Difference between revisions of "BuKyung Create a flat text file database of protein sequences with hash function in Perl"

From Biolecture.org
imported>Baik BuKyung
imported>Baik BuKyung
Line 4: Line 4:
 
<p><span style="font-size:24px">Source code:</span></p>
 
<p><span style="font-size:24px">Source code:</span></p>
  
−
<p>&nbsp;</p>
+
<p>#!/usr/bin/perl<br />
−
 
+
&nbsp;use strict;<br />
−
<hr />
 
−
<div>
 
−
<div>#!/usr/bin/perl
 
−
<p>&nbsp;use strict;<br />
 
 
&nbsp;use warnings;<br />
 
&nbsp;use warnings;<br />
−
&nbsp;open FH, &quot;&gt;&quot;, &quot;outer.fasta&quot; or die &quot;$!\n&quot;;<br />
+
&nbsp;open FH, &quot;&gt;&quot;, &quot;outerl.fasta&quot; or die &quot;$!\n&quot;;<br />
−
&nbsp;<br />
+
&nbsp;my %sequence=();<br />
−
&nbsp;my $Original_sequence=&quot;ASMKATAHQMKKTGIKGMSTYALLRL&quot;;<br />
+
&nbsp;my $seq_name;<br />
−
&nbsp;my $Extracted_sequence=&quot;MKKTGIKG&quot;;<br />
+
&nbsp;my $seq;<br />
−
&nbsp;if($Original_sequence =~ /$Extracted_sequence/){<br />
+
&nbsp;while(&lt;&gt;){<br />
−
&nbsp;&nbsp;print FH (&quot;Original sequence is&nbsp;:&quot;,$Original_sequence,&quot;\nExtracted sequence is&nbsp;:&quot;,$Extracted_sequence);<br />
+
&nbsp;if($_=~ /&gt;/){<br />
 +
&nbsp;&nbsp;$seq_name=$_;<br />
 +
&nbsp;&nbsp;$seq_name=~ s/\n//;<br />
 
}<br />
 
}<br />
 
&nbsp;else{<br />
 
&nbsp;else{<br />
−
&nbsp;&nbsp;print FH ($Extracted_sequence, &quot; is not in the &quot;, $Original_sequence);</p>
+
&nbsp;&nbsp;$seq=$_;<br />
−
&nbsp;}</div>
+
&nbsp;&nbsp;$seq=~ s/\n//;<br />
 +
}<br />
 +
&nbsp;$sequence{$seq_name}=$seq;<br />
 +
}</p>
  
 
<div>
 
<div>
 +
<div>
 +
<div>&nbsp;</div>
 +
 +
<div><br />
 +
foreach my $key (sort keys %sequence) {<br />
 +
&nbsp;&nbsp;&nbsp; print FH $key, &quot; : &quot;, $sequence{$key}, &quot;&nbsp;&nbsp; \n&quot;;<br />
 +
}
 
<hr />
 
<hr />
−
<p>&nbsp;</p>
+
<p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9824.PNG" style="height:350px; width:472px" /></p>
−
 
+
</div>
−
<p><img alt="" src="http://biolecture.org/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9820(1).PNG" style="height:272px; width:767px" /></p>
 
 
</div>
 
</div>
 
</div>
 
</div>
−
 
−
<p>&nbsp;</p>
 
  
 
<div>
 
<div>
Line 36: Line 41:
 
<p><span style="font-size:24px">Result</span></p>
 
<p><span style="font-size:24px">Result</span></p>
  
−
<p>&nbsp;</p>
+
<p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9825.PNG" style="height:24px; width:327px" /></p>
 +
 
 +
<p><span style="font-size:16px">After execution of 10.pl with outer.fasta, the outerl.fasta file is generated.</span></p>
 +
 
 +
<p><span style="font-size:16px">The content of outer.fasta is</span></p>
 +
 
 +
<p><em>&gt;0<br />
 +
LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI<br />
 +
&gt;1<br />
 +
KHGGRDNLQSMPSLMNDNERRSMRSQRDWHGFWQVLRFMPFHGNNNMHQDCNSHSDQGFIRMDHCKHHRVNGLVISRRRPDHPNQFISWRYGDDSIQFYQ<br />
 +
&gt;2<br />
 +
YWCYISQDNRAERASYYKEVQPNPPNGNRGFPWEPFDQCGVALNAMWKLCIHVNGNRPQNPGQGPYLKHMRVAVDELRSDPAVYFKEDKVDCRHEKFGDK<br />
 +
&gt;3<br />
 +
KAHIQRVRQNNKRSIWGCKRAHGCQEWYNGMFWNHKCIWCREGGEESRPHNNEQIRPDMSGQRKAISPELAPLEGWMEYQCFRKDPKANEMRVNLEMAHM<br />
 +
&gt;4<br />
 +
SRVRVCFKPMYGMIKHHSVHQECGIKDPSYGWLGRPEASHICIWGQHGNNINFMYGKIYRQSYRIPCEDKCPPAPAPLVIQEVWLAPAHRNNKLHKRRGR</em><br />
 +
&nbsp;</p>
 +
 
