awk

for screening, filtering, and extracting rows and columns of text tables Examples print column 3 and 4 of file 'table.txt' awk '{ print $3, $4 }' table.txt     file input/output: read from file 'table.txt' and write to file 'newTable.txt' awk < table.txt '{ print $3, $4 }' > newTable.txt    to use in a pipe cat table.txt | awk '{ print $3, $4 }' > newTable.txt print only columns 3 and 4 when column 3 contains "gene123" awk '$3=="gene123"{ print $3, $4}' table.txt print complete line when column 3 contains "gene123" awk '$3=="gene123"' table.txt print complete line when column 3 contains NOT "NA" (alternatively use grep, see below) awk '$3!="NA"' table.txt print lines in which the ratio between columns 4 and 5 is smaller than 0.4 awk '$4/$5<0.4' table.txt print columns separated by tab change output field separator (OFS) to tabular "\t", instead of using space by default additionally, fix also input field separator (-F) to tabular "\t", in case of empty fields  awk -F"\t" '$3=="gene123"{OFS = "\t"; print $3, $4}' table.txt   switch column 3 and 4 awk '{tmp=$3; $3=$4; $4=tmp}; {print }'  switch only in lines where field 3 is larger than field 4 awk '$3>$4{tmp = $3; $3=$4; $4=tmp;}; {print }'  print columns in any specific order awk '{ print $2, $1, $4, $3 }' For extracting columns from text files, see also: cut combine multiple conditions AND operator: && awk '$3=="gene01" && $4>95 { print $3, $4}' table.txt OR operator: || awk '$3=="gene01" || $3=="gene02" { print $3, $4}' table.txt Count number of columns in each line # file separator 'FS' can be replaced by any column separator FS="\t" or FS="|" or  FS=":" ... awk '{ FS = "\t" } ; { print NF}'  table.txt Sum and mean average of numbers in column 2 awk 'BEGIN{C=0}; {C=C+$2}; END{print C "\t" C/NR}' table.csv 2345 56 For getting word frequencies, see also: uniq -c Remove lines using sed or grep # remove all empty lines (d - delete) sed '/^$/d' textfile.txt > new.txt # remove all lines containing 'NA' grep -vw NA textfile.txt > new.txt # remove all lines that contain multiple strings from the unwanted word list file grep -Fwf unwanted_word_list.txt -v textfile.txt > new.txt   -w search for full word, not substring   -F read pattern as plain text, not interpreting special characters as regular expressions   -f read pattern from file   -v keep non-matching lines (remove lines that contain the searched word)