comparison rapsodyn/extractseq.pl @ 10:0a6c1cfe4dc8 draft

Uploaded

9:0e7c6fe60646

#!/usr/bin/perl
#V1.01 #Ajout d'un _ a la fin du nom pour eviter les problemes avec ncbi blast+

use strict;
use warnings;
use Getopt::Long;

"input_assembly_file=s" => \$input_assembly_file,
"window_length=i" => \$WINDOWS_LENGTH
) or die("Error in command line arguments\n");

open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n");
open(INA, $input_assembly_file) or die ("Can't open $input_assembly_file\n");

my @variant_list;

		else {
			$descriptor.="?_?";
		}
		$variant{"desc"}=$descriptor;
		
		print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n";

		
		
		#print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n";
		
		push(@variant_list,\%variant);
	}
}
close (INV);

10:0a6c1cfe4dc8

#!/usr/bin/perl
#V1.10 manage empty files
#V1.02 Trop de pb avec nbci blast+, changment du header des fasta
#V1.01 #Ajout d'un _ a la fin du nom pour eviter les problemes avec ncbi blast+

use strict;
use warnings;
use Getopt::Long;

"input_assembly_file=s" => \$input_assembly_file,
"window_length=i" => \$WINDOWS_LENGTH
) or die("Error in command line arguments\n");

open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n");

if ( -z INV){
	print ">empty\nAAAAA";
	exit(0);
}

open(INA, $input_assembly_file) or die ("Can't open $input_assembly_file\n");

my @variant_list;

		else {
			$descriptor.="?_?";
		}
		$variant{"desc"}=$descriptor;
		
		#print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n";

		
		
		#V1.02 : changement du header
		#print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n";
		print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n";
		
		push(@variant_list,\%variant);
	}
}
close (INV);