how to calculate all pairwise distances in two dimensions and transform them into a matrix
Hello to all,
I am very new in the shell scripting and I need help. I have data for several individuals in several rows followed by a tag and by 5 values per row, with the name of the individual in the first column, e.g.:
I would like to calculate the sum of the absolute values of the pairwise differences between individuals. For instance:
Code:
Distance between IND1 and IND2=|12-12|+|13-12|+|12-15|+|15-14|+|14-14|= 5
Distance between IND1 and IND3=|12-12|+|13-15|+|12-12|+|15-14|+|14-11|= 6
Distance between IND2 and IND3=|12-12|+|12-15|+|15-12|+|14-14|+|14-11|= 9
Additionally, if the tags of two individuals are different, I would like to sum 100 to the final number. So finally the distance between:
IND1 and IND2 would be = 5 + 100 = 105
IND1 and IND3 would be = 6 + 0 = 6
IND2 and IND3 would be = 9 + 100 = 109
After this, I would like to transform this list of distances into a matrix:
Code:
IND1 IND2 IND3
IND1
IND2 105
IND3 6 109
Could some one help me with this? Thanks a lot in advance! Best!
File 1 contains the list of words that needed to be randomly paired:
Tiger
Cat
Fish
Frog
Dog
Mouse
Elephant
Monkey
File 2 contains the pairs that should not be used (in any solution) during random pairing.
Elephant-Dog
Cat-Fish
Monkey-Frog
Dog-Elephant, Fish-Cat, Frog-Monkey... (1 Reply)
The following code transform the matrix to columns. Is it possible to do it other way around ( get the input from the output) ?
input
y1 y2 y3 y4 y5
x1 0.3 0.5 2.3 3.1 5.1
x2 1.2 4.1 3.5 1.7 1.2
x3 3.1 2.1 1.0 4.1 2.1
x4 5.0 4.0 6.0 7.0 1.1
output
x1 y1 0.3
x2 y1 1.2
x3... (1 Reply)
This matrix represents correlation values.
Is it possible to calculate the percentage of columns (a1, a2, a3) that have a value >= |0.5| and report the percentage that has positive correlation >0.5 and negative correlation <-0.5 separately. thanx in advance!
input
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The second file looks something like this:
Sequences.txt
>Sample1 Freq 59
ggatatgatgatgaactggt
>Sample1 Freq 54
ggatatgatgttgaactggt
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I have an input matrix file like this
Col1 Col2 Col3 Col4
R1 1 2 3 4
R2 4 5 6 7
R3 5 6 7 8
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11-28-2011
