replace all (globally): replace at all position, not only the first where the search text appeared
# use variables: requires double quotes "s/old/new/g"
FILENAME=myfile.txt
SEARCH_FOR=oldtext
REPLACE_WITH=newtext
sed -i "s/${SEARCH_FOR}/${REPLACE_WITH}/g" ${FILENAME}
# use in a pipe
cat myfile.txt | sed 's/oldtext/newtext/g' > newfile.txt
# replacing text without interpreting special characters
# Example: replace old long taxa with short taxa name in data_abundance_table.txt file
OLDTAXA='k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__[Prevotella]'
NEWTAXA='Prevotella'
# mask/cover special characters: replace [ with \[
OLDTAXA=$(sed -e 's/[]\/ ()$*.^|[]/\\&/g' <<< "${OLDTAXA}")
NEWTAXA=$(sed -e 's/[]\/ ()$*.^|[]/\\&/g' <<< "${NEWTAXA}")
echo ${OLDTAXA} ${NEWTAXA}
# replace taxa names in same file
sed -i "s/${OLDTAXA}/${NEWTAXA}/g" data_abundance_table.txt
# replace multiple taxa present in a two column text file: taxa_old_new_name.txt
cat taxa_old_new_name.txt | while read OLDTAXA NEWTAXA; do
echo ${OLDTAXA} ${NEWTAXA} ;
OLDTAXA=$(sed -e 's/[]\/ ()$*.^|[]/\\&/g' <<< "${OLDTAXA}") ;
NEWTAXA=$(sed -e 's/[]\/ ()$*.^|[]/\\&/g' <<< "${NEWTAXA}") ;
sed -i "s/${OLDTAXA}/${NEWTAXA}/g" data_abundance_table.txt ;
done