Hi Jim,
Thanks again. Very helpful as usual!
T.
On 2013-02-13, at 11:37 PM, Jim Gibson <jimsgib...@gmail.com> wrote:
>
> On Feb 13, 2013, at 6:47 PM, Tiago Hori wrote:
>
>> Hey Guys,
>>
>> I am still at the same place. I am writing these little pieces of code to
>> try to learn the language better, so any advice would be useful. I am again
>> parsing through tab delimited files and now trying to find fish from on id
>> (in these case families AS5 and AS9), retrieve the weights and average
>> them. When I started I did it for one family and it worked (instead of the
>> @families I had a scalar $family set to AS5). But really it is more useful
>> to look at more than one family at time (I should mention that are 2 types
>> of fish per family one ends in PS , the other doesn't). So I tried to use a
>> foreach loop to go through the file twice, once with a the search value set
>> to AS5 and a second time to AS9. It works for AS5, but for some reason, the
>> foreach loop sets $test to AS9 the second time, but it doesn't go through
>> the while loop. What am I doing wrong?
>>
>> here is the code:
>>
>> #! /usr/bin/perl
>> use strict;
>> use warnings;
>>
>> my $file = $ARGV[0];
>> my @family = ('AS5','AS9');
>> my $i;
>> my $ii;
>> my $test;
>>
>> open (my $fh, "<", $file) or die ("Can't open $file: $!");
>>
>> foreach (@family){
>> $test = $_;
>
> You can combine those two lines like this (for and foreach are equivalent, so
> most people use the shorter form):
>
> for my $test ( @family ) {
>
>> my @data_weight_2N = ();
>> my @data_weight_3N = ();
>
> The second time through the for loop, the file has been read and is
> positioned at its end. You are going to get nothing by reading the file the
> second time through. You should rewind the file:
>
> seek($fh,0,0);
>
>> while (<$fh>){
>> chomp;
>> my $line = $_;
>
> Once again, you can do the assignment directly and not use the default
> variable $_. It is shorter and better:
>
> while( my $line = <$fh> ) {
> chomp($line);
>
>> my @data = split ("\t", $line);
>> if ($data[0] !~ /[0-9]*/){
>> next;}
>
> Better syntax for those two lines:
>
> next if $data[0] !~ /[0-9]*/;
>
>> elsif ($data[1] eq "ABF09-$test"){
>
> Then you can make the above line 'if …'
>
>> $i += 1;
>> push (@data_weight_2N, $data[6]);
>> }elsif ($data[1] eq "ABF09-".$test."PS"){
>> $ii += 1;
>> push (@data_weight_3N,$data[6]);
>> }
>> }
>> my $mean_2N = &average (\@data_weight_2N);
>> my $stdev_2N = &stdev (\@data_weight_2N);
>
> You should not be calling subroutines with the ampersand character.
>
>> my $stderr_2N = ($stdev_2N/sqrt($i));
>>
>> print "These are the the avearge weight, stdev and stderr for $test
>> 2N:\t", $mean_2N,"\t",$stdev_2N,"\t",$stderr_2N, "\n";
>
> It is more efficient to print one double-quoted string than a series of short
> strings,
> even if you have to concatenate the string from two shorter strings:
>
> print "These are the the avearge weight, stdev and stderr for $test" .
> " 2N:\t$mean_2N\t$stdev_2N\t$stderr_2N\n";
>
>>
>> my $mean_3N = &average (\@data_weight_3N);
>> my $stdev_3N = &stdev (\@data_weight_3N);
>> my $stderr_3N = ($stdev_3N/sqrt($i));
>>
>> print "These are the the avearge weight, stdev and stderr for $test
>> 3N:\t", $mean_3N,"\t",$stdev_3N,"\t",$stderr_3N, "\n";
>> }
>>
>> close ($fh);
>>
>> sub average{
>> my($data) = @_;
>> if (not @$data) {
>> print ("Empty array\n");
>> return 0;
>> }
>> my $total = 0;
>> foreach (@$data) {
>> $total += $_;
>> }
>
> Shorter:
>
> $total += $_ for @$data;
>
>> my $average = $total / @$data;
>> return $average;
>> }
>>
>> sub stdev{
>> my($data) = @_;
>> if(@$data == 1){
>> return 0;
>> }
>> my $average = &average($data);
>> my $sqtotal = 0;
>> foreach(@$data) {
>> $sqtotal += ($average-$_) ** 2;
>> }
>> my $std = ($sqtotal / (@$data-1)) ** 0.5;
>> return $std;
>> }
>>
>> Thanks,
>
>
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