BOL: Wire posts tagged with 'Fasta'

Wire post by Neel

Neel — Wed, 09 Mar 2016 08:23:46 -0600

Delete space from FASTA header: perl -pe 's/>\S+\K.+//' < file.fasta > new_file.fasta #PerlOneLiner #Trick #Perl #Space #Fasta

Wire post by Rahul Nayak

Rahul Nayak — Wed, 09 Sep 2015 16:05:55 -0500

Remove the fasta description and just keep the identifier. perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa #Perl #Oneliner #Trick #Tips #Fasta #Identifier #Remove

Wire post by Rahul Nayak

Rahul Nayak — Wed, 09 Sep 2015 16:01:53 -0500

Extract sequences by their ID from a fasta file. perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.txt sample1.fa #Extract #Sequences #IDs #Fasta #Perl #Trick #Oneliner

Wire post by Rahul Nayak

Rahul Nayak — Thu, 13 Aug 2015 00:36:31 -0500

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

Wire post by Jit

Jit — Mon, 21 Jul 2014 06:37:42 -0500

To count number of fasta entries, I use: grep -c '^>' mySequences.fasta #Perl #Count #Number #Fasta #Linux #Grep

Wire post by Jit

Jit — Fri, 06 Jun 2014 02:55:27 -0500

Remove the blank space from a fasta file. perl -nlwe 'tr/ //d; print if length' fileName #Delete #Space #Fasta #Perl #Oneliner

Wire post by Jit

Jit — Fri, 06 Jun 2014 02:54:18 -0500

Remove N from a fasta file. Go to vi editor, type :%s/N\{25,\}//g and press enter. #Vim #vi #N #Replace #Fasta

Wire post by Jit

Jit — Fri, 06 Jun 2014 02:38:28 -0500

perl -nle 'if (/^>/) { $sl = 0; print; next } next if ($sl >= 200); $_ = substr($_, 0, 200-$sl) if ($sl + length($_) > 200); $sl += length($_); print;' file.fa >new.fa #Perl #Extract #Fasta

Wire post by Jitendra Narayan

Jitendra Narayan — Fri, 30 May 2014 06:08:14 -0500

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. https://github.com/lh3/seqtk #FASTA #FASTAQ #NGS

Wire post by Jit

Jit — Fri, 23 May 2014 10:10:20 -0500

FastaQ 2 Fasta Oneliner: paste - - - -< totalRNA_placental_1.fastq | perl -pale'$_="@F[0..1]"'|tr "\^@" "\>" | perl -pale 's/\s/\n/g' #Oneliner #NGS #FastaQ #Fasta

Wire post by Neel

Neel — Mon, 12 May 2014 04:47:30 -0500

zcat input_file.fastq.gz | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > output_file.fa #fastaQ2fasta #fastaq #fasta #Oneliner

Wire post by Rahul Nayak

Rahul Nayak — Wed, 02 Oct 2013 09:15:50 -0500

GenBank to FASTA format conversion, Written By Junguk HUR http://tinyurl.com/ntp7w5v #Perl #FASTA #Genbank