我想使用 R 从特定 XML 节点中提取信息:http : //www.uniprot.org/uniprot/P38949.xml。它涉及以下块:
<feature type="initiator methionine" description="Removed" evidence="1">
<location>
<position position="1"/>
</location>
</feature>
<feature type="chain" description="Major pollen allergen Car b 1 isoforms 1A and 1B" id="PRO_0000154185">
<location>
<begin position="2"/>
<end position="160"/>
</location>
</feature>
<feature type="sequence variant" description="In isoform 1B.">
<original>V</original>
<variation>A</variation>
<location>
<position position="38"/>
</location>
</feature>
<feature type="sequence variant" description="In isoform 1B.">
<original>I</original>
<variation>S</variation>
<location>
<position position="63"/>
</location>
</feature>
<feature type="sequence variant" description="In isoform 1B.">
<original>K</original>
<variation>E</variation>
<location>
<position position="133"/>
</location>
</feature>
我尝试使用以下代码提取特征类型=“序列变体”节点:
TabName = "P38949"
http = paste0("http://www.uniprot.org/uniprot/",TabName,".xml")
data = xmlParse(http)
nd = getNodeSet(data, "//ns:entry", namespaces=c(ns=getDefaultNamespace(data)[[1]]$uri))
original = sapply(nd, xpathSApply, './/*[local-name()="original"]', xmlValue)
variation = sapply(nd, xpathSApply, './/*[local-name()="variation"]', xmlValue)
description = sapply(nd, xpathSApply, './/*[local-name()="feature" and @type="sequence variant"]', xmlGetAttr, 'description')
position = sapply(nd, xpathSApply, './/*[local-name()="position"]', xmlGetAttr, 'position')
table = rbind(table, data.frame(description,original,variation,position))
我无法正确提取位置属性,因为脚本还提取了我不想要的功能类型=“启动器蛋氨酸”的位置属性。输出表应如下所示:
description original variation position
In isoform 1B. V A 38
In isoform 1B. I S 63
In isoform 1B. K E 133
使用rvest
(稍微方便的xml2
“版本”)和purrr
:
library(rvest)
library(purrr)
read_xml('http://www.uniprot.org/uniprot/P38949.xml') %>%
xml_nodes(xpath = '//d1:feature[@type="sequence variant"]') %>%
map_df(~{
description <- xml_attr(.x, 'description')
original <- xml_node(.x, xpath = 'd1:original') %>%
xml_text()
variation <- xml_node(.x, xpath = 'd1:variation') %>%
xml_text()
position <- xml_node(.x, xpath = 'd1:location/d1:position') %>%
xml_attr('position')
data.frame(description, original, variation, position,
stringsAsFactors = FALSE)
})
#> description original variation position
#> 1 In isoform 1B. V A 38
#> 2 In isoform 1B. I S 63
#> 3 In isoform 1B. K E 133
本文收集自互联网,转载请注明来源。
如有侵权,请联系[email protected] 删除。
我来说两句