Results for "Awk"

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  • Print all the values beetween a pattern "abc" > awk '/abc/{flag=1;next}/mno/{flag=0}flag' file #awk #print #range #pattern

    Tags: awk, print, range, pattern

    2972 days ago

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

    Tags: awk, oneliner

    2502 days ago

  • Replace space with tab. $ awk -v OFS="\t" '$1=$1' file1 #tab #space #replace #awk

    Tags: tab, space, replace, awk

    2425 days ago

  • Remove duplicated lines from text file. $ awk '!seen[$0]++' allIds #duplicate #lines #remove #awk

    Tags: duplicate, lines, remove, awk

    2423 days ago

  • Converting FASTQ to FASTA

    There are several ways you can convert fastq to fasta sequences. Some methods are listed below. Using SED sed can be used to selectively print the desired lines from a file, so if you print the first and 2rd line of every 4 lines, you get the sequence header and sequence need...

    Tags: fasta, fastq, convert, sed, awk, seqtk, bioawk, fastx, Emboss, fastq2fasta

    2268 days ago

  • Multiline to singleline covert. $ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa #Multi #Single #Convert #awk

    Tags: Multi, Single, Convert, awk

    1586 days ago

  • Extract the underscore separated values. $ awk '{split($0,a,"_"); print a[1]"_"a[2]}' aaa.txt | sort | uniq -u > all_ids_sm.txt #awk #bash #underscore #list

    Tags: awk, bash, underscore, list

    1454 days ago

  • Run bash script in Perl program !

    BioPerl is a compilation of Perl modules that can be used to build bioinformatics-related Perl scripts. It is used, for example, in the development of source codes, standalone software/tools, and algorithms in bioinformatics programmes. Different modules are easy to instal and include, making it ...

    Tags: Perl, Bash, Script, awk, Module

    600 days ago

  • Most Commonly used Awk by Bioinformatician

      Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases. Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single ...

    Tags: Awk, Bioinformatics

    3875 days ago