One-liners - Revision history

Rf at 21:02, 17 April 2017

2017-04-17T21:02:36Z

Rf at 20:42, 17 April 2017

2017-04-17T20:42:42Z

Rf at 09:16, 30 March 2017

2017-03-30T09:16:44Z

Rf at 09:15, 30 March 2017

2017-03-30T09:15:10Z

Rf at 08:58, 30 March 2017

2017-03-30T08:58:30Z

Rf at 08:53, 30 March 2017

2017-03-30T08:53:40Z

Rf: Rf moved page Awk one-liners and scripts to One-liners

2017-03-30T08:39:51Z

Rf moved page Awk one-liners and scripts to One-liners

Rf at 18:00, 13 March 2017

2017-03-13T18:00:12Z

Rf: Created page with " You have a genome coverage file in bedgraph format (final, fourth column is the coverage for a particular section) amd would like to find the max value: awk '{if($4>mxc) m..."

2017-03-13T17:50:49Z

Created page with " You have a genome coverage file in bedgraph format (final, fourth column is the coverage for a particular section) amd would like to find the max value: awk '{if($4>mxc) m..."

New page

You have a genome coverage file in bedgraph format (final, fourth column is the coverage for a particular section) amd would like to find the max value:

awk '{if($4>mxc) mxc=$4} END {print mxc}' v30chronly_s.cov

A genome coverage file what is the average coverage per base?

awk '{tot=tot+$4/($3-$2); la=$3} END {print tot/la}' v30chronly_s.cov

← Older revision		Revision as of 21:02, 17 April 2017
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	Given a multifasta fasta file, you are able to list out the ID lines, Now you want a certain sequence. the following will list out the fourth sequence.		Given a multifasta fasta file, you are able to list out the ID lines, Now you want a certain sequence. the following will list out the fourth sequence.
	awk '{if(/^>/) c++; if(c==4) print}' hexaseqs.fasta		awk '{if(/^>/) c++; if(c==4) print}' hexaseqs.fasta
		+
		+	With an even better idea of the lines of interest, it's possible to use a head and tail combination. These two two are highly optmised and may quickly on very big files. However, you do need the line numbers as given by <code>grep -n ">"</code>. If the indicated lines are n1 and n2, then:
		+
		+	head -n2-1 <file> \|tail +n1

@@ Line 24: / Line 24: @@
 = One-liners featuring awk =
-You have a genome coverage file in bedgraph format (final, fourth column is the coverage for a particular section) amd would like to find the max value:
+You have a genome coverage file in bedgraph format (with the final, fourth column giving the coverage for a particular section) and would like to find the max coverage value across all the ranges:
   awk '{if($4>mxc) mxc=$4} END {print mxc}' v30chronly_s.cov
@@ Line 33: / Line 33: @@
 Note how in the above, for '''la''' (last), we want the  third column on the last line which is the endpoint, but we don't know when it will occur so the third column on all lines get assigned to this variable. This will not do if there is more than one chromosome.

@@ Line 20: / Line 20: @@
 * here we lean heavily on bash's formatted print statement, '''printf''', to generate a regular expression which can be submitted to grep.
 * the regular expression should be designed to guarantee a unique entry in the manicured filelisting.
 = One-liners featuring awk =

@@ Line 16: / Line 16: @@
 <ins>Explanation</ins>
-* lst0 is the original filelisting
+* '''lst0''' is the original filelisting
-* lst is the manicured filelisting
+* '''lst''' is the manicured filelisting
-* here we lean heavily ob bash's formatted print statement to generate a regular expression which should be designed to guarantee a unique entry in the manicured filelisting.
+* here we lean heavily on bash's formatted print statement, '''printf''', to generate a regular expression which can be submitted to grep.
 = One-liners featuring awk =

@@ Line 11: / Line 11: @@
 ==Renaming multiple files==
-There are various way of doing this. Here we have a complicated situation where we have made a filelisting and copied it, and manicured the names in the copy, and now want to rename each file in the original to its corresponding manicured version. Here follows one such example
+There are various way of doing this. Here we have a complicated situation where we have made a filelisting and copied it, and manicured the names in the copy, and now want to rename each file in the original to its corresponding manicured version. The key difficulty is getting the right corresponding name in the manicured list. Here follows one such example
- for i in $(cat lst0); do j=${i#*_}; R=$(printf "%s_\\w\\+_R%s\n" ${i%%_*} ${j%.*}); mv $i $(grep $R lst); done
+<ins>Explanation</ins>
 You have a genome coverage file in bedgraph format (final, fourth column is the coverage for a particular section) amd would like to find the max value:

← Older revision	Revision as of 08:53, 30 March 2017
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	+	= Introduction =
	+
	+	Within command-line usage, there is a common situation whereby a single command-line starts to become quite complicated, and can take quite a while to build up.
	+
	+	In bioinformatics, one is often forced into this situation as many of the tools have quite complicated options and parameter settings.
	+
	+	It also is the usual mode of building simple for loops that can turn out to be quite powerful.
	+
	+	= Examples =
	+
	+	==Renaming multiple files==
	+
	+	There are various way of doing this. Here we have a complicated situation where we have made a filelisting and copied it, and manicured the names in the copy, and now want to rename each file in the original to its corresponding manicured version. Here follows one such example
	+
	+
	+	for i in $(cat lst0); do j=${i#_}; R=$(printf "%s_\\w\\+_R%s\n" ${i%%_} ${j%.*}); mv $i $(grep $R lst); done

← Older revision	Revision as of 08:39, 30 March 2017
(No difference)

← Older revision		Revision as of 18:00, 13 March 2017
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	awk '{tot=tot+$4/($3-$2); la=$3} END {print tot/la}' v30chronly_s.cov		awk '{tot=tot+$4/($3-$2); la=$3} END {print tot/la}' v30chronly_s.cov
		+
		+	Note how in the above, for '''la''' (last), we want the third column on the last line which is the endpoint, but we don't know when it will occur so the third column on all lines get assigned to this variable. This will not do if there is more than one chromosome.