Question: Usage of 'xtract'
1
gravatar for cvjuanjo87
3 months ago by
cvjuanjo8710
cvjuanjo8710 wrote:

Hello everyone, I tried to use 'xtract' for converting a xml file of taxonomy data, but i got:

$ efetch -db taxonomy -id 10090 -format xml | xtract -Pattern Taxon -first TaxId ScientificName GenbankCommonName Division

Unable to locate xtract executable. Please execute the following:

ftp-cp ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract.Linux.gz gunzip -f xtract.Linux.gz chmod +x xtract.Linux

I tried to do this, but i still the same.

I hope what I have requested is possible.

xtract edirect • 215 views
ADD COMMENTlink modified 3 months ago by DCGenomics300 • written 3 months ago by cvjuanjo8710
1
gravatar for genomax
3 months ago by
genomax42k
United States
genomax42k wrote:

The executable appears to be named xtract.linux. You could try cp -pi xtract.linux xtract and see if that works.

ADD COMMENTlink modified 3 months ago • written 3 months ago by genomax42k
1
gravatar for DCGenomics
3 months ago by
DCGenomics300
United States
DCGenomics300 wrote:

Try a fresh download of Entrez Direct. The current version has an xtract wrapper that launches the appropriate precompiled binary, in this case xtract.Linux.

Xtract was rewritten two years ago, replacing the original Perl implementation, and now always handles recursive data structures. Thus, the capitalized -Pattern is deprecated in favor of the normal -pattern. Furthermore, by default it will only show the top-level data. Additional exploration with -group or -block can go down one level at a time (e.g., -block /Taxon), or do a recursive exploration of each level for deeply-nested data (e.g., -block */Gene-commentary_accession).

ADD COMMENTlink written 3 months ago by DCGenomics300
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