Fancy Oneliner for Bioinformatics !!
This webpage lists some of the one-liners that we frequently use in metagenomic analyses. You can click on the following links to browse through different topics. You ca...2868 days ago
2227 days ago
Bash oneliner to extract all ids from a multifasta file
#List of ids - one per line in allIds.txt $ awk 'BEGIN{while((getline0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa # You can play with this f=!l[$1 ] if wanted to extract or not extract the ids1547 days ago
Reformat the multifasta for sequence length !
#awk oneliner to reformat the multifasta sequences awk '!/^>/ {printf "%s", $0; n = "\n"} /^>/ {print n $0; n = ""}' file.fasta | fold -w 1001401 days ago
Perl one-liner for bioinformatician !!!
With the emergence of NGS technologies, and sequencing data most of the bioinformaticians mung and wrangle around massive amounts of genomics text. There are several "standardized" file formats (FASTQ, SAM, VCF, etc.) and some tools for manipulating them (fastx toolkit, samtools, vcftools, etc.),...Tags: Bioinformatics, Computational Biology, Perl, NGS, Genome, Hacking, One-liner, Oneliner
3637 days ago
Tags: Bioinformatics, Oneliner
2227 days ago
2699 days ago
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/Oneliner3638 days ago