☰

2つのDNA配列の比較

tag-icon • tag-icon text-processing bioinformatics
2つのDNA配列の比較

ATGCATGC2つのDNA配列がありますTACGTTGC

A比較がソートされたら「+」を提供し、TそれG以外の場合はC「-」を印刷するプログラムを作成したいと思います。

良い

ATGCATGC
TACGTTGC
+++++---

誰でも私を助けることができますか？

上記は予想される結果を提供します。

私が試したことは次のとおりです。

#!/bin/bash


declare -a seq1=()
declare -a seq2=()


read -p 'Enter the ncleotide seq (charactor by charactor followe\d by space0) ' -a seq1

read -n1 seq1

read -p 'Enter the ncleotide seq (charactor by charactor followe\d by space0) ' -a seq2

read -n1 seq2

for a in ${seq1[*]} ; do
for b in ${seq2[*]} ; do
if [ $a == A ] || [ $b == T ] ; then
echo -n "+"
elif [ $a == A ] || [ $b == C ] ; then
echo -n " -"
elif [ $a == A ] || [ $b == G ] ; then
echo -n "-"
elif [ $a == T ] || [ $b == A ] ; then
echo -n "+"
elif [ $a == T ] || [ $b == C ] ; then
echo -n "-"
elif [ $a == T ] || [ $b == G ] ; then
echo -n "-"
elif [ $a == C ] || [ $b == G ] ; then
echo -n "+"
elif [ $a == C ] || [ $b == A ] ; then
echo -n "-"
elif [ $a == C ] || [ $b == T ] ; then
echo -n "-"
elif [ $a == G ] || [ $b == C ] ; then
echo -n "+"
elif [ $a == G ] || [ $b == A ] ; then
echo -n "-"
elif [ $a == G ] || [ $b == T ] ; then
echo -n "-"
else  
echo $a $b
fi
done
done

ベストアンサー1

使用awk:

awk -v seq1='CATGCATGCTCAT' -v seq2='ATACGTTGCGTTA' '
function sign(s) { cmp=(cmp==""?"":cmp) s }
BEGIN{
    split(seq1, tmp1, ""); split(seq2, tmp2, "");
    for(i in tmp1) {
        if( tmp1[i] == tmp2[i] ){ sign("-"); continue }
        if( (tmp1[i] ~/[AT]/ && tmp2[i] ~/[AT]/) || 
            (tmp1[i] ~/[GC]/ && tmp2[i] ~/[GC]/) ) { sign("+"); continue }
        sign("-")
    }
    print seq1 ORS seq2 ORS cmp
}'

出力：

CATGCATGCTCAT
ATACGTTGCGTTA
-+++++-----++

コメントを含む同じコード：

awk -v seq1='CATGCATGCTCAT' -v seq2='ATACGTTGCGTTA' '
# set sequences one in seq1 another in seq2

function sign(s) { cmp=(cmp==""?"":cmp) s }
# function to join the the changes on +/- for each pair of chars

BEGIN{
    split(seq1, tmp1, ""); split(seq2, tmp2, "");
    # split each sequences characters into individual arrays

    for(i in tmp1) {
    # loop over keys on one of the arrays (assuming length of both seq will be same)

        if( tmp1[i] == tmp2[i] ){ sign("-"); continue }
        # if both chars were same AA, TT, CC, GG, ..., sign should be "-"

        if( (tmp1[i] ~/[AT]/ && tmp2[i] ~/[AT]/) || 
            (tmp1[i] ~/[GC]/ && tmp2[i] ~/[GC]/) ) { sign("+"); continue }
        # if one was "A" and another was "T" or vice-versa as well as
        # if one was "G" and another was "C" or vice-versa, sign should be "+"

        sign("-")
        # otherwise "-"

    }
    print seq1 ORS seq2 ORS cmp
    # print the last result, first printing the sequences then 
    # the comparison result in 'cmp'
}'

おすすめ記事