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我在这里得到了很好的输入，即对一串核苷酸进行搜索以搜索 3 个核苷酸的重复模式，并要求通过为其构建正则表达式来连续发生 7 次重复。

my $regex1 = qr/( ([ACGT]{3}) \2{6,} )/x;

我了解如何扩展它以在 10 行中搜索 2 个 nucs 以及在 7 行中搜索 4 个。

但我想扩展代码，以便用户可以指向他们的输入文件，并检查上述正则表达式以及我需要为其他两个搜索创建的另外两个正则表达式。

编辑：我如何让我的输入文件像上面那样使用多个正则表达式？我在代码中创建了另外两个正则表达式（被哈希符号淘汰）

这是我当前的代码

print "Please specify the file location (DO NOT DRAG/DROP files!) then press ENTER:\n";
$seq = <STDIN>;

#Remove the newline from the filename
chomp $seq;

#open the file or exit
open (SEQFILE, $seq) or die "Can't open '$seq': $!";

#read the dna sequence from the file and store it into the array variable @seq1
@seq1 = <SEQFILE>;

#Close the file
close SEQFILE;

#Put the sequence into a single string as it is easier to search for the motif
$seq1 = join( '', @seq1);

#Remove whitespace
$seq1 =~s/\s//g;

#Count of number of nucleotides
#Initialize the variable
$number = 0;
$number = length $seq1;

#Use regex to say "Find 3 nucelotides and match at least 6 times
# qr(quotes and compiles)/( ([nucs]{number of nucs in pattern}) \2{number of repeats,}/x(permit within pattern)
my $regex1 = qr/( ([ACGT]{3}) \2{6,} )/x;
#my $regex = qr/( ([ACGT]){2}) \2{9,} )/x;
#my $regex2 = qr/( ([ACGT]{4}) \2{6,} )/x;

#Tell program to use $regex on variable that holds the file
$seq1 =~ $regex1;

#Now print the results to screen
#This will need to change to printing to a file (WHAT KIND OF FILE?)in the following manner :site, nucelotide match, # of times, length of full sequence
printf "MATCHED %s exactly %d times\n", $2, length($1)/3;
print "Length of sequence: $number\n";
exit;
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1 回答 1

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只需使用一个for循环。就像是

for my $regex ($regex1, $regex2, $regex3) {
  next unless $seq1 =~ $regex;
  printf "MATCHED %s exactly %d times\n", $2, length($1)/length($2);
}

But you will probably want to change the output to describe the results better.

于 2013-02-23T03:39:05.653 回答