Difference between revisions of "BuKyung Create a flat text file database of protein sequences with hash function in Perl"
imported>Baik BuKyung (Created page with "<p>Back to Baik BuKyung</p> <hr /> <p> </p>") |
imported>Baik BuKyung |
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<hr /> | <hr /> | ||
+ | <p><span style="font-size:24px">Source code:</span></p> | ||
+ | |||
+ | <p>#!/usr/bin/perl<br /> | ||
+ | use strict;<br /> | ||
+ | use warnings;<br /> | ||
+ | open FH, ">", "outerl.txt" or die "$!\n";<br /> | ||
+ | my %sequence=();<br /> | ||
+ | my $seq_name;<br /> | ||
+ | my $seq;<br /> | ||
+ | while(<>){<br /> | ||
+ | if($_=~ />/){<br /> | ||
+ | $seq_name=$_;<br /> | ||
+ | $seq_name=~ s/\n//;<br /> | ||
+ | }<br /> | ||
+ | else{<br /> | ||
+ | $seq=$_;<br /> | ||
+ | $seq=~ s/\n//;<br /> | ||
+ | }<br /> | ||
+ | $sequence{$seq_name}=$seq;<br /> | ||
+ | }</p> | ||
+ | |||
+ | <div> | ||
+ | <div> | ||
+ | <div> </div> | ||
+ | |||
+ | <div><br /> | ||
+ | foreach my $key (sort keys %sequence) {<br /> | ||
+ | print FH $key, " : ", $sequence{$key}, " \n";<br /> | ||
+ | } | ||
+ | <hr /> | ||
+ | <p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9824(1).PNG" style="height:393px; width:418px" /></p> | ||
+ | </div> | ||
+ | </div> | ||
+ | </div> | ||
+ | |||
+ | <div> | ||
+ | <hr /> | ||
+ | <p><span style="font-size:24px">Result</span></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>>0<br /> | ||
+ | LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI<br /> | ||
+ | >1<br /> | ||
+ | KHGGRDNLQSMPSLMNDNERRSMRSQRDWHGFWQVLRFMPFHGNNNMHQDCNSHSDQGFIRMDHCKHHRVNGLVISRRRPDHPNQFISWRYGDDSIQFYQ<br /> | ||
+ | >2<br /> | ||
+ | YWCYISQDNRAERASYYKEVQPNPPNGNRGFPWEPFDQCGVALNAMWKLCIHVNGNRPQNPGQGPYLKHMRVAVDELRSDPAVYFKEDKVDCRHEKFGDK<br /> | ||
+ | >3<br /> | ||
+ | KAHIQRVRQNNKRSIWGCKRAHGCQEWYNGMFWNHKCIWCREGGEESRPHNNEQIRPDMSGQRKAISPELAPLEGWMEYQCFRKDPKANEMRVNLEMAHM<br /> | ||
+ | >4<br /> | ||
+ | SRVRVCFKPMYGMIKHHSVHQECGIKDPSYGWLGRPEASHICIWGQHGNNINFMYGKIYRQSYRIPCEDKCPPAPAPLVIQEVWLAPAHRNNKLHKRRGR</em><br /> | ||
+ | </p> | ||
+ | |||
+ | <p><span style="font-size:16px">generated by the [[BuKyung Randomly generate five 100 AA long protein sequences and store them in a FASTA file]] assignment program.</span></p> | ||
+ | |||
<p> </p> | <p> </p> | ||
+ | |||
+ | <p><span style="font-size:16px">The contents of the outerl.txt is</span></p> | ||
+ | |||
+ | <p><em>>0 : LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI <br /> | ||
+ | >1 : KHGGRDNLQSMPSLMNDNERRSMRSQRDWHGFWQVLRFMPFHGNNNMHQDCNSHSDQGFIRMDHCKHHRVNGLVISRRRPDHPNQFISWRYGDDSIQFYQ <br /> | ||
+ | >2 : YWCYISQDNRAERASYYKEVQPNPPNGNRGFPWEPFDQCGVALNAMWKLCIHVNGNRPQNPGQGPYLKHMRVAVDELRSDPAVYFKEDKVDCRHEKFGDK <br /> | ||
+ | >3 : KAHIQRVRQNNKRSIWGCKRAHGCQEWYNGMFWNHKCIWCREGGEESRPHNNEQIRPDMSGQRKAISPELAPLEGWMEYQCFRKDPKANEMRVNLEMAHM <br /> | ||
+ | >4 : SRVRVCFKPMYGMIKHHSVHQECGIKDPSYGWLGRPEASHICIWGQHGNNINFMYGKIYRQSYRIPCEDKCPPAPAPLVIQEVWLAPAHRNNKLHKRRGR </em><br /> | ||
+ | </p> | ||
+ | </div> |
Latest revision as of 06:06, 17 June 2016
Back to Baik BuKyung
Source code:
#!/usr/bin/perl
use strict;
use warnings;
open FH, ">", "outerl.txt" 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 BuKyung Randomly generate five 100 AA long protein sequences and store them in a FASTA file assignment program.
The contents of the outerl.txt is
>0 : LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI
>1 : KHGGRDNLQSMPSLMNDNERRSMRSQRDWHGFWQVLRFMPFHGNNNMHQDCNSHSDQGFIRMDHCKHHRVNGLVISRRRPDHPNQFISWRYGDDSIQFYQ
>2 : YWCYISQDNRAERASYYKEVQPNPPNGNRGFPWEPFDQCGVALNAMWKLCIHVNGNRPQNPGQGPYLKHMRVAVDELRSDPAVYFKEDKVDCRHEKFGDK
>3 : KAHIQRVRQNNKRSIWGCKRAHGCQEWYNGMFWNHKCIWCREGGEESRPHNNEQIRPDMSGQRKAISPELAPLEGWMEYQCFRKDPKANEMRVNLEMAHM
>4 : SRVRVCFKPMYGMIKHHSVHQECGIKDPSYGWLGRPEASHICIWGQHGNNINFMYGKIYRQSYRIPCEDKCPPAPAPLVIQEVWLAPAHRNNKLHKRRGR