Ignoring
moritz's very good suggestion, you could perform a naive search by storing the contents of the first file in an
array of arrays. This would end up looking something like (untested):
my @file1 = ();
open(FILE, @ARGV[0]) ||
die ("could not open file @ARGV[0]\n");
while (my $line = <FILE>) {
chomp $line;
my ($chr, $start, $stop) = split(/\t/, $line);
push @file1, [$chr, $start, $stop];
}
close FILE;
open(FILE, @ARGV[1])||die ("could not open file @ARGV[1]\n");
while(<FILE>){
($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,$SizeKB)= s
+plit;
# foreach (line in genes.db){ # I don't know what to put here
+.
foreach my $line (@file1){
my ($chr, $start, $stop) = @$line;
if ($chr eq $Chrom && $start gt $ModStart && $end lt $ModE
+nd){
$Count++;
print ;($Gene,$Chrom,$ModStart,$ModEnd,$Strand,$ExonCount,
+$SizeKB,$Count)
}
}
Note that your original concept had some scoping issues.
-
Are you posting in the right place? Check out Where do I post X? to know for sure.
-
Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
<code> <a> <b> <big>
<blockquote> <br /> <dd>
<dl> <dt> <em> <font>
<h1> <h2> <h3> <h4>
<h5> <h6> <hr /> <i>
<li> <nbsp> <ol> <p>
<small> <strike> <strong>
<sub> <sup> <table>
<td> <th> <tr> <tt>
<u> <ul>
-
Snippets of code should be wrapped in
<code> tags not
<pre> tags. In fact, <pre>
tags should generally be avoided. If they must
be used, extreme care should be
taken to ensure that their contents do not
have long lines (<70 chars), in order to prevent
horizontal scrolling (and possible janitor
intervention).
-
Want more info? How to link
or How to display code and escape characters
are good places to start.