Mercurial > repos > dereeper > pangenome_explorer
annotate PanExplorer_workflow/Perl/translate.pl @ 1:032f6b3806a3 draft
Uploaded
| author | dereeper |
|---|---|
| date | Thu, 30 May 2024 11:16:08 +0000 |
| parents | |
| children |
| rev | line source |
|---|---|
| 1 | 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); |