Sleep or delay for batching EDirect search
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Entering edit mode
3.6 years ago

Hi,

I am new to any programming so I think I have a relative simple problem.

I am trying to automate performing multiple searches from pubmed through Edirect by inputing a file that contains different search terms on each line that outputs to a text file. The formula below works when the input file only has a few search terms, but I get timed out when I have a file with more search terms. I think I need to put a "sleep" parameter somewhere to slow down the query, but can't quite figure out where.

IFS=$'\n'; for next in$(cat testsearch.txt) ; do esearch -db pubmed -query $next >>output.txt ;done  Thanks! Ana edirect pubmed • 727 views ADD COMMENT 0 Entering edit mode How about IFS=$'\n'; for next in $(cat testsearch.txt) ; do esearch -db pubmed -query$next  >>output.txt; sleep 60 ;done

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Entering edit mode

I think esearch has a batch mode as well off the top of my head, so you may be able to pass it your file of search terms directly (been a while since I played with it though). I don't imagine it'll alter the time out issue though - more FYI.