UNIX for Dummies Questions & Answers

 real 9m13.651s
 user 9m13.210s
 sys 0m0.436s

 sed -n '0,/AATTCCGG/s/^[ATCG]*AATTCCGG\(.\)\(.\)\(.\)\(.\)[ATCG]*$/\1\2\3\4/p; 0,/CCGGAATT/y/ATCG/TAGC/; s/^[ATCG]*\(.\)\(.\)\(.\)\(.\)GGCCTTAA[ATCG]*$/\4\3\2\1/p'

 real 1m10.950s
 user 1m10.715s
 sys 0m0.234s

sed -n '0,/AATTCCGG/s/^[ATCG]*AATTCCGG\(.\)\(.\)\(.\)\(.\)[ATCG]*$/\1\2\3\4/p; 0,/CCGGAATT/{y/ATCG/TAGC/; s/^[ATCG]*\(.\)\(.\)\(.\)\(.\)GGCCTTAA[ATCG]*$/\4\3\2\1/p;}' file*

 sed -n '/AATTCCGG/s/^[ATCG]*AATTCCGG\(....\)[ATCG]*$/\1/p; /CCGGAATT/{y/ATCG/TAGC/; s/^[ATCG]*\(.\)\(.\)\(.\)\(.\)GGCCTTAA[ATCG]*$/\4\3\2\1/p;}'

 sed -n '/AATTCCGG/s/^[ATCG]*AATTCCGG\(....\)[ATCG]*$/\1/pg; /CCGGAATT/{y/ATCG/TAGC/; s/^[ATCG]*\(.\)\(.\)\(.\)\(.\)GGCCTTAA[ATCG]*$/\4\3\2\1/pg;}'

awk -v len=4 -v string=AATTCCGG -v max=10 '
  BEGIN {
    FS=RS; RS=">"; OFS=""
    C["A"]="T"; C["T"]="A"; C["C"]="G"; C["G"]="C"  
  }
  function reverse_complement(s,        t,i,n,F) {
    n=split(s,F,"")
    for(i=1;i<=n;i++)
      t=C[F[i]] t
    return t
  }
  FNR==1{
    split(FILENAME, F, ".")
    c=1
    next
  } 
  { 
    label=$1
    $1=""
    rec=$0 FS reverse_complement($0)
    while(c<=max && match(rec,string)) { 
      print F[1] ":" label ":" substr(rec,RSTART+RLENGTH, len)
      rec=substr(rec, RSTART+RLENGTH+len)
      c++
    }
  }
' file*.txt