Re^3: Looking for series in consecutive lines of a file

Hello mbp,

Since the input lines are known to be sorted, it is feasible to reduce memory requirements by reading the input file line-by-line. Here is one approach:

#! perl
use strict;
use warnings;
use constant MIN_DEPTH => 5;

my  ($chromosome, $position, undef, $coverage_depth) = split /\s+/, <D
+ATA>;
my   %series =
(
    name  => $chromosome,
    start => $position,
    end   => $position,
    depth => $coverage_depth,
);

while (<DATA>)
{
    ($chromosome, $position, undef, $coverage_depth) = split /\s+/;

    if ($series{name}   eq $chromosome   &&
        $series{end}    == $position - 1 &&
        $series{depth}  >= MIN_DEPTH     &&
        $coverage_depth >= MIN_DEPTH)
    {
        $series{end}     = $position;
    }
    else
    {
        display_series();

        %series =
        (
            name  => $chromosome,
            start => $position,
            end   => $position,
            depth => $coverage_depth,
        );
    }
}

display_series();

sub display_series
{
    if ($series{depth} >= MIN_DEPTH)
    {
        print join(',', $series{name}, $series{start}, $series{end},
                        $series{end} - $series{start} + 1), "\n";
    }
}

__DATA__
C10000035    12    C    4    ....^>.    HHFCC
C10000035    13    C    6    .....^>.    HHFFCC
C10000035    14    C    6    ......    JHFFCC
C10000035    15    C    6    ......    IHFFFC
C10000035    16    A    4    .GG...^>G    JGHFFFC
C10000035    17    C    7    .......    JGHFFFC
C10000035    18    C    8    .......^].    JIHHFFC@
C10000035    19    A    8    ........    IJHHFFFC
C10000035    20    C    9    ..T...T.^].    JIHGHFF@C
C10000035    21    G    10    A........^].    AJJHHHFDCC
C10000040    30    C    5    ....^>.    HHFCC
C10000040    31    C    6    .....^>.    HHFFCC
C10000040    32    C    6    ......    JHFFCC
C10000040    33    C    6    ......    IHFFFC
C10000040    34    C    4    ......    IHFFFC
C10000040    35    C    4    ......    IHFFFC
C10000040    36    C    4    ......    IHFFFC
C10000040    37    C    6    ......    IHFFFC
C10000040    38    C    6    ......    IHFFFC
[download]

Output:

16:48 >perl 1157_SoPW.pl
C10000035,13,15,3
C10000035,17,21,5
C10000040,30,33,4
C10000040,37,38,2

16:50 >
[download]

Hope that helps,

Athanasius <°(((>< contra mundum Iustus alius egestas vitae, eros Piratica,

Comment on Re^3: Looking for series in consecutive lines of a file Select or Download Code

Replies are listed 'Best First'.
Re^4: Looking for series in consecutive lines of a file by Anonymous Monk on Feb 17, 2015 at 08:04 UTC
I see you're trying not to overwhelm the new guy, but introducing "use constant" and not introducing subroutine arguments, references? Eeew :) `... display_series( \%series ); ... display_series( \%series ); ... sub display_series { my( $series ) = @_; if ($series->{depth} >= MIN_DEPTH) { print join(',', $series->{name}, $series->{start}, $series->{e +nd}, $series->{end} - $series->{start} + 1), "\n"; } }` [download]	[reply] [d/l]
Re^5: Looking for series in consecutive lines of a file by mbp (Novice) on Feb 17, 2015 at 23:16 UTC
Anonymous Monk, haha, yes I do have a ways to go, but thanks for your addition!	[reply]
Re^4: Looking for series in consecutive lines of a file by mbp (Novice) on Feb 17, 2015 at 23:12 UTC
Hi Anathasius, Brilliant, that works a treat! Thank you very much for your time and help, I really appreciate it. Best, mbp	[reply]