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Bash script to handle Multifasta files
By BioStar 1357 days ago
#Convert all lowercase residues to uppercase in a FASTA sequence file
$ awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' input.fasta > output.fasta
#Rearrange FASTA sequences according to their length
$ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""), $0);N++;next;} {printf("%s",$0);} END {printf("\n");}' input.fasta |\
>awk -F '\t' '{printf("%d\t%s\n",length($2),$0;)}' |\
>sort -k1,1n | cut -f 2- |tr "\t" "\n" > output.fasta
#Add ‘>’ at the beginning of headers in a FASTA file
$ awk '{if ($0 ~/_/) {printf ">";} print $0; }' input.fasta > output.fasta
#Match FASTA headers in two different multi-FASTA files
$ awk 'NR=FNR{a[$0];next}$0 in a{print $0}' input1.fasta input2.fasta
#Merge all FASTA files in a directory into a single FASTA file
$ awk'1' *.fa > all.fa
