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

Uploaded

--- a/rapsodyn/extractseq.pl	Mon Oct 20 05:58:31 2014 -0400
+++ b/rapsodyn/extractseq.pl	Mon Jan 19 04:33:21 2015 -0500
@@ -1,4 +1,6 @@
 #!/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;
@@ -16,6 +18,12 @@
 ) 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;
@@ -89,11 +97,13 @@
 		}
 		$variant{"desc"}=$descriptor;
 		
-		print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n";
+		#print ">",$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);
 	}