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Inserting shell script input data automatically from a text file


 
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# 1  
Old 01-23-2016
Linux Inserting shell script input data automatically from a text file

Dear experts,

I am new to linux programming. I have a shell script which i should run it on all my samples.
I only define input and out put for this script. The inputs are 3 numbers(coordination numbers) which are available in a series of text file.
Since i have a lots of samples, it takes a lot of time to manually insert the numbers to the script.
Is it possible to write a script which automatically insert the numbers from the text files to the script?

An example of my text fileSmiliein this example only 49 75 48 are used as inputs, so i need to extract them automatically from the text file and insert them as inputs to the script)

Code:
Cluster Index	Voxels	MAX	MAX X (vox)	MAX Y (vox)	MAX Z (vox)	COG X (vox)	COG Y (vox)	COG Z (vox)
15	17	5.07	49	75	48	48.1	73.5	47.4
14	16	5.52	42	80	50	41.3	79.7	49.7

I will be grateful for any help you can provide.

Best,
Mohamad

Last edited by Scrutinizer; 01-23-2016 at 04:18 PM.. Reason: CODE tags
# 2  
Old 01-23-2016
Try:
Code:
TAB=$(printf "\t")
while IFS=$TAB read ci voxels max max_x max_y max_z cog_x cog_y cog_z
do
  echo "$max_x, $max_y, $max_z"
done < infile


If you only need those the three values you could simplify like this :
Code:
TAB=$(printf "\t")
while IFS=$TAB read x x x max_x max_y max_z x
do
  echo "$max_x, $max_y, $max_z"
done < infile

where "x" contains dummy values..


--
In bash ksh93 and zsh you can use:
Code:
while IFS=$'\t' read ...

in other shells you can use a hard-TAB (entered through CTRL-V TAB)
This User Gave Thanks to Scrutinizer For This Post:
# 3  
Old 01-23-2016
Thanks for your prompt answer,i really really appreciate it.

Sorry, if I ask, but I don't know how to read the text file and also i don't know how to give the outputs to my script.
First i should copy your script to a text file, next i should make it executable and finally i should set the path,right?

i only need the first row parameters, does this scripts only echo values of max_x max_y and max_z in the first row?

my script is:

Code:
fslmaths InputImage -mul 0 -add 1 -roi max_x 1 max_y 1 max_z 1 0 1 outputName

(Inputimage and max_x, max_y and max_z are the inputs)

Since i am new to Linux programming, i will be grateful for your help with this situation

Best,
Mohamad

Last edited by Scrutinizer; 01-23-2016 at 09:04 PM.. Reason: code tags
# 4  
Old 01-23-2016
To read only the first row you can leave out the while loop, you could try something like:

Code:
TAB=$(printf "\t")
IFS=$TAB read x x x max_x max_y max_z x < input_file
fslmaths InputImage -mul 0 -add 1 -roi "$max_x" 1 "$max_y" 1 "$max_z" 1 0 1 outputName

This User Gave Thanks to Scrutinizer For This Post:
# 5  
Old 01-24-2016
I guess you should read and throw away the header line:
Code:
TAB=$(printf "\t")
{ read x; IFS=$TAB read x x x max_x max_y max_z x; } < input_file
fslmaths InputImage -mul 0 -add 1 -roi "$max_x" 1 "$max_y" 1 "$max_z" 1 0 1 outputName

These 2 Users Gave Thanks to RudiC For This Post:
# 6  
Old 01-24-2016
I appreciate the time you have put into detailing these requirements. Thank you.

Its working.

Best
Mohamad
 

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