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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

  2673 days ago

• • Shruti Paniwala@shruti

  

  Remove all blank lines from file. perl -i.bak -n -e "print if /\S/" ../finalSample.fa #Perl #Tricks #PerlOneliner

  2636 days ago

• • Abhimanyu Singh@abhimanyu

  

  #Extract a #sequence from #multi-fasta file: $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file

  2624 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

  2585 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

  2553 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

  2522 days ago

• • Jit@jit.aber

  

  Find a pattern in first 7 characters of reads. bioawk -c fastx 'substr($seq,0,7) == $TAG { print }' reads.fq.gz #Reads #NGS #Extract #Pattern

  2515 days ago

• • Jit@jit.aber

  

  Print each command before executing? Bash script to print each command before executing. $ bash -x myscript.sh #Print #Command #Bash

  2486 days ago

• • Jit@jit.aber

  

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

  2384 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

  2359 days ago

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