Extracting specific strings from sets of multiple lines

[plasma33]

Hello again,

I would like to extract specific strings from a set of aligned strings. That is, I would like to extract only the aligned single string that is exactly matched to one another from several sets of aligned multiple strings avoiding gaps (i.e. hyphens). Please see below for a better picture:
Input:

Code: Select all

IGRNRKGDGARGRGRGRGRHRIKLRGIG
||||||||||||||||||||||||||||
------GDGARGRGRGRGRHRIKLRGIG

IGKKRHIG
||||||||
IG------

GDGARGRGRGRGRHRIKMRGIG
||||||||||||||||||||||
GDGARGRGRGRGRHRIKMRGIG

LIGRGRIIGKK
|||||||||||
LIGR------K

GDGARGRGRGRGRHRLRLRGIGKLKIIGRHR
|||||||||||||||||||||||||||||||
GDGARGRGRGRGRHRLRLRGIGK------HR

IGRHRK------GDGARGRGRGRGRHRLRPRGIGR
|||||||||||||||||||||||||||||||||||
IGRHRKIGRKRLGDGARGRGRGRGRHRLRPRGIGR

and so on
.
.
.

Output:

Code: Select all

GDGARGRGRGRGRHRIKLRGIG
IG
GDGARGRGRGRGRHRIKMRGIG
LIGR
K
GDGARGRGRGRGRHRLRLRGIGK
HR
IGRHRK
GDGARGRGRGRGRHRLRPRGIGR
and so on
.
.
.

Thanks.

Plasma33

[Aacini]

Code: Select all

@echo off
setlocal EnableDelayedExpansion

set "i=0"
(for /F "delims=" %%a in (input.txt) do (
   set /A i=i%%3+1
   set "line!i!=%%a"
   if !i! equ 3 (
      if "!line1:-=!" neq "!line1!" (
         for /F "tokens=1,2 delims=-" %%b in ("!line1!") do (
            echo %%b
            if "%%c" neq "" echo %%c
         )
      ) else if "!line3:-=!" neq "!line3!" (
         for /F "tokens=1,2 delims=-" %%b in ("!line3!") do (
            echo %%b
            if "%%c" neq "" echo %%c
         )
      ) else (
         echo !line1!
      )
   )
)) > output.txt

[plasma33]

@Aacini, you are a legend! Your code works like a charm. Fast and accurate!! Thanks heaps!!

Plasma33