Split the multifasta in separate files !
cat Avaga_allPalindrome.fa | awk '{ if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")} print $0 > filename }'1970 days ago
Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1628 days ago
Python script to check sequence length in multifasta file
#!/usr/bin/python from Bio import SeqIO import sys cmdargs = str(sys.argv) for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): output_line = '%s\t%i' % \ (seq_record.id, len(seq_record)) print(output_line)1228 days ago
Onliner to split the multifasta to singlefasta files !
#Split the multifasta to singlefasta # Multi fasta #Single fasta awk '$0 ~ "^>" { match($1, /^>([^:]+)/, id); filename=id[1]} {print >> filename".fa"}' sequence.fasta1413 days ago
Reformat the multifasta for sequence length !
#awk oneliner to reformat the multifasta sequences awk '!/^>/ {printf "%s", $0; n = "\n"} /^>/ {print n $0; n = ""}' file.fasta | fold -w 1001405 days ago
Bash script to handle Multifasta files
#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 #R...1370 days ago
Remove dupcates in multifasta file !
#Using seqkit for duplicate sequence removal seqkit rmdup -n seqs.fa -o seqs_without_duplicate.fa #Awk for duplicate sequence removal awk '/^>/ { f = !a[$0]++ } f' seqs.fa989 days ago
Run Pango on your multifasta file !
#More at https://cov-lineages.org/resources/pangolin/usage.html (base) [jnarayan@hn1 FASTA]$ conda activate pangolin (pangolin) [jnarayan@hn1 FASTA]$ ls Input_for_Co...900 days ago
Bash script to split multifasta file !
#Using awk, we can easily split a file (multi.fa) into chunks of size N (here, N=500), by using the following one-liner: awk 'BEGIN {n=0;} /^>/ {if(n%500==0){file=spri...836 days ago