User:Timothee Flutre/Notebook/Postdoc/2012/05/25 - Revision history

Timothee Flutre: /* One-liners with GNU tools */ add "loop over pairs"

2013-04-22T18:11:45Z

One-liners with GNU tools: add "loop over pairs"

←Older revision		Revision as of 18:11, 22 April 2013
Line 44:		Line 44:
	g1 s2 0.002		g1 s2 0.002
	g2 s3 0.05		g2 s3 0.05
		+
		+
		+	* '''Loop over pairs''':
		+
		+	$ subgroups=("s1" "s2" "s3" "s4"); for i in {0..2}; do let a=$i+1; for j in $(seq $a 3); do s1=${subgroups[$i]}; s2=${subgroups[$j]}; echo $s1 $s2; done; done

Timothee Flutre: /* One-liners with GNU tools */ add "extract the best snp per gene"

2013-04-19T14:40:55Z

One-liners with GNU tools: add "extract the best snp per gene"

←Older revision		Revision as of 14:40, 19 April 2013
Line 25:		Line 25:

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


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

		+
		+	* '''Extract the best snp per gene''':
		+
		+	$ echo -e "gene\tsnp\tpvalue\ng1\ts1\t0.3\ng1\ts2\t0.002\ng2\ts2\t0.7\ng2\ts3\t0.05" > dat.txt
		+	gene snp pvalue
		+	g1 s1 0.3
		+	g1 s2 0.002
		+	g2 s2 0.7
		+	g2 s3 0.05
		+
		+	$ cat dat.txt \| sed 1d \| sort -k1,1 -k3,3 \| awk '{print $3"\t"$2"\t"$1}' \| uniq -f2
		+	g1 s2 0.002
		+	g2 s3 0.05


Line 36:		Line 49:

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

Timothee Flutre: /* One-liners with GNU tools */ add sed examples

2012-11-29T15:42:51Z

One-liners with GNU tools: add sed examples

←Older revision		Revision as of 15:42, 29 November 2012
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)}'

Timothee Flutre: /* One-liners with GNU tools */ add tutorial + list of other tools

2012-11-22T07:01:38Z

One-liners with GNU tools: add tutorial + list of other tools

←Older revision		Revision as of 07:01, 22 November 2012
Line 8:		Line 8:
	==One-liners with GNU tools==		==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.~~	+	* '''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

Timothee Flutre: /* Awk one-liner to convert fasta file into fastq format */ dedicate this page for one-liners

2012-11-21T15:19:11Z

Awk one-liner to convert fasta file into fastq format: dedicate this page for one-liners

←Older revision		Revision as of 15:19, 21 November 2012
Line 6:		Line 6:
	\| colspan="2"\|		\| colspan="2"\|
	<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->		<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
-	==~~Awk one~~-~~liner to convert fasta file into fastq format~~==	+	==One-liners with GNU tools==

-	* 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]):	+	* [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.
		+
		+
		+	* '''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>		<nowiki>

Timothee Flutre: /* Entry title */

2012-05-25T20:09:26Z

Entry title

←Older revision		Revision as of 20:09, 25 May 2012
Line 6:		Line 6:
	\| colspan="2"\|		\| colspan="2"\|
	<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->		<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
-	==~~Entry title~~==	+	==Awk one-liner to convert fasta file into fastq format==
-	* Insert content here...	+

		+	* 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>

	<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->		<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->

Timothee Flutre: Autocreate 2012/05/25 Entry for User:Timothee_Flutre/Notebook/Postdoc

2012-05-25T20:03:02Z

Autocreate 2012/05/25 Entry for User:Timothee_Flutre/Notebook/Postdoc

New page

{|{{table}} width="800"
|-
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>      </html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
|-
| colspan="2"|

==Entry title==
* Insert content here...


|}

__NOTOC__