Entrez xtract "unrecognized argument '-match'" error

Question

[Nancy Ouyang]

I can't figure out how to use the "-match" syntax even after reading all the documentation I could find. I get these errors:

$ cat xml.txt | xtract -pattern Gene-commentary -match Gene-commentary_type:1

Unrecognized argum`ent '-match'
No -element before 'Gene`-commentary_type:1'

$ cat xml.txt | xtract **-element** Gene-commentary -match Gene-commentary_type:1

Unrecognized argument '-match'
No -element before 'Gene-commentary_type:1'

What am I doing wrong?

---

What I am trying to do is pull the accession of the reference sequence and the coordinates for the region for a given entry in NCBI Gene (see Retrieve all FASTA RefSeq files for a given entry in NCBI gene?) so that I can run efetch -format FASTA -seqstart -seqend and get the appropriate results.

I could parse the XML in python to do it, but it really seems like I should be able to do this in "one line" using entrez direct if only I could get -match to work :/

Here is what the XML looks like:

Say I have a gene record in XML

epost -db gene -id 672 | efetch -format xml > xml.txt

According to the outline,

cat xml.txt | xtract -outline

 <Gene-commentary>
      <Gene-commentary_type value="genomic">1</Gene-commentary_type>
      <Gene-commentary_heading>Reference assembly</Gene-commentary_heading>
      <Gene-commentary_label>RefSeqGene</Gene-commentary_label>
      <Gene-commentary_accession>NG_005905</Gene-commentary_accession>
      <Gene-commentary_version>2</Gene-commentary_version>
      <Gene-commentary_seqs>
        <Seq-loc>
          <Seq-loc_int>
            <Seq-interval>
              <Seq-interval_from>92500</Seq-interval_from>
              <Seq-interval_to>173688</Seq-interval_to>

I have read:

Attempting To Utilise The New Entrez Direct Package But Having Difficulty With Pubmed And Nucleotide Xml Parsing

http://www.ncbi.nlm.nih.gov/books/NBK179288/ (I followed these instructions to install it, so which epost returns ~/edirect/epost)

http://www.ncbi.nlm.nih.gov/news/02-06-2014-entrez-direct-released/?campaign=facebook-02072014

http://elane.stanford.edu/laneconnex/public/media/documents/EntrezDirect.pdf

Answer 1

[hpmcwill]

From a bit of experimentation with 'xtract' it appears that the order of the command-line arguments is important, and thus a use of '-match' must be followed by an '-element' option. This appears to be the source of the error message you receive.

Using just 'xtract' the closest I've gotten so far is:

cat xml.txt | edirect/xtract \
  -pattern Gene-commentary \
  -match 'Gene-commentary_type:1' \
  -element 'Gene-commentary_accession' Seq-interval

You may be able to further anchor the patterns to make the extraction more specific.

[Nancy Ouyang]

Thanks for answering my specific question! It's weird their error message says "before" :/ I wasn't sure who to give the checkmark to, but I think Pierre Lindenbaum answered my actual question.

Answer 2

[Pierre Lindenbaum]

Using a good old xslt stylesheet:

<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
  <xsl:output method="text"/>
  <xsl:template match="/">
    <xsl:for-each select="/Entrezgene-Set/Entrezgene/Entrezgene_locus">
      <xsl:for-each select="Gene-commentary[Gene-commentary_type/@value='genomic' and Gene-commentary_type/text()='1']">
        <xsl:variable name="acn">
          <xsl:value-of select="concat('(',Gene-commentary_heading,')',Gene-commentary_accession)"/>
        </xsl:variable>
        <xsl:for-each select="Gene-commentary_seqs/Seq-loc/Seq-loc_int/Seq-interval">
          <xsl:value-of select="concat($acn,':',Seq-interval_from,'-',Seq-interval_to)"/>
          <xsl:text>
</xsl:text>
        </xsl:for-each>
      </xsl:for-each>
    </xsl:for-each>
  </xsl:template>
</xsl:stylesheet>

run:

xsltproc --novalid transform.xsl  "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=672&retmode=xml"

output:

(Reference GRCh38 Primary Assembly)NC_000017:43044294-43125482
(Reference assembly)NG_005905:92500-173688
(Alternate CHM1_1.1)NC_018928:41431850-41513017
(Alternate HuRef)AC_000149:36962662-37043808

[Nancy Ouyang]

Hah, my initial reaction was "what sorcery is this?" Neat, I'd never heard of xslt before. Thanks!