我有 2 个输入文件。的每一行都File1
应该与 的每一行进行比较File2
。
逻辑是:
如果
Column1
of 与 的(其下的所有值)File1
不匹配,则在输出文件中打印整行。同样,将 的每个值与的每个值进行比较。Column1
File2
File1
Column1
Column1
File2
如果两个文件中的 匹配,并且的
Column1
值大于或小于,其中的值是,则只能打印 的整行并像这样比较所有行。Column2
File1
N+10
N-10
N
Column2
File2
File1
File2
File1
:
Contig1 23
Contig1 42
Contig2 68
Contig3 89
Contig3 102
Contig7 79
File2
:
Contig1 40
Contig1 49
Contig3 90
Contig2 90
Contig20 200
Contig1 24
预期输出:
Contig2 68
Contig3 102
Contig7 79
任何解决方案,即使是没有awk
或 的解决方案都sed
可以。
我发现了类似的问题,但我不太确定我必须做什么:
这是代码:
`NR==FNR {
lines[NR,"col1"] = $1
lines[NR,"col2"] = $2
lines[NR,"line"] = $0
next
}
(lines[FNR,"col1"] != $1) {
print lines[FNR,"line"]
next
}
(lines[FNR,"col2"]+10 < $2 || lines[FNR,"col2"]-10 > $2) {
print lines[FNR,"line"]
}' file1 file2`
答案1
下面的脚本执行以下操作,我认为这就是您想要的:
- 如果 file2 中不存在 file1 中的重叠群,则打印该重叠群的所有行。
- 如果它存在于 file2 中,则对于 file1 中的每个值,仅当它不小于 file2 中该重叠群的任何值 -10 或大于 file2 的任何值 +10 时才打印它。
#!/usr/bin/env perl
my (%file1, %file2);
## read file1, the 1st argument
open(F1,"$ARGV[0]");
while(<F1>){
chomp;
## Split the line on whitespace into the @F array.
my @F=split(/\s+/);
## Save all lines in the %file1 hash.
## $F[0] is the contig name and $F[1] the value.
## The hash will store a list of all values
## associated with this contig.
push @{$file1{$F[0]}},$F[1];
}
close(F1);
## read file2, the second argument
open(F2,"$ARGV[1]");
while(<F2>){
## remove newlines
chomp;
## save the fields into array @F
my @F=split(/\s+/);
## Again, save all values associated with each
## contig into the %file2 hash.
push @{$file2{$F[0]}},$F[1];
}
close(F2);
## For each of the contigs in file1
foreach my $contig (keys(%file1)) {
## If this contig exists in file 2
if(defined $file2{$contig}){
## get the list of values for that contig
## in each of the two files
my @f2_vals=@{$file2{$contig}};
my @f1_vals=@{$file1{$contig}};
## For each of file1's values for this contig
val1:foreach my $val1 (@f1_vals) {
## For each of file2's value for this contig
foreach my $val2 (@f2_vals) {
## Skip to the next value from file1 unless
## this one falls within the desired range.
unless(($val1 < $val2-10) || ($val1 > $val2+10)){
next val1;
}
}
## We will only get here if none of the values
## fell within the desired range. If so, we should
## print the value from file1.
print "$contig $val1\n";
}
}
## If this contig is not in file2, print the
## lines from file1. This will print all lines
## from file1 whose contig was not in file2.
else {
print "$contig $_\n" for @{$file1{$contig}}
}
}
将其保存在文本文件中(例如foo.pl
),使其可执行(chmod a+x foo.pl
)并像这样运行它:
./foo.pl file1 file2
在您的示例中,它返回:
$ foo.pl file1 file2
Contig2 68
Contig3 102
Contig7 79