Merge pull request #264 from andrewjpage/fix_empty_accessory_binary

Fix empty accessory binary

.travis.yml

@@ -8,7 +8,6 @@ addons:
 cache:
   directories:
   - build/parallel-20150522
-  - build/parallel-20141022
   - build/parallel-20130922
   - build/bedtools2
   - build/cd-hit-v4.6.3-2015-0515
@@ -22,7 +21,6 @@ perl:
   - "5.24"
 env:
   - PARALLEL_VERSION=20150522
-  - PARALLEL_VERSION=20141022
   - PARALLEL_VERSION=20130922
 install:
   - "source ./install_dependencies.sh"

README.md

@@ -94,6 +94,6 @@ The code will not work with perl 5.8 or below (pre-modern perl). We no longer te
 * cdhit 4.6.1
 * ncbi blast+ 2.2.30
 * mcl 14-137
-* bedtools 2.20.1
+* bedtools 2.20.1  2.26.0
 * prank 130410
 * GNU parallel 20130922, 20141022, 20150122

dist.ini

@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.6.5
+version = 3.6.6
 author  = Andrew J. Page <[email protected]>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
@@ -12,7 +12,9 @@ repository.web  = http://sanger-pathogens.github.io/Roary/
 repository.url  = https://github.com/sanger-pathogens/Roary.git
 repository.type = git
 
-[@Starter]
+[@Basic]
+[PruneCruft]
+[ExtraTests]
 [AutoPrereqs]
 [PodWeaver]
 [PkgVersion]

install_dependencies.sh

@@ -11,7 +11,7 @@ PARALLEL_VERSION=${PARALLEL_VERSION:-"20150522"}
 PARALLEL_DOWNLOAD_FILENAME="parallel-${PARALLEL_VERSION}.tar.bz2" 
 PARALLEL_URL="http://ftp.gnu.org/gnu/parallel/${PARALLEL_DOWNLOAD_FILENAME}"
 
-BEDTOOLS_VERSION="2.24.0"
+BEDTOOLS_VERSION="2.26.0"
 BEDTOOLS_DOWNLOAD_FILENAME="bedtools-${BEDTOOLS_VERSION}.tar.gz"
 BEDTOOLS_URL="https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/${BEDTOOLS_DOWNLOAD_FILENAME}"
 

lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm

@@ -18,6 +18,8 @@ use Moose;
 use Bio::SeqIO;
 use File::Path qw(make_path);
 use File::Basename;
+use File::Copy;
+use File::Temp qw/ tempfile /;
 use Bio::Roary::Exceptions;
 use Bio::Roary::AnalyseGroups;
 use Bio::Tools::GFF;
@@ -154,9 +156,36 @@ sub _extract_nucleotide_regions {
     return $self->_extracted_nucleotide_fasta_file_from_bed_filename;
 }
 
+sub _cleanup_fasta {
+    my ($self,$infile) = @_;
+
+    my($fh, $outfile) = tempfile();
+    return unless ( -e $infile );
+
+    open( my $in,  '<', $infile );
+    open( my $out, '>', $outfile );
+    while ( my $line = <$in> ) {
+        chomp $line;
+        $line =~ s/"//g if ( $line =~ /^>/ );
+
+	if($line =~ /^(>[^:]+)/)
+	{
+		$line = $1;
+	}
+        print $out "$line\n";
+    }
+    close $in;
+    close $out;
+
+    move( $outfile, $infile);
+    return $infile;
+}
+
+
 sub _build_fasta_file {
     my ($self) = @_;
-    return $self->_extract_nucleotide_regions;
+    my $fasta_filename  = $self->_extract_nucleotide_regions;
+    return $self->_cleanup_fasta($fasta_filename);
 }
 
 no Moose;