View source for BuKyung In a multi-sequence FASTA file, produce statistics such as sequence number, average seq length, GC content, AT content, etc

<p>Back to [[Baik BuKyung]]</p>

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<p><span style="font-size:24px">Source code:</span></p>

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<div>
<div>#!/usr/bin/perl<br />
&nbsp;use strict;<br />
&nbsp;use warnings;<br />
&nbsp;open FH, &quot;&gt;&quot;, &quot;outer.fasta&quot; or die &quot;$!\n&quot;;<br />
&nbsp;my $numberofseq=0;<br />
&nbsp;my @matrix;<br />
&nbsp;while(&lt;&gt;){<br />
&nbsp;if($_=~ /&gt;/){<br />
&nbsp;&nbsp;$matrix[$numberofseq]{seqname}=$_;<br />
&nbsp;&nbsp;$matrix[$numberofseq]{seqname}=~ s/\n//;<br />
&nbsp;&nbsp;<br />
}<br />
&nbsp;else{<br />
&nbsp;&nbsp;$matrix[$numberofseq]{seq}=$_;<br />
&nbsp;&nbsp; &nbsp;$matrix[$numberofseq]{seq}=~ s/\n//;<br />
&nbsp;&nbsp;$numberofseq++;<br />
}<br />
}</div>

<div>&nbsp;</div>

<div>for(my $i=0;$i&lt;$numberofseq;$i++){<br />
&nbsp;my $count=0;<br />
&nbsp;$matrix[$i]{seqlen}=length($matrix[$i]{seq});<br />
&nbsp;for(my $j=0;$j&lt;$matrix[$i]{seqlen};$j++){<br />
&nbsp;&nbsp;my $seq_char=substr($matrix[$i]{seq},$j,1);<br />
&nbsp;&nbsp;if($seq_char=~/[GC]/){<br />
&nbsp;&nbsp;&nbsp;$count++;<br />
&nbsp;&nbsp;}<br />
&nbsp;&nbsp;$matrix[$i]{GC}=$count;<br />
&nbsp;}<br />
}</div>

<div>&nbsp;</div>

<div>my $total_seqlen=0;<br />
my $total_GC=0;<br />
for(my $i=0;$i&lt;$numberofseq;$i++){<br />
&nbsp;print FH ($matrix[$i]{seqname},&quot;\n&quot;,$matrix[$i]{seq},&quot;\n GC content is:&quot;,$matrix[$i]{GC},&quot;\n&quot;);<br />
&nbsp;$total_seqlen=$total_seqlen+$matrix[$i]{seqlen};<br />
&nbsp;$total_GC=$total_GC+$matrix[$i]{GC};<br />
}<br />
print FH (&quot;Average sequence length is :&quot;,$total_seqlen/$numberofseq,&quot;\n GC contents:&quot;,$total_GC/$total_seqlen,&quot;\n AT contents:&quot;,1-($total_GC/$total_seqlen),&quot;\n&quot;)</div>
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<p>&nbsp;</p>

<p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9818.PNG" style="height:631px; width:1162px" /></p>

<p>&nbsp;</p>
</div>

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<p>&nbsp;</p>

<p><span style="font-size:24px">Result</span></p>

<p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9819.PNG" style="height:20px; width:406px" /></p>

<p>&nbsp;</p>

<p><span style="font-size:16px">After the 6.pl is executed with the 5_100-length_Seq.fasta file, the outer.fasta file is generated.</span></p>

<p><span style="font-size:16px">The original content in the tert_Human.fasta file contains 5 fasta sequences with each&nbsp;length 100. The editted version of&nbsp;[[BuKyung Randomly generate five 100 AA long protein sequences and store them in a FASTA file]]&nbsp;made this file.</span></p>

<p>&nbsp;</p>

<p><em>&gt;0<br />
ACCACTACTAAGCGCATGAACGACTGTTAGGTTTCCGATGGCTGCTTGCGTTCCGTGTTCCAGCTGACTGGGCTGAACTATTTGTAATGTTGGTTGCACT<br />
&gt;1<br />
CAGGTACACGGACTGTTTGGTTTGCCCAATTAATTGGCGGGTCGTAAACCGGTTTTTCGTTGGGCGCGGAGTTGTCGTAAACGGTCGGTATTAACTACCT<br />
&gt;2<br />
ATATTCTGTTCGAAGGCGAGGCCTTAATAAACGGGCTCACACTATACGTTTCTAGCGTGCCAGTACGCGTATGCCCTGAGCAGCATCTTGAATAGTCCTT<br />
&gt;3<br />
CACGTCTTGAGGCATGCTCACATAACTTGGGATTGATACAATCGGGGGACGGTAGCGGGGCTAGTGGGCATCGTCGGCGGTCTACGAGCAAAAGTATCAG<br />
&gt;4<br />
CAGGACGTGAACCGAAAGCTGCACACCTATACTATCGTAGTATACCACCGTTCCGTAAATCCATCGCTGATCCTGCCATGAAGGGCTAAGTACGCATGAG</em><br />
&nbsp;</p>

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<p>&nbsp;</p>

<p><span style="font-size:16px">The content of outer.fasta file&nbsp;is</span></p>

<p>&nbsp;</p>

<div>
<div><em>&gt;0<br />
ACCACTACTAAGCGCATGAACGACTGTTAGGTTTCCGATGGCTGCTTGCGTTCCGTGTTCCAGCTGACTGGGCTGAACTATTTGTAATGTTGGTTGCACT<br />
&nbsp;GC content is:0.49<br />
&gt;1<br />
CAGGTACACGGACTGTTTGGTTTGCCCAATTAATTGGCGGGTCGTAAACCGGTTTTTCGTTGGGCGCGGAGTTGTCGTAAACGGTCGGTATTAACTACCT<br />
&nbsp;GC content is:0.5<br />
&gt;2<br />
ATATTCTGTTCGAAGGCGAGGCCTTAATAAACGGGCTCACACTATACGTTTCTAGCGTGCCAGTACGCGTATGCCCTGAGCAGCATCTTGAATAGTCCTT<br />
&nbsp;GC content is:0.48<br />
&gt;3<br />
CACGTCTTGAGGCATGCTCACATAACTTGGGATTGATACAATCGGGGGACGGTAGCGGGGCTAGTGGGCATCGTCGGCGGTCTACGAGCAAAAGTATCAG<br />
&nbsp;GC content is:0.55<br />
&gt;4<br />
CAGGACGTGAACCGAAAGCTGCACACCTATACTATCGTAGTATACCACCGTTCCGTAAATCCATCGCTGATCCTGCCATGAAGGGCTAAGTACGCATGAG<br />
&nbsp;GC content is:0.5</em></div>

<div>&nbsp;</div>

<div><br />
<em>Average sequence length is :100<br />
&nbsp;GC contents:0.504<br />
&nbsp;AT contents:0.496</em></div>
</div>

<div>&nbsp;</div>

<div>&nbsp;</div>

<div><span style="font-size:16px">I just add GC content of each sequence to the end of each sequence. At the end of the file, Average sequence length, GC contents and AT contents are printed out.</span></div>
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