User:Timothee Flutre/Notebook/Postdoc/2012/05/25
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| - | == | + | ==One-liners with GNU tools== |
| - | * | + | * [http://en.wikipedia.org/wiki/AWK AWK] is a programming language very useful to perform, from the command line, quick checks, format conversions and exploratory analyzes on any text file. |
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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 11:19, 21 November 2012
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One-liners with GNU tools
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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