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• • Shruti Paniwala@shruti

  

  Fasta sequence length: awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' file.fa #Length #Linux #OneLiner

  2652 days ago

• • Jit@jit.aber

  

  To clean up a fasta file so only first column of the header is outputted:$ awk '{print $1}' file.fa > output.fa #Sed #Clean #Header #Fasta

  2564 days ago

• • Jit@jit.aber

  

  Rename/number the multi-fasta file in ascending order. $ awk '/^>/{print ">" ++i; next}{print}' < Mix_assembly.fasta > Mix_assembly2.fasta #awk #oneliner

  2532 days ago

• • Rahul Nayak@rahul

  

  Count the number of bases in fasta file. grep -v ">" file.fasta | wc | awk '{print $3-$1}' #Fasta #Count #Bases

  2501 days ago

• • Neelam Jha@neelam

  

  Replace space with tab. $ awk -v OFS="\t" '$1=$1' file1 #tab #space #replace #awk

  2455 days ago

• • Jit@jit.aber

  

  Remove duplicated lines from text file. $ awk '!seen[$0]++' allIds #duplicate #lines #remove #awk

  2453 days ago

• • Jit@jit.aber

  

  Get the reads in fastq file: awk '{s++}END{print s/4}' file.fastq #reads #count #ngs #fastq

  2363 days ago

• • Radha Agarkar@radhaagarkar

  

  Remove the fasta with zero size: awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas #fasta #remove

  2338 days ago

• • Poonam Mahapatra@poonam

  

  Remove duplicate fasta ids: awk '/^>/{f=!d[$1];d[$1]=1}f' in.fa > out.fa #duplicate #fasta #ids

  2330 days ago

• • Jit@jit.aber

  

  awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} {if ($2) print ">"$0}' all_p_ctg.fa > all_p_ctg_CORRECTED.fa #remove #empty #clean #fasta

  2327 days ago

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