Bash: Merging 4 lines in 4 files into one single file

Question

I'm looking for a way to merge 4 lines of dna probing results into one line.

The problem here is:

I don't want to append the lines. But associating them

The 4 lines of dna probing:

A----A----------A----A-A--AAAA-

-CC----CCCC-C-----CCC-C-------C

------G----G--G--G------G------

---TT--------T-T---------T-----

I need these to be 1 line, not just appended but intermixed without the dashes.

First characters of the result:

 ACCTTAGCCCCGC...

This seem to be a kind of general problem, so the language choosed to solve this don't matter.

Answer 1

For fun: one bash way:

lines=(
    A----A----------A----A-A--AAAA-
    -CC----CCCC-C-----CCC-C-------C
    ------G----G--G--G------G------
    ---TT--------T-T---------T-----
)

result=""
for ((i=0;i<${#lines};i++)) ;do
    chr=- c=()
    for ((l=0;l<${#lines[@]};l++)) ;do
        [ "${lines[l]:i:1}" != "-" ] &&
            chr="${lines[l]:i:1}" &&
            c+=($l)
      done
    [ ${#c[@]} -eq 0 ] && printf 'Char #%d not replaced.\n' $i
    [ ${#c[@]} -gt 1 ] && c="${c[*]}" && chr="*" &&
         printf "Conflict at char #%d (lines: %s).\n" $i "${c// /, }"
    result+=$chr
  done
echo $result

With provided input, there is no conflict and all characters is replaced. So the output is:

ACCTTAGCCCCGCTGTAGCCCACAGTAAAAC

Note: Question stand for 4 different files, so lines= syntax could be:

lines=($(cat file1 file2 file3 file4))

But with a wrong input:

lines=(
    A----A---A-----A-----A-A--AAAA-
    -CC----CCCC-C-----CCC-C-------C
    ------G----G---G-G------G------
    ---TT--------T-T---------T-----
)

output could be:

Conflict at char #9 (lines: 0, 1).
Char #14 not replaced.
Conflict at char #15 (lines: 0, 2, 3).
Char #16 not replaced.

and

echo $result
ACCTTAGCC*CGCT-*-GCCCACAGTAAAAC

Small perl filter

But if input are not to be verified, this little perl filter could do the job: (Thanks @jm666 for }{ syntax)

perl -nlE 'y+-+\0+;$,|=$_}{say$,' <(cat file1 file2 file3 file4)

where

-n          process all lines without output
-l          whipe leading cariage return at end of lines
y+lhs+rhs+  replace (translate) chars from 'lhs' to 'rhs'
\0          is the *null* character, binary 0.
$,          is a variable
|=          binary or, between himself and current line ($_)
}{          at END, once all lines processed