在R中解析10gbxml文件

我有10GB的XML文件，我需要解析它。XML的示例结构是

<?xml version="1.0" encoding="UTF-8"?>
<proteinAtlas xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://v18.proteinatlas.org/download/proteinatlas.xsd" schemaVersion="2.5">
    <entry version="18" url="http://v18.proteinatlas.org/ENSG00000000003">
        <name>TSPAN6</name>
        <synonym>T245</synonym>
        <synonym>TM4SF6</synonym>
        <synonym>TSPAN-6</synonym>
        <identifier id="ENSG00000000003" db="Ensembl" version="88.38">
            <xref id="O43657" db="Uniprot/SWISSPROT"/>
        </identifier>
        <proteinClasses>
            <proteinClass source="MDM" id="Ma" parent_id="" name="Predicted membrane proteins"/>
            <proteinClass source="MDM" id="Md" parent_id="" name="Membrane proteins predicted by MDM"/>
            <proteinClass source="MEMSAT3" id="Me" parent_id="" name="MEMSAT3 predicted membrane proteins"/>
            <proteinClass source="MEMSAT-SVM" id="Mf" parent_id="" name="MEMSAT-SVM predicted membrane proteins"/>
            <proteinClass source="Phobius" id="Mg" parent_id="" name="Phobius predicted membrane proteins"/>
            <proteinClass source="SCAMPI" id="Mh" parent_id="" name="SCAMPI predicted membrane proteins"/>
            <proteinClass source="SPOCTOPUS" id="Mi" parent_id="" name="SPOCTOPUS predicted membrane proteins"/>
            <proteinClass source="THUMBUP" id="Mj" parent_id="" name="THUMBUP predicted membrane proteins"/>
            <proteinClass source="TMHMM" id="Mk" parent_id="" name="TMHMM predicted membrane proteins"/>
            <proteinClass source="MDM" id="M1" parent_id="" name="1TM proteins predicted by MDM"/>
            <proteinClass source="MDM" id="M4" parent_id="" name="4TM proteins predicted by MDM"/>
            <proteinClass source="SignalP" id="Sb" parent_id="Se" name="SignalP predicted secreted proteins"/>
            <proteinClass source="HPA" id="Za" parent_id="" name="Predicted intracellular proteins"/>
            <proteinClass source="UniProt" id="Ua" parent_id="" name="UniProt - Evidence at protein level"/>
            <proteinClass source="Kim et al 2014" id="Ea" parent_id="" name="Protein evidence (Kim et al 2014)"/>
            <proteinClass source="Ezkurdia et al 2014" id="Eb" parent_id="" name="Protein evidence (Ezkurdia et al 2014)"/>
        </proteinClasses>
        <proteinEvidence evidence="Evidence at protein level">
            <" source="HPA" evidence="Evidence at transcript level"/>
            <evidence source="MS" evidence="Evidence at protein level"/>
            <evidence source="UniProt" evidence="Evidence at protein level"/>
        </proteinEvidence>
        <tissueExpression source="HPA" technology="IHC" assayType="tissue">
            <summary type="tissue"><![CDATA[Cytoplasmic and membranous expression in most tissues.]]></summary>
            <verification type="reliability" description="Antibody staining mainly consistent with RNA expression data. Pending external verification. ">approved</verification>
            <image imageType="selected">
         </tissueExpression>
    </entry>

TSPAN6
T245
TM4SF6
TSPAN-6
不确定它是否更节省内存，但尝试一下也无妨：

library( xml2 )
library( data.table )

#first, parse the xml document
doc <- read_xml( "./test.xml" )

#get all entry-nodes
entry.nodes <- xml_find_all( doc, "//entry")

#if necessary, you can now delete the read-in document 'doc' to free up memory
#  rm( doc )
#   

#build data.table
# will also handle missing attributes/nodes. 
# because xml_find_first will return NA if node is not found
data.table( name = xml_text( xml_find_first( entry.nodes, ".//name" ) ),
            eviden = xml_attr( xml_find_first( entry.nodes, ".//proteinEvidence" ), "evidence" ) 
            )


#      name                    eviden
# 1: TSPAN6 Evidence at protein level

库（xml2）
库（data.table）
#首先，解析xml文档
doc不确定它是否更节省内存，但尝试一下也无妨：

library( xml2 )
library( data.table )

#first, parse the xml document
doc <- read_xml( "./test.xml" )

#get all entry-nodes
entry.nodes <- xml_find_all( doc, "//entry")

#if necessary, you can now delete the read-in document 'doc' to free up memory
#  rm( doc )
#   

#build data.table
# will also handle missing attributes/nodes. 
# because xml_find_first will return NA if node is not found
data.table( name = xml_text( xml_find_first( entry.nodes, ".//name" ) ),
            eviden = xml_attr( xml_find_first( entry.nodes, ".//proteinEvidence" ), "evidence" ) 
            )


#      name                    eviden
# 1: TSPAN6 Evidence at protein level

库（xml2）
库（data.table）
#首先，解析xml文档
doc我在网上发现，R可能不是解析如此大的XML文件的最佳语言。Python确实有这样的库，它们工作得很好。我试过其中一种，似乎效果不错
 我在网上发现，R可能不是解析如此大的XML文件的最佳语言。Python确实有这样的库，它们工作得很好。我试过其中一种，似乎效果不错
 我在网上发现，R可能不是解析如此大的XML文件的最佳语言。Python确实有这样的库，它们工作得很好。我尝试了其中一种，但没有完全探索，但似乎效果不错。我在网上发现，R可能不是解析如此大的XML文件的最佳语言。Python确实有这样的库，它们工作得很好。我试过其中一个，但没有完全探索，但似乎效果不错。