in reply to Hash_of_Hash_Would do it?

I thought I would provide another approach that doesn't use a hash. It processes line by line.

Chris 

#!/usr/bin/perl
use strict;
use warnings;

chomp(my @previous = split /\t/, <DATA>);

my $from = 1;
my $to = $previous[2]-9 > 0 ? $previous[2]-9 : 0;

# print '0 values' up to 8 less of margin
for my $pos ($from..$to) {
    print join("\t", $previous[1], $pos, '','','0'), "\n";
}

$from = $previous[2]-8 > 0 ? $previous[2]-8 : 1;
$to = $previous[2]-1;

# print margin of '1 values' up to first record
for my $pos ($from .. $to) {
    print join("\t", $previous[1], $pos, '','','1'), "\n";
}

# print first record
print join("\t", @previous[1..4], '1'), "\n";
my $pos_count = $previous[2];

while (<DATA>) {
    chomp;
    my @current= split /\t/;
    
    if ($current[1] eq $previous[1]) {
        if (++$pos_count != $current[2]) {
            for my $pos ($pos_count .. $current[2]-1) {
                print join("\t", $current[1], $pos, '','', '1'), "\n";
            }
        }
        print join("\t", @current[1..4], 1), "\n";
    }
    else {
        # print '1 values' for margin of 8 past last pos for previous 
+record
        for my $pos ($previous[2] + 1 .. $previous[2] + 8) {
            print join("\t", $previous[1], $pos, '','','1'), "\n";
        }
        
        $from = 1;
        $to = $current[2]-9 > 0 ? $current[2]-9 : 0;
        
        # print '0 values' up to 8 less of margin for current record
        for my $pos ($from .. $to) {
            print join("\t", $current[1], $pos, '','','0'), "\n";
        }
        
        $from = $current[2]-8 > 0 ? $current[2]-8 : 1;
        $to = $current[2]-1;
        
        # print '1 values' up to current record
        for my $pos ($from .. $to) {
            print join("\t", $current[1], $pos, '','','1'), "\n";
        }
        
        print join("\t", @current[1..4], 1), "\n";
    }
    
    $pos_count = $current[2];
    @previous = @current;
}

# after last record printed, print out margin of 8 more
for my $pos ($previous[2] + 1 .. $previous[2] + 8) {
    print join("\t", $previous[1], $pos, '','','1'), "\n";
}


__DATA__
CLS_S3_Contig100_st    CLS_S3_Contig100    53    10    0.3717
CLS_S3_Contig100_at    CLS_S3_Contig100    55    11    0.4321
CLS_S3_Contig100_st    CLS_S3_Contig100    57    10    0.3223
CLS_S3_Contig100_at    CLS_S3_Contig100    59    11    0.4055
CLS_S3_Contig100_st    CLS_S3_Contig100    61    11    0.4511
CLS_S3_Contig100_at    CLS_S3_Contig100    63    11    0.474
CLS_S3_Contig10031_st    CLS_S3_Contig10031    53    12    0.5548
CLS_S3_Contig10031_st    CLS_S3_Contig10031    57    10    0.4871
CLS_S3_Contig10031_st    CLS_S3_Contig10031    61    12    0.547
CLSS3627.b1_F19.ab1    CLS_S3_Contig10031    62    11    0.5129
CLSS3627.b1_F19.ab1    CLS_S3_Contig10031    64    11    0.5789

[download]
It printed out this solution. 

