View source for 6) Producing statistics of a multi-sequence FASTA file: sequence number, average seq length, GC content, AT content

<p><strong>Here I created sub function, which opens the file and removes a header, also combine all lines; Further, each&nbsp;nucleatide in fasta file placed to arrays, then counted their content:&nbsp;</strong>&nbsp;</p>

<p>#!/usr/bin/perl<br />
use strict;<br />
use warnings;</p>

<p>&nbsp;my $file = $ARGV[0];<br />
<strong>&nbsp;open (FILE, &quot;$file&quot;) or die </strong>&quot;Can&#39;t open the file: $_\n&quot;;</p>

<p><strong>sub readingfa</strong><br />
{<br />
&nbsp; &nbsp;my $string = &quot;&quot;;<br />
&nbsp; &nbsp; while(&lt;FILE&gt;){<br />
&nbsp; &nbsp; &nbsp; &nbsp; chomp($_);<br />
&nbsp; &nbsp; &nbsp; &nbsp; if($_ =~ /^&gt;/){ next; }<br />
&nbsp; &nbsp; &nbsp; &nbsp; else { $string .= $_; }<br />
&nbsp; &nbsp; }<br />
&nbsp; &nbsp; return($string); }<br />
&nbsp;<strong>my $seq = &amp;readingfa();</strong><br />
&nbsp;my $C = 0; &nbsp;my $G = 0;<br />
&nbsp;my $A = 0;&nbsp;&nbsp;my $T = 0;&nbsp;&nbsp;my $N = 0;</p>

<p>my $length = length $seq;</p>

<p><strong>&nbsp;my @nucleatides = split &quot;&quot;,$seq;</strong><br />
<strong>&nbsp;foreach my $nuc (@nucleatides) {</strong><br />
&nbsp; <strong>&nbsp;if ($nuc eq &quot;C&quot;){<br />
&nbsp; $C &nbsp;= $C+1; }<br />
&nbsp;elsif ($nuc eq &quot;G&quot;){<br />
&nbsp; $G = $G+1; }<br />
&nbsp; elsif ($nuc eq &quot;A&quot;){<br />
&nbsp;$A = $A+1; }<br />
&nbsp;elsif ($nuc eq &quot;T&quot;){<br />
&nbsp;$T = $T+1;}<br />
&nbsp;elsif ($nuc eq &quot;N&quot;) { $N = $N+1;<br />
}}</strong></p>

<p>&nbsp;<strong>my $GC_content = (($C+$G)/$length)*100;<br />
&nbsp; my $AT_content = (($A+$T)/$length)*100;</strong></p>

<p>&nbsp;print &quot;Fasta file statistics: \n&quot;;<br />
&nbsp;print &quot;Sequence length = $length\n&quot;;<br />
&nbsp;print &quot;Number of A: $A\n&quot;;<br />
&nbsp;print &quot;Number of C: $C\n&quot;;<br />
&nbsp;print &quot;Number of T: $T\n&quot;;<br />
&nbsp;print &quot;Number of G: $G\n&quot;;<br />
&nbsp;print &quot;Number of N: $N\n&quot;;<br />
&nbsp;print &quot;GC content is = $GC_content\n&quot;;<br />
&nbsp;print &quot;AT content is = $AT_content\n&quot;;</p>

<p>----------------------------------------------------------------------------------------------</p>

<p><strong>Perl script output will be:&nbsp;</strong></p>

<p>Fasta file statistics:&nbsp;<br />
Sequence length = 156040895<br />
Number of A: 46754807<br />
Number of C: 30523780<br />
Number of T: 46916701<br />
Number of G: 30697741<br />
Number of N: 1147861<br />
GC content is = 39.2342795777991<br />
AT content is = 60.0301017242948<br />
&nbsp;</p>