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Avoiding errors for missing files #95

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Avoiding errors for missing files #95

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6 changes: 6 additions & 0 deletions genomics/4-Variation/fetch_sra_acc.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,12 @@ curl -s 'https://www.ebi.ac.uk/ena/browser/api/xml/links/taxon?accession=2697049

cat ena.txt genbank.txt sra.txt | sort | uniq > union.txt
rm ena.txt

if [ ! -f acc2exclude.txt ]

@bgruening bgruening Mar 30, 2020

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I guess you can just do touch without the if as touch only updates the access times.

@scapella scapella Mar 30, 2020

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You are right. Didn't think about it. Shall I do a new PR?

@bgruening bgruening Mar 30, 2020

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I guess you can do it here directly ...

then
touch acc2exclude.txt;
fi

grep -f acc2exclude.txt -v union.txt > current.txt

# Annotate combined accession with metadata
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