我是一個完整的業餘perl,我想問一個問題來幫助我找到和替換函數,我試圖應用於更改SAM文件上的參考名稱,以便我可以通過FindPeaks運行它。這些文件對於我來說能夠在文本編輯器中打開它們並且無需使用編程語言來運行匹配,這些文件是很大的(從5到17個演出)。如何讓Perl用幾個|來識別一個字符串在它作爲一個單一的字符串?
基本上,我希望Perl匹配整個字符串,如「gi | 149288852 | ref | NC_000067.5 | NC_000067」,並用「chr1」替換整個事物。
然而,到目前爲止,我只能似乎使它要麼代之以 「CHR 1 | CHR1 | CHR1 | CHR1 | CHR 1」 或 「GI | CHR1 |裁判| NC000067.g | NC_000067」
能人幫幫我?
編輯:
我已經嘗試了一些不同的東西,但我想要做的是修改程序我的上司從別人得到正確做到這一點,我會發布它下面:
#!/usr/bin/perl
use strict;
use warnings;
my %Chr = (
"gi|149288852|ref|NC_000067.5|NC_000067" => "chr1",
"gi|149288869|ref|NC_000076.5|NC_000076" => "chr10",
"gi|149288871|ref|NC_000077.5|NC_000077" => "chr11",
"gi|149292731|ref|NC_000078.5|NC_000078" => "chr12",
"gi|149292733|ref|NC_000079.5|NC_000079" => "chr13",
"gi|149292735|ref|NC_000080.5|NC_000080" => "chr14",
"gi|149301884|ref|NC_000081.5|NC_000081" => "chr15",
"gi|149304713|ref|NC_000082.5|NC_000082" => "chr16",
"gi|149313536|ref|NC_000083.5|NC_000083" => "chr17",
"gi|149321426|ref|NC_000084.5|NC_000084" => "chr18",
"gi|149323268|ref|NC_000085.5|NC_000085" => "chr19",
"gi|149338249|ref|NC_000068.6|NC_000068" => "chr2",
"gi|149352351|ref|NC_000069.5|NC_000069" => "chr3",
"gi|149354223|ref|NC_000070.5|NC_000070" => "chr4",
"gi|149354224|ref|NC_000071.5|NC_000071" => "chr5",
"gi|149361431|ref|NC_000072.5|NC_000072" => "chr6",
"gi|149361432|ref|NC_000073.5|NC_000073" => "chr7",
"gi|149361523|ref|NC_000074.5|NC_000074" => "chr8",
"gi|149361524|ref|NC_000075.5|NC_000075" => "chr9",
"gi|149361525|ref|NC_000086.6|NC_000086" => "chrX",
"gi|149361526|ref|NC_000087.6|NC_000087" => "chrY",
);
my $usage = "\n\n\tUsage: convert.pl <SAM file>\n\nThis script converts NCBI ref#s to chr #s\n\n";
die $usage unless (@ARGV == 1);
my $file = $ARGV[0];
open (IN, "$file") or die "Can't open file: $file\n";
while (<IN>){
if (/\S+\s+\d+\s+(gi\S+)/){
my $tag = $1;
if (exists $Chr{$tag}){
my $line = $_;
$line =~ s/'$tag'/$Chr{$tag}/;
print $line;
}
else {
die "\n\n\nHash value doesn't exist for $tag $_\n\n";
}
}
else {
print $_;
}
}
它與出來: 「GI | CHR1 |裁判| NC000067.g | NC_000067」
我也試過這樣:
perl -pi -w -e 's/gi|149288852|ref|NC_000067.5|NC_000067/chr1/g;' *.sam
,看看我能做到這一點一個接一個,但出來的 「CHR 1 | CH1 | CHR1 | CHR1 | CHR1」
聽起來像一個貪婪/非貪婪匹配問題? – John 2012-08-02 19:45:10
你可以包含你正在使用的正則表達式嗎? – Dancrumb 2012-08-02 19:45:38
胖逗號自動引用左值,所以你不需要''gi | 149361526 | ref | NC_000087.6 | NC_000087「=>」chrY「',你應該只有'gi | 149361526 | ref | NC_000087.6 | NC_000087 =>「chrY」' – 2012-08-02 19:56:40