homemade blat: insert query from keyboard to find an oligo in an hashtable

Question

[nico_ce90]

I wrote a script that given a sequence extracts a 'n' dimension hashtable of oligos, and tells how many times and where a certain oligo is located.

I want to insert from keyboard an oligo and extract the positions, but I can't write it down. Any suggestions?

Thank you very much!

That's my script, that when asked to insert query returns the name of the file I opened first.

use strict;

my $f;
my $nomefile;
my $line;

my %oligo = ();
my %pos = ();
my $piece;
my $query;
my $sequenza;
my $i;

$nomefile = $ARGV[0];

open $f, "< $nomefile" or die "cannot open $nomefile: $!";

$sequenza = <$f>;

while($line = <$f>)
{
    chomp($line);
    if(substr($line, 0, 1) ne ">")
    {
        $sequenza = $sequenza.$line;
    }
}

$sequenza = uc $sequenza;

for($i = 0; $i < length($sequenza) - 4; $i++)
{
    $piece = substr($sequenza, $i, 4);
    if(exists $oligo{$piece})
    {
        $oligo{$piece} = $oligo{$piece} + 1;
        push(@{$pos{$piece}} , $i + 1);
    }
    else
    {
        $oligo{$piece} = 1;
        push(@{$pos{$piece}} , $i + 1);
    }
}

foreach $piece (sort keys %oligo)
{
    print("$piece\t$oligo{$piece}\t@{$pos{$piece}}\n");
}

print("Insert query:\n");
$query = <>;

chomp($query);

$query = uc $query;

if(exists $oligo{$query})
{
    print("$query\t compare $oligo{$query} volte\t in posizione @{$pos{$query}}\n");
}
else
{
    print("$query does not appear in the sequence");
}

Answer 1

[Jean-Karim Heriche]

Use <STDIN> to read from STDIN. When @ARGV is not empty, <> reads from the files in @ARGV. If you still want to keep using <>, then empty @ARGV first e.g. $nomefile = shift @ARGV;

[nico_ce90]

Thank you very much for your kind answer, it was very simple, I'm new in using Perl but I'm enjoying it very much! Can I ask a little enlightment please?

How can I make it work with a query not the length used to create the index (for example a query >n or a multiple of n)?

Thanks!