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POPerl: How to pass information to a function in module?
 

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  1. POPerl: How to pass information to a function in module?
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    <p>Completely new to Perl here. Anyway, I was given a certain task and I found a perl module online that does <em>exactly</em> what I want. </p> <p><a href="http://jaspar.genereg.net/html/DOWNLOAD/jaspar_CORE/non_redundant/by_tax_group/vertebrates/matrix_only/matrix_only.txt" rel="nofollow">Matrix</a></p> <p><a href="http://tfbs.genereg.net/DOC/" rel="nofollow">Documentation</a></p> <p>This is the documentation for the perl module -- under Ext there is one called pwmsearch, which does exactly what I need.</p> <p>So I tried to write a script that starts out something like this:</p> <pre><code>#!/usr/bin/env perl -w use strict; use TFBS::Ext::pwmsearch; #this was how the documentation said in synopsis part for pwmsearch so I figured this was how to do it </code></pre> <p>The problem is that I cannot figure out how I am supposed to pass objects to pwmsearch. The source code of pwmsearch as shown in the documentation above says it takes in $matrixobj and $seqobj, which I have stored as files matrix and sequence. </p> <p>So after googling around on what I could try, I tried doing things like:</p> <pre><code>pwmsearch('matrix','sequence'); </code></pre> <p>or</p> <pre><code>open FILE, 'matrix.txt' or die "Couldn't open file"; $matrix.=&lt;FILE&gt; close FILE; open FILE, 'sequence' or die "Couldn't open file"; $seq.=&lt;FILE&gt; close FILE; pwmsearch($matrix,$seq) </code></pre> <p>But all of them makes perl bark at me with various errors. What am I doing wrong and what could I do to fix them?</p>
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    1. CO`$matrixobj` has to be some kind of object (since I see a method called on it), as the name implies. It probably has to be an object of one of the TFBS::Matrix::* classes.
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      1. USikegami
    2. CO`$seqobj` also has to be an object of some kind (since I see a method called on it), though I see no class with "Sequence" in the name.
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    3. COProbably a [Bio::Seq](http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Seq.pm) object - see http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO.pm.
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      1. USMvanGeest
 

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