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

(Difference between revisions)
 Revision as of 03:01, 22 November 2012 (view source) (→One-liners with GNU tools: add tutorial + list of other tools)← Previous diff Revision as of 11:42, 29 November 2012 (view source) (→One-liners with GNU tools: add sed examples)Next diff → Line 20: Line 20: - * '''Use absolute values:''' + * '''Skip a subset of successive lines''': + for i in {1..10}; do echo \$i; done | sed 3,6d - awk 'function abs(x){return (((x < 0.0) ? -x : x) + 0.0)} {print abs(\$1)}' input.txt + + * '''Extract a subset of successive lines''': + for i in {1..20}; do echo \$i; done | sed -n 3,5p + + + * '''Use absolute values:''' + for i in {-5..5}; do echo \$i; done | awk 'function abs(x){return (((x < 0.0) ? -x : x) + 0.0)} {print abs(\$1)}'

Revision as of 11:42, 29 November 2012

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One-liners with GNU tools

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

• Skip a subset of successive lines:
```for i in {1..10}; do echo \$i; done | sed 3,6d
```

• Extract a subset of successive lines:
```for i in {1..20}; do echo \$i; done | sed -n 3,5p
```

• Use absolute values:
```for i in {-5..5}; do echo \$i; done | awk 'function abs(x){return (((x < 0.0) ? -x : x) + 0.0)} {print abs(\$1)}'
```

```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

```