Difference between revisions of "BuKyung Create a flat text file database of protein sequences with hash function in Perl"
imported>Baik BuKyung |
imported>Baik BuKyung |
||
| Line 7: | Line 7: | ||
use strict;<br /> | use strict;<br /> | ||
use warnings;<br /> | use warnings;<br /> | ||
| − | open FH, ">", "outerl. | + | open FH, ">", "outerl.txt" or die "$!\n";<br /> |
my %sequence=();<br /> | my %sequence=();<br /> | ||
my $seq_name;<br /> | my $seq_name;<br /> | ||
| Line 32: | Line 32: | ||
} | } | ||
<hr /> | <hr /> | ||
| − | <p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9824.PNG" style="height: | + | <p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9824(1).PNG" style="height:393px; width:418px" /></p> |
</div> | </div> | ||
</div> | </div> | ||
| Line 61: | Line 61: | ||
<p><span style="font-size:16px">generated by the [[]] assignment program.</span></p> | <p><span style="font-size:16px">generated by the [[]] assignment program.</span></p> | ||
| − | <p><span style="font-size:16px">The contents of the outerl. | + | <p><span style="font-size:16px">The contents of the outerl.txt is</span></p> |
<p><em>>0 : LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI <br /> | <p><em>>0 : LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI <br /> | ||
Revision as of 06:05, 17 June 2016
Back to Baik BuKyung
Source code:
#!/usr/bin/perl
use strict;
use warnings;
open FH, ">", "outerl.txt" or die "$!\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 [[]] assignment program.
The contents of the outerl.txt is
>0 : LIEYMVYQVHECCMKNIKKSQVSARMRARGHMVQLYYEDWEPIISDQRNSAANRSDDRVIESQSKQNVKHSNWEQCMCWFKILINMWLGQMREPPIYEDI
>1 : KHGGRDNLQSMPSLMNDNERRSMRSQRDWHGFWQVLRFMPFHGNNNMHQDCNSHSDQGFIRMDHCKHHRVNGLVISRRRPDHPNQFISWRYGDDSIQFYQ
>2 : YWCYISQDNRAERASYYKEVQPNPPNGNRGFPWEPFDQCGVALNAMWKLCIHVNGNRPQNPGQGPYLKHMRVAVDELRSDPAVYFKEDKVDCRHEKFGDK
>3 : KAHIQRVRQNNKRSIWGCKRAHGCQEWYNGMFWNHKCIWCREGGEESRPHNNEQIRPDMSGQRKAISPELAPLEGWMEYQCFRKDPKANEMRVNLEMAHM
>4 : SRVRVCFKPMYGMIKHHSVHQECGIKDPSYGWLGRPEASHICIWGQHGNNINFMYGKIYRQSYRIPCEDKCPPAPAPLVIQEVWLAPAHRNNKLHKRRGR
