User:Timothee Flutre/Notebook/Postdoc/2012/05/25: Difference between revisions
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== | ==Awk one-liner to convert fasta file into fastq format== | ||
* 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 13:09, 25 May 2012
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Awk one-liner to convert fasta file into fastq format
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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