 +
<p><span style="font-size:16px">generated by the [[]] assignment program.</span></p>
 +
 
 +
<p><span style="font-size:16px">The contents of the outerl.fasta is</span></p>
  
−
<p>&nbsp;</p>
+
<p><em>&gt;0 : LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI&nbsp;&nbsp;<br />
 +
&gt;1 : KHGGRDNLQSMPSLMNDNERRSMRSQRDWHGFWQVLRFMPFHGNNNMHQDCNSHSDQGFIRMDHCKHHRVNGLVISRRRPDHPNQFISWRYGDDSIQFYQ&nbsp;&nbsp;<br />
 +
&gt;2 : YWCYISQDNRAERASYYKEVQPNPPNGNRGFPWEPFDQCGVALNAMWKLCIHVNGNRPQNPGQGPYLKHMRVAVDELRSDPAVYFKEDKVDCRHEKFGDK&nbsp;&nbsp;<br />
 +
&gt;3 : KAHIQRVRQNNKRSIWGCKRAHGCQEWYNGMFWNHKCIWCREGGEESRPHNNEQIRPDMSGQRKAISPELAPLEGWMEYQCFRKDPKANEMRVNLEMAHM&nbsp;&nbsp;<br />
 +
&gt;4 : SRVRVCFKPMYGMIKHHSVHQECGIKDPSYGWLGRPEASHICIWGQHGNNINFMYGKIYRQSYRIPCEDKCPPAPAPLVIQEVWLAPAHRNNKLHKRRGR&nbsp;&nbsp;</em><br />
 +
&nbsp;</p>
 
</div>
 
</div>

Revision as of 06:03, 17 June 2016

Back to Baik BuKyung

Source code:

#!/usr/bin/perl
 use strict;
 use warnings;
 open FH, ">", "outerl.fasta" or die "$!\n";
 my %sequence=();
 my $seq_name;
 my $seq;
 while(<>){
 if($_=~ />/){
  $seq_name=$_;
  $seq_name=~ s/\n//;
}
 else{
  $seq=$_;
  $seq=~ s/\n//;
}
 $sequence{$seq_name}=$seq;
}

 

foreach my $key (sort keys %sequence) {
    print FH $key, " : ", $sequence{$key}, "   \n";
}

Result

After execution of 10.pl with outer.fasta, the outerl.fasta file is generated.

The content of outer.fasta is

>0
LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI
>1
KHGGRDNLQSMPSLMNDNERRSMRSQRDWHGFWQVLRFMPFHGNNNMHQDCNSHSDQGFIRMDHCKHHRVNGLVISRRRPDHPNQFISWRYGDDSIQFYQ
>2
YWCYISQDNRAERASYYKEVQPNPPNGNRGFPWEPFDQCGVALNAMWKLCIHVNGNRPQNPGQGPYLKHMRVAVDELRSDPAVYFKEDKVDCRHEKFGDK
>3
KAHIQRVRQNNKRSIWGCKRAHGCQEWYNGMFWNHKCIWCREGGEESRPHNNEQIRPDMSGQRKAISPELAPLEGWMEYQCFRKDPKANEMRVNLEMAHM
>4
SRVRVCFKPMYGMIKHHSVHQECGIKDPSYGWLGRPEASHICIWGQHGNNINFMYGKIYRQSYRIPCEDKCPPAPAPLVIQEVWLAPAHRNNKLHKRRGR
 

generated by the [[]] assignment program.

The contents of the outerl.fasta is

>0 : LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI  
>1 : KHGGRDNLQSMPSLMNDNERRSMRSQRDWHGFWQVLRFMPFHGNNNMHQDCNSHSDQGFIRMDHCKHHRVNGLVISRRRPDHPNQFISWRYGDDSIQFYQ  
>2 : YWCYISQDNRAERASYYKEVQPNPPNGNRGFPWEPFDQCGVALNAMWKLCIHVNGNRPQNPGQGPYLKHMRVAVDELRSDPAVYFKEDKVDCRHEKFGDK  
>3 : KAHIQRVRQNNKRSIWGCKRAHGCQEWYNGMFWNHKCIWCREGGEESRPHNNEQIRPDMSGQRKAISPELAPLEGWMEYQCFRKDPKANEMRVNLEMAHM  
>4 : SRVRVCFKPMYGMIKHHSVHQECGIKDPSYGWLGRPEASHICIWGQHGNNINFMYGKIYRQSYRIPCEDKCPPAPAPLVIQEVWLAPAHRNNKLHKRRGR  
 

Retrieved from "http://Biolecture.org/index.php?title=BuKyung_Create_a_flat_text_file_database_of_protein_sequences_with_hash_function_in_Perl&oldid=9743"