Coverage for Bio.SeqIO.SeqXmlIO : 16%

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# Copyright 2010 by Thomas Schmitt. # All rights reserved. # # This module is for reading and writing SeqXML format files as # SeqRecord objects, and is expected to be used via the Bio.SeqIO API.
You are expected to use this module via the Bio.SeqIO functions.
SeqXML is a lightweight XML format which is supposed be an alternative for FASTA files. For more Information see http://www.seqXML.org and Schmitt et al (2011), http://dx.doi.org/10.1093/bib/bbr025 """
"""Base class for building iterators for record style XML formats.
It is assumed that all information for one record can be found within a record element or above. Two types of methods are called when the start tag of an element is reached. To receive only the attributes of an element before its end tag is reached implement _attr_TAGNAME. To get an element and its children as a DOM tree implement _elem_TAGNAME. Everything that is part of the DOM tree will not trigger any further method calls. """
"""Creating the object and initializing the XML parser."""
self._recordTag = recordTag self._namespace = namespace self._events = pulldom.parse(handle)
"""Iterate over the records in the XML file. Returns the last parsed record."""
record = None try: for event, node in self._events:
if event == "START_ELEMENT" and node.namespaceURI == self._namespace:
if node.localName == self._recordTag: #create an empty SeqRecord record = SeqRecord('', id='')
#call matching methods with attributes only if hasattr(self, "_attr_" + node.localName): getattr(self, "_attr_" + node.localName)( self._attributes(node), record)
#call matching methods with DOM tree if hasattr(self, "_elem_" + node.localName): #read the element and all nested elements into a DOM tree self._events.expandNode(node) node.normalize()
getattr(self, "_elem_" + node.localName)(node, record)
elif event == "END_ELEMENT" and node.namespaceURI == self._namespace and node.localName == self._recordTag: yield record
except SAXParseException as e:
if e.getLineNumber() == 1 and e.getColumnNumber() == 0: #empty file pass else: import os if e.getLineNumber() == 1 and e.getColumnNumber() == 1 \ and os.name == "java": #empty file, see http://bugs.jython.org/issue1774 pass else: raise
"""Return the attributes of a DOM node as dictionary."""
return dict((node.attributes.item(i).name, node.attributes.item(i).value) for i in range(node.attributes.length))
"""Breaks seqXML file into SeqRecords.
Assumes valid seqXML please validate beforehand."""
"""Create the object.""" XMLRecordIterator.__init__(self, handle, "entry")
self._source = None self._source_version = None self._version = None self._speciesName = None self._ncbiTaxId = None
"""Parse the document metadata."""
if "source" in attr_dict: self._source = attr_dict["source"] if "sourceVersion" in attr_dict: 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"]
"""Parse key value pair properties and store them as annotations."""
if "name" not in attr_dict: raise ValueError("Malformed property element.")
value = attr_dict.get("value", None)
if attr_dict["name"] not in record.annotations: record.annotations[attr_dict["name"]] = value elif isinstance(record.annotations[attr_dict["name"]], list): record.annotations[attr_dict["name"]].append(value) else: record.annotations[attr_dict["name"]] = [ record.annotations[attr_dict["name"]], value]
"""Parse the species information."""
if "name" not in attr_dict or "ncbiTaxID" not in attr_dict: raise ValueError("Malformed species element!")
#the keywords for the species annotation are taken from SwissIO record.annotations["organism"] = attr_dict["name"] #TODO - Should have been a list to match SwissProt parser: record.annotations["ncbi_taxid"] = attr_dict["ncbiTaxID"]
"""New entry set id and the optional entry source."""
if "id" not in attr_dict: raise ValueError("Malformed entry! Identifier is missing.")
record.id = attr_dict["id"] if "source" in attr_dict: record.annotations["source"] = attr_dict["source"] elif self._source is not 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 is not None: record.annotations["ncbi_taxid"] = self._ncbiTaxId if self._speciesName is not None: record.annotations["organism"] = self._speciesName
"""Parse DNA sequence."""
if not (node.hasChildNodes() and len(node.firstChild.data) > 0): raise ValueError("Sequence length should be greater than 0.")
record.seq = Seq(node.firstChild.data, Alphabet.generic_dna)
"""Parse RNA sequence."""
if not (node.hasChildNodes() and len(node.firstChild.data) > 0): raise ValueError("Sequence length should be greater than 0.")
record.seq = Seq(node.firstChild.data, Alphabet.generic_rna)
"""Parse protein sequence."""
if not (node.hasChildNodes() and len(node.firstChild.data) > 0): raise ValueError("Sequence length should be greater than 0.")
record.seq = Seq(node.firstChild.data, Alphabet.generic_protein)
"""Parse the description."""
if node.hasChildNodes() and len(node.firstChild.data) > 0: record.description = node.firstChild.data
"""Parse a database cross reference"""
if "source" not in attr_dict or "id" not in attr_dict: raise ValueError("Invalid DB cross reference.")
if "%s:%s" % (attr_dict["source"], attr_dict["id"]) not in record.dbxrefs: record.dbxrefs.append( "%s:%s" % (attr_dict["source"], attr_dict["id"]))
"""Writes SeqRecords into seqXML file.
