The new tool appears to do exactly what I want and I was keen to try it out, but I'm having some dificulty.
I am attempting to pull out sequences from a taxon tree matching a single gene and give me a table of Accession, Author(s), Affiliation, Title. This is to give to collaborators for them to authenticate trusted sources, and I will pull out the chosen fasta sequences at a later date.
When parsing pubmed records the documentation is quite clear, and I can confirm it works for me:
esearch -db pubmed -query "Garber ED [AUTH] AND PNAS [JOUR]" | elink -related | efilter -query "mouse" | efetch -format docsum | xtract -pattern DocumentSummary -element Id SortFirstAuthor Title
I am attempting to search the nucleotide database, but I cannot return the 'Authors' or other details using the 'xtract' command, and I can't find any examples on doing so
My best attempt is as follows, but it only gives the Id:
esearch -db nucleotide -query "txid2836[Organism:exp] AND rbcl[GENE]" | efetch -format docsum | xtract -pattern DocumentSummary -element Id Authors
Alternatively, I have been attempting to use efetch -format xml and xtract-ing the information from there, but I can't understand how to select the correct hierarchy level (documentation):
The xtract function is used for processing XML data:
Exploration Argument Hierarchy
-pattern (Highest Rank)
-division
-group
-branch
-block
-section
-subset
-unit (Lowest Rank)
One such attempt looks like this:
esearch -db nucleotide -query "txid2836[Organism:exp] AND rbcl[GENE]" | efetch -format xml | xtract -division Authors -unit Name
1 answer
Currently, I'm unable to get your second example to run to completion. So I'm trying a simpler query:
esearch -db nucleotide -query "NM_182762.3"
The first step is to run xtract with the -outline option, to see what is in the XML:
esearch -db nucleotide -query "NM_182762.3" | efetch -format xml | xtract -outline > ed.out
If you examine the file ed.out, you will see the hierarchy for an author:
Author
Author_name
Person-id
Person-id_ml
Running xtract again: -pattern is the element in the hierarchy "one level" above the -element that you want:
esearch -db nuccore -query "NM_182762.3" | efetch -format xml | xtract -pattern Person-id -element Person-id_ml | head -10
Ren B
Zakharov V
Yang Q
McMahon L
Yu J
Cao W
Xie C
Wu J
Yun J
Lai J
It's worth spending some time with the complete edirect documentation as opposed to the simplified introduction.
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