UNIX for Dummies Questions & Answers

>ID 1
AATAATTCCGGATCGTGC
>ID 2
TTTGACAGTAGAC
>ID 3
AGACGATGACGAT

awk 'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)} { print n "\t" (/AATTCCGGATCG|CGATCCGGAATT/ ? "ATCG" : "NOT Present" ) }

>ID 1
AATAATTTTGGATCGTGC
>ID 2
TTTGACGTTCCGGAATTCAGTAGAC
>ID 3
AGACGATGACGAT

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

file1:ID 1:ATCG
file2:ID 2:AACG

real    0m28.877s
user    0m28.734s
sys     0m0.015s

awk 'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)} { print n "\t" (/AATTCCGGATCG|CGATCCGGAATT/ ? "ATCG" : "NOT Present" ) }'

real    0m0.074s
user    0m0.031s
sys     0m0.030s

sed -n 's/^[ATCG]*AATTCCGG\(.\)\(.\)\(.\)\(.\)[ATCG]*$/\1\2\3\4/p' file
sed -n 's/^[ATCG]*\(.\)\(.\)\(.\)\(.\)CCGGAATT[ATCG]*$/\4\3\2\1/p' file | tr ATGC TACG

real    0m0.482s
user    0m0.405s
sys     0m0.138s

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

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

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'

rec=substr(rec, RSTART+1)

rec=substr(rec, RSTART+RLENGTH+len+1)

rec=substr(rec, RSTART+RLENGTH+len)

  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
  }