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I've been tricked by this several times, and thought it would be a good addition to the Cookbook. When using while loops without adding the </dev/null after the input the input, only the first line will be processed. Here is the (slightly modified) example from the docs:
while read org
do
esearch -db taxonomy -query "$org [LNGE] AND family [RANK]" < /dev/null |
efetch -format docsum |
xtract -pattern DocumentSummary -lbl "$org" \
-element ScientificName Division
done < organisms
(The "< /dev/null" input redirection construct prevents esearch from "draining" the remaining lines from stdin.)
I can make a pull request is this is repo is still being supported.
The text was updated successfully, but these errors were encountered:
I've been tricked by this several times, and thought it would be a good addition to the Cookbook. When using
while
loops without adding the</dev/null
after the input the input, only the first line will be processed. Here is the (slightly modified) example from the docs:I can make a pull request is this is repo is still being supported.
The text was updated successfully, but these errors were encountered: