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cyklee/find.replace.sh

Created November 25, 2018 01:40
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sed and shell script to find pattern from a column and replacing it with entries from another column - handy for tidying up a newick phylogenetic tree
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find.replace.sh
paste Short.name.txt Proper.name.txt | while read n k; do sed -i "s/$n/$k/g" tree.nwk; done
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cyklee commented Nov 25, 2018

If the name files contained "/", it will clash with sed. In that case, the delimiter can be replaced with other characters e.g. "s@$n@$k@g"

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cyklee commented Nov 25, 2018

In addition, newick tree uses ":" as separator, so it can be used within the branch tip names.

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