Question: Usage of 'xtract'
0
gravatar for cvjuanjo87
6 days ago by
cvjuanjo870
cvjuanjo870 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 • 115 views
ADD COMMENTlink modified 23 hours ago by DCGenomics300 • written 6 days ago by cvjuanjo870
1
gravatar for genomax
6 days ago by
genomax37k
United States
genomax37k 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 6 days ago • written 6 days ago by genomax37k
1
gravatar for DCGenomics
23 hours 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 23 hours ago by DCGenomics300
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