Hi, Jim
Thanks very much!
It works now!
All the best
Li
________________________________________
From: Jim Gibson [jimsgib...@gmail.com]
Sent: Sunday, August 26, 2012 12:13 PM
To: Perl Beginners
Subject: Re: a condition
On Aug 26, 2012, at 10:03 AM, Wang, Li wrote:
> Dear All
>
> 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"
next if $tmp[$i] eq 'N/N';
is probably an easier test here.
> @arr = split("\t",$tmp[$i]); #assign the filtered data to a new array
> @arr
At this point, since you split the original line on "\t", there aren't going to
be any tab characters in the elements of @tmp. You are going to have a
one-element @arr array here. I think you want the following instead of the
above line:
push(@arr,$tmp[$i]);
This will accumulate all of the tokens in the line, other than the first, that
are not equal to 'N/N';
> }
> if (@arr == grep $arr[0] eq $_, @arr) {
Your one-element array will always pass this test.
> print OUT "here\n";
> }
> else{
> print OUT "@tmp\n";
> }
> }
>
> close IN;
> close OUT;
>
> It returns me all "here".
> I struggled but failed at figuring out what is the problem. Could you please
> point out the problem?
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