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POHow do I average column values from a tab-separated data file, ignoring a header row and the left column?
 

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  1. POHow do I average column values from a tab-separated data file, ignoring a header row and the left column?
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    <p>First and foremost I apologise if this, or a similar query, has been posted before but I did follow the steps and looked here and beyond and that is why I'm resorting to asking a question, something I rarely ever do.</p> <p>Background before my query - I'm a final year biomedical student, and I decided to take a Bioinformatics paper - a paper that has only begun to be offered at my university this year. I thought it would be a good change, but now that I've had experience two weeks in, I'm not finding it particularly engaging. Challenging, yes, but not engaging, in that I've never done any programming in my life, and I'm expecting to learn this so suddenly. As such, anything I present to you is as a complete 'newbie', and I admit that I literally have little to no clue on how to go about doing things and I really do want to try and learn.</p> <p>Anyway, onto my query…</p> <p>My task is to compute averages from the following data file, titled <code>Lab1_table.txt</code>:</p> <pre><code>retrovirus genome gag pol env HIV-1 9181 1503 3006 2571 FIV 9474 1353 2993 2571 KoRV 8431 1566 3384 1980 GaLV 8088 1563 3498 2058 PERV 8072 1560 3621 1532 </code></pre> <p>I have to write a script that will open and read this file, read each line by splitting the contents into an array and computer the average of the numerical values (<code>genome</code>, <code>gag</code>, <code>pol</code>, <code>env</code>), and write to a new file the average from each of the aforementioned columns.</p> <p>I've been trying my best to figure out how to not take into account the first row, or the first column, but every time I try to execute on the command line I keep coming up with 'explicit package name' errors.</p> <pre><code>Global symbol @average requires explicit package name at line 23. Global symbol @average requires explicit package name at line 29. Execution aborted due to compilation errors. </code></pre> <p>I understand that this involves <code>@</code> and <code>$</code>, but even knowing that I've not been able to change the errors.</p> <p>This is my code, but I emphasise that I'm a beginner having started this just last week:</p> <pre><code>#!/usr/bin/perl -w use strict; my $infile = "Lab1_table.txt"; # This is the file path open INFILE, $infile or die "Can't open $infile: $!"; my $count = 0; my $average = (); while (&lt;INFILE&gt;) { chomp; my @columns = split /\t/; $count++; if ( $count == 1 ) { $average = @columns; } else { for( my $i = 1; $i &lt; scalar $average; $i++ ) { $average[$i] += $columns[$i]; } } } for( my $i = 1; $i &lt; scalar $average; $i++ ) { print $average[$i]/$count, "\n"; } </code></pre> <p>I'd appreciate any insight, and I would also great appreciate letting me know by list numbering what you're doing at each step - if appropriate. I'd like to learn and it would make more sense to me if I was able to read through what someone's process was.</p>
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    1. COok, I see you've taken to heart the `use warnings` and `use strict` commandments. And that's where your error is coming from. You declared 'average' to be an array ref (kinda) then you used it as an array. try one or the other (but NOT both) of these: 1. change line to be @average OR 2. dereference properly with `$average->[i]` Note, this won't solve the whole problem, but it will get rid of the error messages for you, allowing you to focus on the logic.
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      1. POHow do I average column values from a tab-separated data file, ignoring a header row and the left column?
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    2. COOh, I just had to dereference it. That did get rid of the last two errors, and you're right it doesn't solve the whole problem as I come up with this now: Can't use string ("5") as an ARRAY ref while "strict refs" in use at line 23, <INFILE> line 2. I'm unsurewhat's happened here though...
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    3. CO@PkC you may want to update your code sample to display the latest state of your code. That would be more helpful for debugging.
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      1. USoalders
 

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