CLS_S3_Contig100    1            0
CLS_S3_Contig100    2            0
CLS_S3_Contig100    3            0
CLS_S3_Contig100    4            0
CLS_S3_Contig100    5            0
CLS_S3_Contig100    6            0
CLS_S3_Contig100    7            0
CLS_S3_Contig100    8            0
CLS_S3_Contig100    9            0
CLS_S3_Contig100    10            0
CLS_S3_Contig100    11            0
CLS_S3_Contig100    12            0
CLS_S3_Contig100    13            0
CLS_S3_Contig100    14            0
CLS_S3_Contig100    15            0
CLS_S3_Contig100    16            0
CLS_S3_Contig100    17            0
CLS_S3_Contig100    18            0
CLS_S3_Contig100    19            0
CLS_S3_Contig100    20            0
CLS_S3_Contig100    21            0
CLS_S3_Contig100    22            0
CLS_S3_Contig100    23            0
CLS_S3_Contig100    24            0
CLS_S3_Contig100    25            0
CLS_S3_Contig100    26            0
CLS_S3_Contig100    27            0
CLS_S3_Contig100    28            0
CLS_S3_Contig100    29            0
CLS_S3_Contig100    30            0
CLS_S3_Contig100    31            0
CLS_S3_Contig100    32            0
CLS_S3_Contig100    33            0
CLS_S3_Contig100    34            0
CLS_S3_Contig100    35            0
CLS_S3_Contig100    36            0
CLS_S3_Contig100    37            0
CLS_S3_Contig100    38            0
CLS_S3_Contig100    39            0
CLS_S3_Contig100    40            0
CLS_S3_Contig100    41            0
CLS_S3_Contig100    42            0
CLS_S3_Contig100    43            0
CLS_S3_Contig100    44            0
CLS_S3_Contig100    45            1
CLS_S3_Contig100    46            1
CLS_S3_Contig100    47            1
CLS_S3_Contig100    48            1
CLS_S3_Contig100    49            1
CLS_S3_Contig100    50            1
CLS_S3_Contig100    51            1
CLS_S3_Contig100    52            1
CLS_S3_Contig100    53    10    0.3717    1
CLS_S3_Contig100    54            1
CLS_S3_Contig100    55    11    0.4321    1
CLS_S3_Contig100    56            1
CLS_S3_Contig100    57    10    0.3223    1
CLS_S3_Contig100    58            1
CLS_S3_Contig100    59    11    0.4055    1
CLS_S3_Contig100    60            1
CLS_S3_Contig100    61    11    0.4511    1
CLS_S3_Contig100    62            1
CLS_S3_Contig100    63    11    0.474    1
CLS_S3_Contig100    64            1
CLS_S3_Contig100    65            1
CLS_S3_Contig100    66            1
CLS_S3_Contig100    67            1
CLS_S3_Contig100    68            1
CLS_S3_Contig100    69            1
CLS_S3_Contig100    70            1
CLS_S3_Contig100    71            1
CLS_S3_Contig10031    1            0
CLS_S3_Contig10031    2            0
CLS_S3_Contig10031    3            0
CLS_S3_Contig10031    4            0
CLS_S3_Contig10031    5            0
CLS_S3_Contig10031    6            0
CLS_S3_Contig10031    7            0
CLS_S3_Contig10031    8            0
CLS_S3_Contig10031    9            0
CLS_S3_Contig10031    10            0
CLS_S3_Contig10031    11            0
CLS_S3_Contig10031    12            0
CLS_S3_Contig10031    13            0
CLS_S3_Contig10031    14            0
CLS_S3_Contig10031    15            0
CLS_S3_Contig10031    16            0
CLS_S3_Contig10031    17            0
CLS_S3_Contig10031    18            0
CLS_S3_Contig10031    19            0
CLS_S3_Contig10031    20            0
CLS_S3_Contig10031    21            0
CLS_S3_Contig10031    22            0
CLS_S3_Contig10031    23            0
CLS_S3_Contig10031    24            0
CLS_S3_Contig10031    25            0
CLS_S3_Contig10031    26            0
CLS_S3_Contig10031    27            0
CLS_S3_Contig10031    28            0
CLS_S3_Contig10031    29            0
CLS_S3_Contig10031    30            0
CLS_S3_Contig10031    31            0
CLS_S3_Contig10031    32            0
CLS_S3_Contig10031    33            0
CLS_S3_Contig10031    34            0
CLS_S3_Contig10031    35            0
CLS_S3_Contig10031    36            0
CLS_S3_Contig10031    37            0
CLS_S3_Contig10031    38            0
CLS_S3_Contig10031    39            0
CLS_S3_Contig10031    40            0
CLS_S3_Contig10031    41            0
CLS_S3_Contig10031    42            0
CLS_S3_Contig10031    43            0
CLS_S3_Contig10031    44            0
CLS_S3_Contig10031    45            1
CLS_S3_Contig10031    46            1
CLS_S3_Contig10031    47            1
CLS_S3_Contig10031    48            1
CLS_S3_Contig10031    49            1
CLS_S3_Contig10031    50            1
CLS_S3_Contig10031    51            1
CLS_S3_Contig10031    52            1
CLS_S3_Contig10031    53    12    0.5548    1
CLS_S3_Contig10031    54            1
CLS_S3_Contig10031    55            1
CLS_S3_Contig10031    56            1
CLS_S3_Contig10031    57    10    0.4871    1
CLS_S3_Contig10031    58            1
CLS_S3_Contig10031    59            1
CLS_S3_Contig10031    60            1
CLS_S3_Contig10031    61    12    0.547    1
CLS_S3_Contig10031    62    11    0.5129    1
CLS_S3_Contig10031    63            1
CLS_S3_Contig10031    64    11    0.5789    1
CLS_S3_Contig10031    65            1
CLS_S3_Contig10031    66            1
CLS_S3_Contig10031    67            1
CLS_S3_Contig10031    68            1
CLS_S3_Contig10031    69            1
CLS_S3_Contig10031    70            1
CLS_S3_Contig10031    71            1
CLS_S3_Contig10031    72            1

