Wang, Li wrote:
Dear All
Hello,
Thanks very much for your help!
I tried the script with my real data and found out that the situation gets more
complicate.
The following is part of my data:
scaffold_1_13528 T/T C/T T/T C/T T/T C/T T/T
T/T N/N T/T C/T T/T C/C C/T C/T T/T T/T
T/T T/T T/T T/T C/T C/T C/T C/T T/T T/T
T/T N/N T/T (keep)
scaffold_1_13531 G/G G/G G/G G/G G/G G/C G/G
G/G N/N G/G G/C G/G G/G G/G G/G G/G G/G
G/G G/G G/G G/G G/G G/G G/G G/G G/G G/G
G/G N/N G/G (keep)
scaffold_1_13546 A/A A/A A/A A/A A/A C/A A/A
A/A N/N A/A C/A N/N A/A A/A N/N N/N A/A
N/N A/A N/N A/A A/A A/A C/A C/A A/A A/A
N/N N/N A/A (keep)
scaffold_1_22222 N/N C/C N/N C/C N/N N/N C/C
C/C N/N N/N C/C C/C N/N C/C C/C C/C N/N
N/N C/C N/N C/C N/N C/C N/N C/C C/C C/C
N/N N/N C/C (delete)
scaffold_1_113139 C/C C/C N/N C/C N/N C/C C/C
C/G N/N C/C N/N C/C N/N C/C C/C N/N N/N
C/C N/N C/G C/G N/N C/C C/C N/N C/C C/C
N/N C/C C/C (keep)
scaffold_1_113140 G/G G/G N/N G/G N/N G/G G/G
G/G N/N G/G G/G G/G N/N G/G G/G N/N N/N
G/G N/N G/G G/G N/N G/G G/G N/N G/G G/A
N/N G/A G/G (keep)
scaffold_1_113207 A/A A/A N/N A/A N/N A/A A/A
A/A N/N A/A A/A A/A N/N A/A A/A N/N N/N
A/A N/N A/A A/A N/N A/A A/A N/N A/A A/A
N/N A/A A/A (delete)
scaffold_1_114021 C/C C/C N/N C/C N/N C/C C/C
C/T C/C C/C C/C N/N N/N C/C C/C C/T N/N
C/C N/N C/T C/C N/N C/C C/C C/C C/C C/C
N/N C/C C/C (keep)
scaffold_1_114213 A/C C/C A/A C/C N/N A/C A/A
A/A A/A A/C A/C A/C N/N A/A A/A A/A N/N
A/A A/A A/A A/A N/N A/A C/C A/A A/A A/A
N/N A/A A/A (keep)
If in each line, without count of "N/N", all the other SNPs are the same, delete this
line. The "scaffold" indicates the position of the SNP.
My code is as follows:
#! /usr/bin/perl
use strict;
use warnings;
my $usage="perl $0<infile>\n";
my $in=shift or die $usage;
open (IN,$in) or die "Error: not found the $in\n";
my $outfile = "SNPFilterSeg.txt";
open (OUT, ">$outfile");
my $i;
while (<IN>){
next if /^#/;
$_=~s/\n//;
$_=~s/\r//;
my @tmp=split("\t",$_);
my @arr;
for ($i=1; $i<=30; $i++){
next if $tmp[$i] =~ m/N\/N/; #filter out all "N/N"
@arr = split("\t",$tmp[$i]); #assign the filtered data to a new array
@arr
}
if (@arr == grep $arr[0] eq $_, @arr) {
print OUT "here\n";
}
else{
print OUT "@tmp\n";
}
}
close IN;
close OUT;
#!/usr/bin/perl
use strict;
use warnings;
my $usage = "perl $0 <infile>\n";
my $in = shift or die $usage;
open IN, '<', $in or die "Cannot open '$in' because: $!";
my $outfile = "SNPFilterSeg.txt";
open OUT, '>', $outfile or die "Cannot open '$outfile' because: $!";
while ( <IN> ) {
next if /^#/;
my ( undef, @tmp ) = grep $_ ne 'N/N', split;
print OUT $_ if @tmp != grep $tmp[ 0 ] eq $_, @tmp;
}
close IN;
close OUT;
John
--
Any intelligent fool can make things bigger and
more complex... It takes a touch of genius -
and a lot of courage to move in the opposite
direction. -- Albert Einstein
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