write_parse_and_compare(read1_records)
 
+    def test_read_write_globalSpecies(self):
+
+        read1_records = list(SeqIO.parse(test_files["globalSpecies"][2],"seqxml"))
+        self._write_parse_and_compare(read1_records)
+
 
     def _write_parse_and_compare(self,read1_records):