Mercurial > repos > dereeper > pangenome_explorer
comparison Perl/translate.pl @ 3:e42d30da7a74 draft
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author | dereeper |
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date | Thu, 30 May 2024 11:52:25 +0000 |
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2:97e4e3e818b6 | 3:e42d30da7a74 |
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1 #!/usr/bin/perl | |
2 | |
3 use strict; | |
4 | |
5 use File::Basename; | |
6 my $dirname = dirname(__FILE__); | |
7 | |
8 my $out = $ARGV[1]; | |
9 my $in = $ARGV[0]; | |
10 open(F,$in); | |
11 open(O,">$out"); | |
12 while(<F>){ | |
13 if (/>(.*)/){ | |
14 print O $_; | |
15 } | |
16 else{ | |
17 my $dna = $_; | |
18 my $DNA = uc($dna); | |
19 $DNA =~s/\n//g;$DNA =~s/\r//g; | |
20 system("perl $dirname/DNA_Transcription_Translation.pl $DNA >>translate.log 2>&1"); | |
21 my $result = `cat result.txt`; | |
22 chop($result); | |
23 print O $result."\n"; | |
24 } | |
25 } | |
26 close(F); | |
27 close(O); |