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本帖最后由 climby 于 2010-05-11 14:11 编辑
我帮你翻译了一下,初看看不出来该脚本是做什么的,但我运行了我翻译的perl脚本,看结果我知道了。
这个脚本是求出2个字串中匹配程度最高的子串。
翻译其实没有什么技术含量,多半就是变量名前加$.(估计这也是很多人不屑动手的原因{:3_189:})
perl代码:
- #!/usr/bin/perl
- sub pairaln {
- my ( $seq1, $seq2 ) = @_;
- my $MATCH = 1; # +1 for letters that match
- my $MISMATCH = -1; #-1 for letters that mismatch
- my $GAP = -1; # -1 for any gap
- # initialization
- my $score = [];
- my $pointer = [];
- $score->[0] = [] unless ( defined $score->[0] );
- $score->[0]->[0] = 0;
- $pointer->[0] = [] unless ( defined $pointer->[0] );
- $pointer->[0]->[0] = 0;
- my $l1 = length $seq1;
- my $l2 = length $seq2;
- for ( my $j = 1; $j <= $l1; $j++ ) {
- $score[0][$j] = $GAP * $j;
- $pointer[0][$j] = 2;
- }
- for ( my $i = 1; $i <= $l2; $i++ ) {
- $score->[$i] = [] unless ( defined $score->[$i] );
- $pointer->[$i] = [] unless ( defined $pointer->[$i] );
- $score->[$i]->[0] = $GAP * $i;
- $pointer->[$i]->[0] = 3;
- }
- # fill
- for ( my $i = 1; $i <= $l2; $i++ ) {
- my $letter2 = substr( $seq2, $i - 1, 1 );
- for ( my $j = 1; $j <= $l1; $j++ ) {
- my ( $diagonal_score, $left_score, $up_score );
- # calculate match score
- my $letter1 = substr( $seq1, $j - 1, 1 );
- if ( $letter1 eq $letter2 ) {
- $diagonal_score = $score->[ $i - 1 ]->[ $j - 1 ] + $MATCH;
- }
- else {
- $diagonal_score = $score->[ $i - 1 ]->[ $j - 1 ] + $MISMATCH;
- }
- # calculate gap scores
- $up_score = $score->[ $i - 1 ]->[$j] + $GAP;
- $left_score = $score->[$i]->[ $j - 1 ] + $GAP;
- # choose best score
- if ( $diagonal_score >= $up_score ) {
- if ( $diagonal_score >= $left_score ) {
- $score->[$i]->[$j] = $diagonal_score;
- $pointer->[$i]->[$j] = 1;
- }
- else {
- $score->[$i]->[$j] = $left_score;
- $pointer->[$i]->[$j] = 2;
- }
- }
- else {
- if ( $up_score >= $left_score ) {
- $score->[$i]->[$j] = $up_score;
- $pointer->[$i]->[$j] = 3;
- }
- else {
- $score->[$i]->[$j] = $left_score;
- $pointer->[$i]->[$j] = 2;
- }
- }
- }
- }
- # trace-back
- my $align1 = [];
- my $align2 = [];
- # start at last cell of matrix
- my $j = $l1;
- my $i = $l2;
- while (1) {
- last if ( $pointer->[$i]->[$j] == 0 ); # ends at first cell of matrix
- my $len_align1 = scalar(@$align1);
- my $len_align2 = scalar(@$align2);
- if ( $pointer->[$i]->[$j] == 1 ) {
- $align1->[$len_align1] = substr( $seq1, $j - 1, 1 );
- $align2->[$len_align2] = substr( $seq2, $i - 1, 1 );
- $i--;
- $j--;
- }
- if ( $pointer->[$i]->[$j] == 2 ) {
- $align1->[$len_align1] = substr( $seq1, $j - 1, 1 );
- $align2->[$len_align2] = "-";
- $j--;
- }
- if ( $pointer->[$i]->[$j] == 3 ) {
- $align1->[$len_align1] = "-";
- $align2->[$len_align2] = substr( $seq2 . $i - 1, 1 );
- $i--;
- }
- }
- my @re_align1 = reverse @$align1;
- my @re_align2 = reverse @$align2;
- my $result = "";
- $result .= "序列:\n$seq1\n$seq2\n比对结果:\n@re_align1\n@re_align2";
- return $result;
- }
- my $output = &pairaln( 'CTGGGCTGACTGA', 'GACTAGCTAGACTGA' );
- print $output;
复制代码 运行结果:
- 序列:
- CTGGGCTGACTGA
- GACTAGCTAGACTGA
- 比对结果:
- - - T G G C T - A C T G A
- 1 1 T - G C T 1 A C T G A
复制代码 |
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