From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sat, 6 Jun 2009 20:40:44 +0000 (+0000)
Subject: fixed bug in format_genome
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5b09c82668d3a2aaaee85c219c05abc7ca242129;p=biopieces.git

fixed bug in format_genome

git-svn-id: http://biopieces.googlecode.com/svn/trunk@496 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index d5058ca..f02720c 100755
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -29,6 +29,9 @@
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;
+use Maasha::NCBI;
+use Maasha::Match;
+use Maasha::UCSC;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
diff --git a/code_perl/Maasha/NCBI.pm b/code_perl/Maasha/NCBI.pm
index a94dc4a..6618092 100644
--- a/code_perl/Maasha/NCBI.pm
+++ b/code_perl/Maasha/NCBI.pm
@@ -32,6 +32,7 @@ use strict;
 use Data::Dumper;
 use LWP::Simple;
 use Maasha::Common;
+use Maasha::Filesys;
 use Maasha::Seq;
 
 use vars qw( @ISA @EXPORT );
@@ -458,7 +459,7 @@ sub blast_index
         $type = "F";
     }
 
-    Maasha::Common::dir_create_if_not_exists( $dst_dir );
+    Maasha::Filesys::dir_create_if_not_exists( $dst_dir );
     Maasha::Common::run( "formatdb", "-p $type -i $src_dir/$file -t $index_name -l /dev/null" );
     Maasha::Common::run( "mv", "$src_dir/*hr $dst_dir" );
     Maasha::Common::run( "mv", "$src_dir/*in $dst_dir" );