conversion of rs id to ss id!!

Question

[keerthuguna96]

How to convert the rs id into ss id(s) for multiple rs? Is there any coding or tool available to do this easily, since i was stuck with millions of rs ids!

[cpad0112]

programmatically (i.e mere conversion of text 'rs' to 'ss') or scientifically (fetching corresponding ss IDs for each rsID)?

[keerthuguna96]

scientifically it would be easy... main thing is i want to do it in short time

Answer 1

[Pierre Lindenbaum]

using my tool xsltstream : http://lindenb.github.io/jvarkit/XsltStream.html

 wget -O - -q  "ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/XML/ds_ch1.xml.gz" |\
  gunzip -c |\
  java -jar dist/xsltstream.jar -t transform.xsl --tag '{https://www.ncbi.nlm.nih.gov/SNP/docsum}Rs'

output:

rs171 ss41715810
rs171 ss43026199
rs171 ss96405203
rs242 ss242
rs242 ss287669350
rs242 ss326012704
rs242 ss326012781
rs242 ss498801024
rs242 ss550913725
rs242 ss552749651
(...)

view raw README.md hosted with ❤ by GitHub

	<?xml version='1.0' encoding="UTF-8" ?>
	<xsl:stylesheet xmlns:xsl='http://www.w3.org/1999/XSL/Transform' version='1.0' xmlns:r="https://www.ncbi.nlm.nih.gov/SNP/docsum">
	<xsl:output method="text"/>
	<xsl:template match="/">
	<xsl:apply-templates select="//r:Rs/r:Ss"/>
	</xsl:template>
	<xsl:template match="r:Ss">rs<xsl:value-of select="../@rsId"/> ss<xsl:value-of select="@ssId"/><xsl:text>
	</xsl:text>
	</xsl:template>
	</xsl:stylesheet>

view raw transform.xsl hosted with ❤ by GitHub

[keerthuguna96]

i dont get it installed.. is there any other way?

[Pierre Lindenbaum]

"i dont get it installed"

[keerthuguna96]

sorry.. its not working.. can you tell the other way

[Pierre Lindenbaum]

did you just read the content of the link ? https://meta.stackexchange.com/questions/147616