[download]

Replies are listed 'Best First'.
Re^2: Hash_of_Hash_Would do it?
by sesemin (Beadle) on Sep 16, 2008 at 01:03 UTC
    Hi Chris,

    Thanks for your time and solution. I ran your code and it works great as long as the gap in PIP is not large. In another word if PIP jumps from 240 to 280, it fills all the new col with "1" whereas we want it fill up to 248 from one margin and 272 from the other margin. 

    
for my $pos ($previous[2] + 1 .. $previous[2] + 8) {
            print join("\t", $previous[1], $pos, '','','1'), "\n";
        }

    [download]
    is this the place to control the loop. Not pass more than 8?

    Thank you again.

    Pedro

[reply]
[d/l]
Re^2: Hash_of_Hash_Would do it?
by Cristoforo (Curate) on Sep 16, 2008 at 23:18 UTC
    You would replace
    if (++$pos_count != $current[2]) {
            for my $pos ($pos_count .. $current[2]-1) {
                print join("\t", $current[1], $pos, '','', '1'), "\n";
            }
        }

    [download]

    with

            if (++$pos_count != $current[2]) {
            fill_interval($pos_count, @current);
        }

    [download]

    where fill_interval() is defined as

    sub fill_interval {
    my ($pos_count, @current) = @_;
    my $margin = 8;
    if ($current[2] - $pos_count <= 2*$margin) {
        for my $pos ($pos_count .. $current[2]-1) {
            print join("\t", $current[1], $pos, '','', '1'), "\n";
        }
    }
    else {
        my @bool;
        my ($start, $end) = ($pos_count, $current[2]-1);
        for my $i (0..$margin-1) {
            @bool[ $start + $i, $end - $i ] = (1,1);
        }
        
        for my $pos ($pos_count .. $current[2]-1) {
            print join("\t", $current[1], $pos, '','', $bool[$pos] || 
+0), "\n";
        }        
    }
}

    [download]

    Update: Changed literal values to $margin.

[reply]
[d/l]
[select]
      Thank you very much Chris, It is perfect now. A+++
[reply]

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