Multiply numbers between two different patterns and print the whole file

Question

I would like to replace number between patterns with multiplicated numbers and print the all the lines. The file is a tree file in newick format and consisted only a single line. My targets are all the numbers after ) and before :. I wanted to multiply all the numbers in between the two symbols with 100.

file:

((((A_8:0.000846,(A_5:0.002449,(A_1:1e-06,((A_4:1e-06,((A_7:1e-06,A_6:0.001061)0.714000:1e-06,A_3:1e-06)0.314500:1e-06)0.358667:1e-06,A_2:1e-06)0.361000:1e-06)0.434800:1e-06)0.683500:0.001619)0.888571:0.001931,A_9:0.00069)0.688471:0.000691,...

The easiest way to me seemed to be splitting the file by replacing all the ":" symbols with a new line first. So all my target numbers are now in separate lines and appear after ). Then, I was using the awk script below to multiply the target numbers with 100, but didn't manage to keep the lines without my target number though.

script:

sed 's/:/\n/g' df9.tree | awk -F")" '{OFS=")"} $2=$2*100 {print $0}'
sed 's/:/\n/g' df9.tree | awk '$NF ~/)/ {$NF *=100}1'

How can I multiply the numbers after ) and print the entire file in this case? Or is there other simpler way to directly look for the numbers lie between : and ), multiply them by 100 and print the whole file?

Update: Expected output

((((A_8:0.000846,(A_5:0.002449,(A_1:1e-06,((A_4:1e-06,((A_7:1e-06,A_6:0.001061)71.4000:1e-06,A_3:1e-06)31.4500:1e-06)35.8667:1e-06,A_2:1e-06)36.1000:1e-06)43.4800:1e-06)68.3500:0.001619)88.8571:0.001931,A_9:0.00069)68.8471:0.000691,...)

Answer 1

awk 'BEGIN {OFS=FS=":"; ORS=RS=")"} NR>1 {$1=sprintf("%.4f", $1 * 100)}1' df9.tree

If you accept to separate RS records and FS fields, then the required number will always be in the first field after the first record.

Answer 2

$ perl -pe 's/\)([-0-9.]+):/sprintf ")%.4f:", $1 * 100/eg' df9.tree
((((A_8:0.000846,(A_5:0.002449,(A_1:1e-06,((A:1e-06,((A_7:1e-06,A:0.001061)71.4000:1e-06,A:1e-06)31.4500:1e-06)35.8667:1e-06,A:1e-06)36.1000:1e-06)43.4800:1e-06)68.3500:0.001619)88.8571:0.001931,A:0.00069)68.8471:0.000691,...

replaces all numbers (defined as a sequence of one-or-more digits, periods, or minus characters) immediately following a ) character and terminated by a : character with the number multiplied by 100.

e.g. )0.714000: gets changed to )71.4000:

It uses perl's /e regex evaluation modifier to execute perl code in the RHS of the s/// operator. See man perlop and search for s\/PATTERN for details. sprintf is used to format the number to have 4 decimal places.

---

If the number between ) and : could be in either plain decimal notation ("0.714000") or "C float"-style scientific notation ("1e-06"), the regex needs to be just a tiny bit more complicated to match all the possible variations:

$ perl -pe 's/\)(([+-]?)(?=\d|\.\d)\d*(\.\d*)?([Ee]([+-]?\d+))?):/sprintf ")%.4f:", $1 * 100/eg' df9.tree
((((A_8:0.000846,(A_5:0.002449,(A_1:1e-06,((A_4:1e-06,((A_7:1e-06,A_6:0.001061)71.4000:1e-06,A_3:1e-06)31.4500:1e-06)35.8667:1e-06,A_2:1e-06)36.1000:1e-06)43.4800:1e-06)68.3500:0.001619)88.8571:0.001931,A_9:0.00069)68.8471:0.000691,...)

The following may also work, but there may be some numbers it won't match:

perl -pe 's/\)([-0-9.eE+]+):/sprintf ")%.4f:", $1 * 100/eg'

Answer 3

With perl's s///e, you can use the evaluation step to determine if the match was numeric, and substitute accordingly:

perl -MScalar::Util=looks_like_number -pe '
s{\)\K.*?(?=:)}{ looks_like_number($&) ? $&*100 : $& }ge' file

With GNU awk, using a regular expression for the record separator:

gawk 'prevRT==")" && RT==":" && $0+0 == $0 {$0 *= 100} {ORS = prevRT = RT}
1' RS='[):]' file

This tests the numeric-ness of a record with the comparison $0+0 == $0.

Answer 4

Using POSIX sed in conjunction with the desk calculator dc and bash shell we can get the result as shown. First we compute the form of the string to be synthesized then synthesize it by pushing it onto bash.

echo 'echo "'"$(sed -e '
  s#)\([^:)]\{1,\}\):#)$(echo "4k100 \1*1/p"|dc):#g' < file)"'"'|sh

---

Or, we can eval the variable which has been pre-filled with the command to generate the output.

var='echo "'$(sed -e '
  s#)\([^:)]\{1,\}\):#)$(echo "4k100 \1*1/p"|dc):#g' < inp)\"

eval "$var"

---

Using the 4-argument split function in GNU awk which keeps track of both the fields and the delimiters.

awk '{
  split($0, a, /[:)]/, s)
  for (i=1; i in a; i++)
    print (s[i-1] s[i] == "):" ? sprintf("%.4f",a[i]*100):a[i]) s[i]
  $0=RS
}1' ORS= file