Results for "Oneliner"

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  • rename all *.txt as *.bak: find . -name "*.txt" | sed "s/\.txt$//" | xargs -i echo mv {}.txt {}.bak | sh #Linux #Rename #Oneliner

    Tags: Linux, Rename, Oneliner

    1291 days ago

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

    Tags: Delete, Space, Fasta, Perl, Oneliner

    1291 days ago

  • 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

    Tags: fastaQ2fasta, fastaq, fasta, Oneliner

    1316 days ago

  • 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

    Tags: Oneliner, NGS, FastaQ, Fasta

    1305 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

    1298 days ago

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

    Tags: Linux, Oneliner, NGS

    1254 days ago

  • Perl One liner basics !!

    Perl has a ton of command line switches (see perldoc perlrun), but I'm just going to cover the ones you'll commonly need to debug code. The most important switch is -e, for execute (or maybe "engage" :) ). The -e switch takes a quoted string of Perl code and executes it. For example:$ perl -e 'pr...

    Tags: Bioinformatics, Computational Biology, Education, Study, Script, Perl, Oneliner, Basic

    939 days ago

  • 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

    Tags: Extract, Sequences, IDs, Fasta, Perl, Trick, Oneliner

    830 days ago

  • 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

    Tags: Perl, Oneliner, Trick, Tips, Fasta, Identifier, Remove

    830 days ago

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

    Tags: Fastaq, Count, Number, Grep, Dirty, Oneliner, NGS

    830 days ago