looking for a tool

Question: looking for a tool

3.0 years ago by

olivier.claude • 30

France

olivier.claude • 30 wrote:

hello,

i am tring to play with some datas, but i am facing some problems:

- i want to know the lenght of the sequence (column5) and i didn't found any tool allowing to do it.

-I want to substract column 4 to column 3 . No tools neither.

Any idea?

here is a sample to help:

1	2	3	4	5
posterior	0.865	168	181	NRKRRQRREWEARR
posterior	0.865	120	135	NRKRRQRREWEARR
posterior	0.968	278	290	VEKRPRRKRRTRL

Thanks a lot & have a nice day!

Olivier

count substract galaxy • 1.0k views

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modified 3.0 years ago by Bjoern Gruening ♦ 5.1k • written 3.0 years ago by olivier.claude • 30

3.0 years ago by

Devon Ryan • 1.9k

Germany

Devon Ryan • 1.9k wrote:

This can be done with "awk" under the "Unix tools". To get the length of column 5 the program is:

{print length($5)}

To get the difference between columns 4 and 3 it'd be

{print $4-$3}

ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by Devon Ryan • 1.9k

3.0 years ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

Hi Oliver

I suggest the following for your first question:

1) Text Manipulation -> Add column: Add "1" with Iterate set to 'yes', this will give you unique identifiers for every line in your table

2) FASTA manipulation -> Tabular-to-FASTA: select column 6 as title and column 5 as sequence

3) FASTA manipulation -> compute sequence length:

... for your second question:

1) Text Manipulation -> compute: use expression "c4-c3"

Hope this helps, Hans-Rudolf

ADD COMMENT • link written 3.0 years ago by Hotz, Hans-Rudolf • 1.8k

3.0 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi Olivier,

sorry to be so late to this game. Just to add a very simple solution: Use the tools "Compute an expression on every row" and insert into the "Add expression" field "len(c5)". You will get a file with a new column that has the length of your sequence.

Such nice tricky and more you can find here:

https://github.com/bgruening/galaxy-tricks

Cheers,

Bjoern

ADD COMMENT • link written 3.0 years ago by Bjoern Gruening ♦ 5.1k

Thanks for adding the list of all build-in functions to the help text of "column_maker.xml" (i.e. 'Compute an expression on every row')

ADD REPLY • link written 3.0 years ago by Hotz, Hans-Rudolf • 1.8k

3.0 years ago by

olivier.claude • 30

France

olivier.claude • 30 wrote:

it works fine thanks to both of you !

Olivier.

ADD COMMENT • link written 3.0 years ago by olivier.claude • 30

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