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Results for "awk"

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  Awk

  Awk is widely used these days for extraction and manipulation of large scale biological data in Unix/Linux.Most of the awk code is single liner. Useful Weblinks: http://www.grymoire.com/Unix/Awk.html http://www.hcs.harvard.edu/~dholland/computers/awk.html http://www.pement.org/awk/awk1line.tx...

  Tags: awk, gawk, nawk, sed, data, sequencing, one liner

  3908 days ago

• • Rahul Agarwal@raag

  

  How to merge multiple files (>10) with different length using awk? for e.g. 1st column as unique id (gene name)

  Tags: awk, merge, sed, gawk, nawk

  3503 days ago

• • Jit@jit.aber

  

  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

  2998 days ago

• • Jit@jit.aber

  

  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

  2528 days ago

• • Neelam Jha@neelam

  

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

  Tags: tab, space, replace, awk

  2451 days ago

• • Jit@jit.aber

  

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

  Tags: duplicate, lines, remove, awk

  2449 days ago

• • Neelam Jha@neelam

  

  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

  2294 days ago

• • LEGE@lege

  

  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

  1612 days ago

• • Rahul Nayak@rahul

  

  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

  1480 days ago

• • Neelam Jha@neelam

  

  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

  626 days ago

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