User:Timothee Flutre/Notebook/Postdoc/2012/05/25

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==Awk one-liner to convert fasta file into fastq format==
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==One-liners with GNU tools==
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* We can use the built-in variable "RS" ([http://www.gnu.org/software/gawk/manual/gawk.html#Records split records]) and use "split" ([http://www.gnu.org/software/gawk/manual/gawk.html#String-Functions string function]):
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* '''Tutorial''': [http://www.ibm.com/developerworks/aix/library/au-unixtext/index.html Introduction to text manipulation on UNIX-based systems] by Brad Yoes (IBM)
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* '''Toolbox''':
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** [http://en.wikipedia.org/wiki/AWK AWK]
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** grep
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** sed
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** cut
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** tr
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** wc
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* '''Use absolute values:'''
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awk 'function abs(x){return (((x < 0.0) ? -x : x) + 0.0)} {print abs($1)}' input.txt
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* '''Convert file from fasta to fastq''': we can use the built-in variable "RS" ([http://www.gnu.org/software/gawk/manual/gawk.html#Records split records]) and use "split" ([http://www.gnu.org/software/gawk/manual/gawk.html#String-Functions string function]):
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Revision as of 02:01, 22 November 2012

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One-liners with GNU tools


  • Toolbox:
    • AWK
    • grep
    • sed
    • cut
    • tr
    • wc


  • Use absolute values:
awk 'function abs(x){return (((x < 0.0) ? -x : x) + 0.0)} {print abs($1)}' input.txt


awk 'BEGIN{RS=">"} {if(NF==0)next; split($0,a,"\n"); printf "@"a[1]"\n"a[2]"\n+\n"; \
for(i=1;i<=length(a[2]);i++)printf "}"; printf"\n"}' probes.fa > probes.fq


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