BOL: Wire posts tagged with 'oneliner'

Wire post by LEGE

LEGE — Thu, 02 Sep 2021 06:41:33 -0500

Count number of fasta sequence $ awk '/^>/ { f = !a[$0]++ } f' aaaa.fa > bbbb.fa #count #fasta #oneliner

Wire post by Jit

Jit — Mon, 21 Oct 2019 12:00:22 -0500

https://github.com/stephenturner/oneliners #Bash #Tutorial #OneLiner

Wire post by BioJoker

BioJoker — Sat, 04 May 2019 06:08:20 -0500

Genome Mapping #OneLiner https://bioinformaticsonline.com/snippets/view/39310/one-liner-for-reads-mapping

Wire post by Rahul Nayak

Rahul Nayak — Thu, 08 Jun 2017 09:10:37 -0500

Unmasking the lower case values in genome. $ perl -pe '/^[^>]/ and $_=uc' genomic.fna > genomic.unmasked.fna #Genome #Unmask #Perl #Oneliner

Wire post by Jit

Jit — Tue, 23 May 2017 04:47:49 -0500

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

Wire post by Jit

Jit — Tue, 02 May 2017 09:34:11 -0500

Perl OneLiner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html #Perl #Oneliner #NGS #Script

Wire post by Jit

Jit — Tue, 02 May 2017 09:05:00 -0500

NGS onliner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/subsetFASTAFASTAQ.html #OneLiner #NGS

Wire post by Shruti Paniwala

Shruti Paniwala — Mon, 23 Jan 2017 05:01:08 -0600

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

Wire post by Jit

Jit — Sun, 13 Mar 2016 13:59:21 -0500

Print all text after a matching string perl -ne "print unless 1 .. m(String)" #Perl #OneLiner #String #Perl #Trick

Wire post by Rahul Nayak

Rahul Nayak — Wed, 09 Sep 2015 16:17:11 -0500

Count the number of sequences in fastaq file. grep -c '^@' sample1.fq #Fastaq #Count #Number #Grep #Dirty #Oneliner #NGS

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 — Fri, 03 Jul 2015 01:50:13 -0500

Fancy One-Liner http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/oneliners.html #Perl #OneLiner #Bioinformatics #Quick #Common #Tricks #CommandLine #Terminal

Wire post by Abhimanyu Singh

Abhimanyu Singh — Sat, 12 Jul 2014 15:09:10 -0500

Linux one-liner. https://wikis.utexas.edu/display/bioiteam/Scott%27s+list+of+linux+one-liners #Linux #Oneliner #NGS

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