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Results for "Oneliner"

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• • Rahul Nayak@rahul

  

  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

  3614 days ago

• • Jit@jit.aber

  

  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

  3613 days ago

• • Neelam Jha@neelam

  

  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

  3638 days ago

• • Jit@jit.aber

  

  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

  3627 days ago

• • Abhimanyu Singh@abhimanyu

  

  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

  3620 days ago

• • Abhimanyu Singh@abhimanyu

  

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

  Tags: Linux, Oneliner, NGS

  3577 days ago

• • Abhimanyu Singh@abhimanyu

  

  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

  3261 days ago

• • Rahul Nayak@rahul

  

  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

  3153 days ago

• • Rahul Nayak@rahul

  

  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

  3152 days ago

• • Rahul Nayak@rahul

  

  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

  3152 days ago

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