SeqXML requires the sequence alphabet be explicitly RNA, DNA or protein, i.e. an instance or subclass of Bio.Alphapet.RNAAlphabet, Bio.Alphapet.DNAAlphabet or Bio.Alphapet.ProteinAlphabet. """
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.source = source self.source_version = source_version self.species = species self.ncbiTaxId = ncbiTaxId
"""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/0.4/seqxml.xsd", "seqXMLversion": "0.4"}
if self.source is not None: attrs["source"] = self.source if self.source_version is not None: attrs["sourceVersion"] = self.source_version if self.species is not None: if not isinstance(self.species, basestring): raise TypeError("species should be of type string") attrs["speciesName"] = self.species if self.ncbiTaxId is not 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))
"""Write one record."""
if not record.id or record.id == "<unknown id>": raise ValueError("SeqXML requires identifier")
if not isinstance(record.id, basestring): raise TypeError("Identifier should be of type string")
attrb = {"id": record.id}
if "source" in record.annotations and self.source != record.annotations["source"]: if not isinstance(record.annotations["source"], basestring): raise TypeError("source should be of type string") attrb["source"] = record.annotations["source"]
self.xml_generator.startElement("entry", AttributesImpl(attrb)) self._write_species(record) self._write_description(record) self._write_seq(record) self._write_dbxrefs(record) self._write_properties(record) self.xml_generator.endElement("entry")
"""Close the root node and finish the XML document."""
SequentialSequenceWriter.write_footer(self)
self.xml_generator.endElement("seqXML") self.xml_generator.endDocument()
"""Write the species if given."""
local_ncbi_taxid = None if "ncbi_taxid" in record.annotations: local_ncbi_taxid = record.annotations["ncbi_taxid"] if isinstance(local_ncbi_taxid, list): #SwissProt parser uses a list (which could cope with chimeras) if len(local_ncbi_taxid) == 1: local_ncbi_taxid = local_ncbi_taxid[0] elif len(local_ncbi_taxid) == 0: local_ncbi_taxid = None else: ValueError('Multiple entries for record.annotations["ncbi_taxid"], %r' % local_ncbi_taxid) if "organism" in record.annotations and local_ncbi_taxid: local_org = record.annotations["organism"]
if not isinstance(local_org, basestring): raise TypeError("organism should be of type string")
if not isinstance(local_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 local_org != self.species or local_ncbi_taxid != self.ncbiTaxId:
attr = {"name": local_org, "ncbiTaxID": local_ncbi_taxid} self.xml_generator.startElement( "species", AttributesImpl(attr)) self.xml_generator.endElement("species")
"""Write the description if given."""
if record.description:
if not isinstance(record.description, basestring): raise TypeError("Description should be of type string")
description = record.description if description == "<unknown description>": description = ""
if len(record.description) > 0: self.xml_generator.startElement( "description", AttributesImpl({})) self.xml_generator.characters(description) self.xml_generator.endElement("description")
"""Write the sequence.
Note that SeqXML requires a DNA, RNA or protein alphabet. """
if isinstance(record.seq, UnknownSeq): raise TypeError( "Sequence type is UnknownSeq but SeqXML requires sequence")
seq = str(record.seq)
if not len(seq) > 0: raise ValueError("The sequence length should be greater than 0")
#Get the base alphabet (underneath any Gapped or StopCodon encoding) alpha = Alphabet._get_base_alphabet(record.seq.alphabet) if isinstance(alpha, Alphabet.RNAAlphabet): seqElem = "RNAseq" elif isinstance(alpha, Alphabet.DNAAlphabet): seqElem = "DNAseq" elif isinstance(alpha, Alphabet.ProteinAlphabet): seqElem = "AAseq" else: raise ValueError("Need a DNA, RNA or Protein alphabet")
self.xml_generator.startElement(seqElem, AttributesImpl({})) self.xml_generator.characters(seq) self.xml_generator.endElement(seqElem)
"""Write all database cross references.""" if record.dbxrefs is not None:
for dbxref in record.dbxrefs:
if not isinstance(dbxref, basestring): 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 = {"source": dbsource, "id": dbid} self.xml_generator.startElement("DBRef", AttributesImpl(attr)) self.xml_generator.endElement("DBRef")
"""Write all annotations that are key value pairs with values of a primitive type or list of primitive types."""
for key, value in record.annotations.items():
if key not in ("organism", "ncbi_taxid", "source"):
if value is None:
attr = {"name": key} self.xml_generator.startElement( "property", AttributesImpl(attr)) self.xml_generator.endElement("property")
elif isinstance(value, list):
for v in value: if isinstance(value, (int, float, basestring)): attr = {"name": key, "value": v} self.xml_generator.startElement( "property", AttributesImpl(attr)) self.xml_generator.endElement("property")
elif isinstance(value, (int, float, basestring)):
attr = {"name": key, "value": str(value)} self.xml_generator.startElement( "property", AttributesImpl(attr)) self.xml_generator.endElement("property")
print("Running quick self test")
from Bio import SeqIO import sys
with open("Tests/SeqXML/protein_example.xml", "r") as fileHandle: records = list(SeqIO.parse(fileHandle, "seqxml"))
from Bio._py3k import StringIO stringHandle = StringIO()
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("") |