User:Timothee Flutre/Notebook/Postdoc/2012/05/25: Difference between revisions
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== | ==One-liners with GNU tools== | ||
* '''Tutorial''': [http://www.ibm.com/developerworks/aix/library/au-unixtext/index.html Introduction to text manipulation on UNIX-based systems] by Brad Yoes (IBM) | |||
* '''Toolbox''': | |||
** [http://en.wikipedia.org/wiki/AWK 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 | |||
* '''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]): | |||
<nowiki> | |||
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 | |||
</nowiki> | |||
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Revision as of 00:01, 22 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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