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• • Abhimanyu Singh@abhimanyu

  

  Perl one-liner for bioinformatician !!!

  ...F, etc.) and some tools for manipulating them (fastx toolkit, samtools, vcftools, etc.), there are still times where knowing a little bit of Perl onliner is extremely helpful. Perl o...

  3641 days ago

Wire posts

• • Rahul Nayak@rahul

  

  Linux onliner for bioinformatician https://github.com/stephenturner/oneliners #Linux #Onliner

  3676 days ago

• • Rahul Nayak@rahul

  

  Sort FASTA sequence by length: cat f1.fasta| awk '{if($0 ~ /^>/){printf "%st", $0}else{print length($0)"t"$0}}'| sort -k2n,2| awk '{print $1"n"$3}' > sequence.fasta #Sort #Fasta #Trick #Onliner

  3201 days ago

• +2 more Wire posts

Bio-Scripts

• • BioStar@biostar

  

  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 script

  1628 days ago

• • BioStar@biostar

  

  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.fasta

  1413 days ago

• +3 more Bio-Scripts

Comments

• • Jitendra Narayan@admin

  

  Comment on "Perl one-liner for bioinformatician !!!"

  Nice collection of Perl oneliner. Thank you for the useful list. You can also track other perl onliner posted on wire at http://bioinformaticsonline.com/thewire/tag/Oneliner

  3641 days ago

• • Shruti Paniwala@shruti

  

  Comment on "Most Commonly used Awk by Bioinformatician"

  Some of the useful Unix onliner http://genomics-array.blogspot.in/2010/11/some-unixperl-oneliners-for.html

  3675 days ago