[med-svn] [roary] 01/03: Imported Upstream version 3.6.6+dfsg

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository roary.

commit 56c4c6f86a7ee3a981f1e4d9e519214c86657caf
Author: Sascha Steinbiss <satta at debian.org>
Date:   Tue Jul 26 09:01:33 2016 +0000

    Imported Upstream version 3.6.6+dfsg
---
 .travis.yml                                        |  2 --
 README.md                                          |  2 +-
 dist.ini                                           |  2 +-
 install_dependencies.sh                            |  2 +-
 lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm | 31 +++++++++++++++++++++-
 5 files changed, 33 insertions(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index d1070e2..5d011ac 100644
--- a/.travis.yml
+++ b/.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"
diff --git a/README.md b/README.md
index 307bc49..0e738d0 100644
--- a/README.md
+++ b/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
diff --git a/dist.ini b/dist.ini
index cd28cc0..df48455 100644
--- a/dist.ini
+++ b/dist.ini
@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.6.5
+version = 3.6.6
 author  = Andrew J. Page <ap13 at sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
diff --git a/install_dependencies.sh b/install_dependencies.sh
index e53cf89..451c683 100755
--- a/install_dependencies.sh
+++ b/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}"
 
diff --git a/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm b/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
index 90ebc5d..6f762dc 100644
--- a/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
+++ b/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;

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