Converting to decimal values

Question: Converting to decimal values

8 weeks ago by

Hi everyone,

I have a table like this

A   B   2.9711e-01  6.8662e-10  2/2048
A   C   2.3343e-03  0.0000e+00  1861/2048
A   D   2.9711e-01  6.8666e-10  2/2048
A   E   2.9711e-01  6.8658e-10  2/2048

I would like to convert column 5 into the decimal value, such as

    A   B   2.9711e-01  6.8662e-10  0,0009765625
    A   C   2.3343e-03  0.0000e+00  0,90869140625
    A   D   2.9711e-01  6.8666e-10  0,0009765625
    A   E   2.9711e-01  6.8658e-10  0,0009765625

Could someone help me out?

Cheers!

sequence • 209 views

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modified 7 weeks ago by h.mon ♦ 32k • written 8 weeks ago by genomes_and_MGEs • 10

How is this related to bioinformatics?

ADD REPLY • link written 8 weeks ago by _r_am ♦ 32k

8 weeks ago by

JC ♦ 12k

Mexico

JC ♦ 12k wrote:

This can do the trick:

$ perl -lane '($n,$d)=split(/\//,$F[4]); $F[4]=$n/$d; print join "\t", @F' < table.txt
A       B       2.9711e-01      6.8662e-10      0.0009765625
A       C       2.3343e-03      0.0000e+00      0.90869140625
A       D       2.9711e-01      6.8666e-10      0.0009765625
A       E       2.9711e-01      6.8658e-10      0.0009765625

ADD COMMENT • link written 8 weeks ago by JC ♦ 12k

8 weeks ago by

Kevin Blighe ♦ 69k

Republic of Ireland

Kevin Blighe ♦ 69k wrote:

You can try awk, too, assuming that your file's format is consistent (no empty cells; tab-delimited) and that there is indeed no header:

awk -F "\t" '{
  split($5, div, "/");
  print $1"\t"$2"\t"$3"\t"$4"\t"div[1]/div[2]}' table.txt

A   B   2.9711e-01  6.8662e-10  0.000976562
A   C   2.3343e-03  0.0000e+00  0.908691
A   D   2.9711e-01  6.8666e-10  0.000976562
A   E   2.9711e-01  6.8658e-10  0.000976562

Kevin

ADD COMMENT • link modified 8 weeks ago • written 8 weeks ago by Kevin Blighe ♦ 69k

8 weeks ago by

Devon Ryan ♦ 98k

Freiburg, Germany

Devon Ryan ♦ 98k wrote:

$ awk '{split($5, v, "/"); OFS="\t"; print $1,$2,$3,v[1]/v[2]}' foo.txt
A       B       2.9711e-01      0.000976562
A       C       2.3343e-03      0.908691
A       D       2.9711e-01      0.000976562
A       E       2.9711e-01      0.000976562

ADD COMMENT • link written 8 weeks ago by Devon Ryan ♦ 98k

7 weeks ago by

h.mon ♦ 32k

Brazil

h.mon ♦ 32k wrote:

Just to keep the tradition of questions with no clear relation to bioinformatics attracting lots of answers (and because it is Friday night at times of pandemics), here are some alternative solutions:

Using several bash variables:

while IFS=$'\t' read -r val1 val2 val3 val4 val5
do
    val5=$(echo "scale=10; $val5" | bc -l)
    printf "%s\t%s\t%s\t%s\t%s\n" "$val1" "$val2" "$val3" "$val4" "$val5"
done < table.tsv

With an array, slicing the array to delete the last element and replace by the result of the division:

while IFS=$'\t' read -r -a array
do
    val=$(echo "scale=10; ${array[-1]}" | bc -l)
    array=("${array[@]::${#array[@]}-1}")
    array+=($val)
    printf "%s\t" "${array[@]}"; echo
done < table.tsv

For modern (later than 4.2, I think) bash, one can use a nicer syntax to delete the last array element:

while IFS=$'\t' read -r -a array
do
    val=$(echo "scale=10; ${array[-1]}" | bc -l)
    unset array[-1]
    printf "%s\t" "${array[@]}"
    printf "%s\n" "$val"
done < table.tsv

ADD COMMENT • link written 7 weeks ago by h.mon ♦ 32k

These are my favorite posts because we get to see multiple ways people tackle the same problem!

ADD REPLY • link written 7 weeks ago by bioinformatics2020 • 570

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