Mercurial > repos > mcharles > rapsosnp
diff rapsodyn/extractseq.pl @ 10:0a6c1cfe4dc8 draft
Uploaded
author | mcharles |
---|---|
date | Mon, 19 Jan 2015 04:33:21 -0500 |
parents | 0e7c6fe60646 |
children |
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--- 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); }