----- Original Message -----
From: "Li, Aiguo (NIH/NCI)" <[EMAIL PROTECTED]>
Date: Monday, January 24, 2005 5:14 pm
Subject: How to go back to a line and do something with it in an input fil
e?
> hello, all.
Hello
Seems like there is a problem with your data, or problem is miss-read. See
comments in data.
>
> I need to transform the column3 data from an input file as
> indicated below
> into three values: 0, 0.4, 1.
> if there are more than 3 NoCall continuously in column3, change
> NoCall into
> "1". this option has the highest precedence.
> for the rows where column2 is between 52 and 105 (range from a file),
> transform the values in column3 into "0.4".
> for the rows outside of this region, change the values in column3
> into "0"
>
> print into an output file.
>
> I am struggling with how to go back to the line to change the
> column 3 after
> 3 consecutive NoCall has been counted???
>
> I currently read the input data into an array and used this line
> to go back
> to the beginning of first NoCall line: my $nocalline =
> $contents[$line_num -
> 3];
> Perl does not like it and an error message says: ""my" variable
> $nocallinemasks earlier declaration in same scope a
> line 38. Use of implicit split to @_ is deprecated at
> trynocall.pl line 38.
> syntax error at trynocall.pl line 38, near ");"
>
> Can anyone give some hints?
>
> Thanks
>
> Aiguo
>
>
> input data is: output data should be:
> ====================== ========================
> 1 22 AA 1 22 0
> 1 24 AA 1 24 0
> 1 26 NoCall 1 26 0
> 1 27 BB 1 27 0
> 1 30 AB 1 30 0
> 1 35 NoCall 1 35 1
> 1 40 NoCall 1 40 1
^ ony 2 ahead have a "NoCall" ahead; Shouldnt this change to "1 40 0" ?
> 1 41 NoCall 1 41 1
same problem in this raw and next one
> 1 42 NoCall 1 42 1
> 1 48 AB 1 48 0
> 1 50 AB 1 50 0
> 1 52 BB 1 52 0.4
> 1 53 NoCall 1 53 0.4
> 1 55 NoCall 1 55 0.4
> 1 56 BB 1 56 0.4
> 1 66 AA 1 66 0.4
> 1 70 NoCall 1 70 1
> 1 90 NoCall 1 90 1
> 1 99 NoCall 1 99 1
> 1 100 NoCall 1 100 1
> 1 101 NoCall 1 101 1
> 1 103 AA 1 103 0.4
> 1 105 BB 1 105 0.4
> 2 22 AA 2 22 0
> 2 24 BB 2 24 0
> 2 26 AB 2 26 0
> 2 27 BB 2 27 0
> 2 30 AA 2 30 0
> 2 35 AA 2 35 0
> 2 40 AA 2 40 0
>
>
> the code I have
> =================
> #!usr/local/bin/perl
>
> use strict;
> use warnings;
>
> open (DATA, "C:/Aiguo_2004/SNP_Johnpark/work
> files/summary/testnocall1.txt")or die "Can not open file \n";
> open (LOH, "C:/Aiguo_2004/SNP_Johnpark/work
> files/summary/loh.txt") or die
> "Can not open file \n";
> open (OUT1, ">C:/perl/work/nocallout.txt") or "die can not open
> file \n";
>
> my @contents = <DATA>;
> my $chro_num;
> my $lohbegin;
> my $lohend;
> my $line_num = 0;
>
>
> while(my $lohline = <LOH>) #this file contain regions for changing
> to 0.4
> {
> ($chro_num, $lohbegin, $lohend) = split(/\t/, $lohline);
> foreach my $line (@contents)
> {
> while($line =~ /^[1..9]/)
> {
> $line_num++;
> #print $line_num;
> (my $chro, my $position, my $call) = split (/\t/, $line);
>
> if(($chro_num == $chro)&&($position >= $lohbegin) &&
> ($position <= $lohend))
> {
> call = 0.4;
> unless($call =~ "NoCall")
> {
> my $n++;
> my $m++;
>
> if($n >= 3)
> {
> my $nocalline = $contents[$line_num - 3];
> my ($nocall_chro, $nocall_begin, $nocall =
> split(/\t/, $nocalline);
> print "Nocall chro = $nocall_chro, Nocall
> begin = $nocall_begin \n";
> $nocall = "Nocall";
> }
> #else{$call = 0.4;}
> print $call;
> $contents[$line_num] = join('\t', $chro, $position,
> $call);
> }
> }
> #print "Chro:$chro, Position:$position, call=$call\n";
> }
> #print @contents;
> }
> }
>
> close DATA;
> close OUT1;
> close LOH;
>
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>
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