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AWK one-liners for FASTA manipulation

bioinfogal Mar 22nd, 2019 58 Never
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  1. 1. To find sequences with matching name
  2. awk 'BEGIN{RS=">";FS="\n"}NR>1{if ($1~/name/) print ">"$0}' file.fa
  3. 2. To extract sequences using a list
  4. awk 'BEGIN{RS=">";FS="\n"}NR==FNR{a[$1]++}NR>FNR{if ($1 in a && $0!="") printf ">%s",$0}' list file.fa
  5. #The names in the list must start with ">" and each name is separated by a newline ("\n")
  6. 3. To join multiple lines into single line
  7. awk 'BEGIN{RS=">";FS="\n"}NR>1{seq="";for (i=2;i<=NF;i++) seq=seq""$i; print ">"$1"\n"seq}' file.fa
  8. #Single line sequence is desirable when a sequence is long and spans many lines. Furthermore, single line sequence is much easier to be manipulated using AWK oneliners as showed in the next few examples.
  9. 4. To print specified sequence region
  10. #To print the sequence starting from position 1 until 2213
  11. awk 'BEGIN{RS=">";FS="\n"}NR>1{seq="";for (i=2;i<=NF;i++) seq=seq""$i; print ">"$1"\n"substr(seq,1,2213)}' file.fa
  12. #To print sequence starting from position 399 until 704
  13. awk 'BEGIN{RS=">";FS="\n"}NR>1{seq="";for (i=2;i<=NF;i++) seq=seq""$i; print ">"$1"\n"substr(seq,399,704-399+1)}' file.fa
  14. #To print sequence with matching name from position 399 until 704
  15. awk 'BEGIN{RS=">";FS="\n"}NR>1{seq="";for (i=2;i<=NF;i++) seq=seq""$i; if ($1~/name/) print ">"$1"\n"substr(seq,399,704-399+1)}' file.fa
  16. #Useful to print sequence region when given start position and stop position or length
  17. 5. To reformat into 100 characters per line
  18. awk 'BEGIN{RS=">";FS="\n"}NR>1{seq="";for (i=2;i<=NF;i++) seq=seq""$i;a[$1]=seq;b[$1]=length(seq)}END{for (i in a) {k=sprintf("%d", (b[i]/100)+1); printf ">%s\n",i;for (j=1;j<=int(k);j++) printf "%s\n", substr(a[i],1+(j-1)*100,100)}}' fasta.txt
  19. 6. To substitute nucleotide sequences
  20. #To substitute small letter with capital letter
  21. awk 'BEGIN{RS=">";FS="\n"}NR>1{printf ">%s\n",$1;for (i=2;i<=NF;i++) {gsub(/c/,"C",$i);gsub(/a/,"A",$i);gsub(/g/,"G",$i);gsub(/t/,"T",$i); printf "%s\n",$i}}' file.fa
  22. 7. To convert DNA to RNA
  23. awk 'BEGIN{RS=">";FS="\n"}NR>1{printf ">%s\n",$1;for (i=2;i<=NF;i++) {gsub(/T/,"U",$i); printf "%s\n",$i}}' file.fa
  24. 8. To summarize sequence content
  25. awk 'BEGIN{RS=">";FS="\n";print "name\tA\tC\tG\tT\tN\tlength\tGC%"}NR>1{sumA=0;sumT=0;sumC=0;sumG=0;sumN=0;seq="";for (i=2;i<=NF;i++) seq=seq""$i; k=length(seq); for (i=1;i<=k;i++) {if (substr(seq,i,1)=="T") sumT+=1; else if (substr(seq,i,1)=="A") sumA+=1; else if (substr(seq,i,1)=="G") sumG+=1; else if (substr(seq,i,1)=="C") sumC+=1; else if (substr(seq,i,1)=="N") sumN+=1}; print $1"\t"sumA"\t"sumC"\t"sumG"\t"sumT"\t"sumN"\t"k"\t"(sumC+sumG)/k*100}' file.fa
  26. #Calculate number of each nucleotide, total length and GC content
  27. 9. To reverse complement nucleotide sequences
  28. awk 'BEGIN{RS=">";FS="\n";a["T"]="A";a["A"]="T";a["C"]="G";a["G"]="C";a["N"]="N"}NR>1{for (i=2;i<=NF;i++) seq=seq""$i;for(i=length(seq);i!=0;i--) {k=substr(seq,i,1);x=x a[k]}; printf ">%s\n%s",$1,x}' file.fa
  29. #This will produce a single line sequence
  30. 10. To convert FASTQ to FASTA format
  31. awk 'NR%4==1{print ">"substr($0,2)}NR%4==2{print $0}' file.fq
  32. #print first and second line of every four lines. Replace the first character of the first line with ">".
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