diff -Nru roary-3.11.0+dfsg/debian/changelog roary-3.12.0+dfsg/debian/changelog --- roary-3.11.0+dfsg/debian/changelog 2017-10-11 08:18:22.000000000 +0000 +++ roary-3.12.0+dfsg/debian/changelog 2018-01-26 10:17:54.000000000 +0000 @@ -1,3 +1,18 @@ +roary (3.12.0+dfsg-1) unstable; urgency=medium + + * New upstream release. + + -- Sascha Steinbiss Fri, 26 Jan 2018 11:17:54 +0100 + +roary (3.11.4+dfsg-1) unstable; urgency=medium + + * New upstream release. + * Bump Standards-Version. + * Add patch to use a shebang line of #!/usr/bin/perl, as + mandated by policy 10.4 (>= Standards version 4.1.2) + + -- Sascha Steinbiss Mon, 15 Jan 2018 13:40:31 +0100 + roary (3.11.0+dfsg-1) unstable; urgency=medium * New upstream release. diff -Nru roary-3.11.0+dfsg/debian/control roary-3.12.0+dfsg/debian/control --- roary-3.11.0+dfsg/debian/control 2017-10-11 08:18:22.000000000 +0000 +++ roary-3.12.0+dfsg/debian/control 2018-01-26 10:17:10.000000000 +0000 @@ -35,7 +35,7 @@ mafft, fasttree Build-Depends-Indep: perl -Standards-Version: 4.1.1 +Standards-Version: 4.1.3 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/roary.git Vcs-Git: https://anonscm.debian.org/git/debian-med/roary.git Homepage: http://sanger-pathogens.github.io/Roary/ diff -Nru roary-3.11.0+dfsg/debian/patches/series roary-3.12.0+dfsg/debian/patches/series --- roary-3.11.0+dfsg/debian/patches/series 2017-10-11 08:18:22.000000000 +0000 +++ roary-3.12.0+dfsg/debian/patches/series 2018-01-26 10:17:10.000000000 +0000 @@ -1,2 +1,3 @@ rename_R_script.patch use-dz-starter.patch +use-debian-perl-path.patch diff -Nru roary-3.11.0+dfsg/debian/patches/use-debian-perl-path.patch roary-3.12.0+dfsg/debian/patches/use-debian-perl-path.patch --- roary-3.11.0+dfsg/debian/patches/use-debian-perl-path.patch 1970-01-01 00:00:00.000000000 +0000 +++ roary-3.12.0+dfsg/debian/patches/use-debian-perl-path.patch 2018-01-26 10:17:10.000000000 +0000 @@ -0,0 +1,612 @@ +Description: use Debian Perl path + According to Policy 10.4 (introduced in Standards version 4.1.2) + the shebang at the top of Perl command scripts must be "#!/usr/bin/perl". + This patches changes the included scripts to conform to this. +Author: Sascha Steinbiss +--- a/bin/create_pan_genome ++++ b/bin/create_pan_genome +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::CreatePanGenome; + +--- a/bin/extract_proteome_from_gff ++++ b/bin/extract_proteome_from_gff +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::ExtractProteomeFromGFF; + +--- a/bin/iterative_cdhit ++++ b/bin/iterative_cdhit +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::IterativeCdhit; + +--- a/bin/pan_genome_assembly_statistics ++++ b/bin/pan_genome_assembly_statistics +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::AssemblyStatistics; + +--- a/bin/pan_genome_core_alignment ++++ b/bin/pan_genome_core_alignment +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::RoaryCoreAlignment; + +--- a/bin/pan_genome_post_analysis ++++ b/bin/pan_genome_post_analysis +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::RoaryPostAnalysis; + +--- a/bin/pan_genome_reorder_spreadsheet ++++ b/bin/pan_genome_reorder_spreadsheet +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::RoaryReorderSpreadsheet; + +--- a/bin/parallel_all_against_all_blastp ++++ b/bin/parallel_all_against_all_blastp +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::ParallelAllAgainstAllBlastp; + +--- a/bin/protein_alignment_from_nucleotides ++++ b/bin/protein_alignment_from_nucleotides +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::GeneAlignmentFromNucleotides; + +--- a/bin/query_pan_genome ++++ b/bin/query_pan_genome +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::QueryRoary; + +--- a/bin/roary ++++ b/bin/roary +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::Roary; + +--- a/bin/roary-pan_genome_reorder_spreadsheet ++++ b/bin/roary-pan_genome_reorder_spreadsheet +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::RoaryReorderSpreadsheet; + +--- a/bin/roary-query_pan_genome ++++ b/bin/roary-query_pan_genome +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::QueryRoary; + +--- a/bin/roary-unique_genes_per_sample ++++ b/bin/roary-unique_genes_per_sample +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::UniqueGenesPerSample; + +--- a/bin/transfer_annotation_to_groups ++++ b/bin/transfer_annotation_to_groups +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + package Bio::Roary::Main::TransferAnnotationToGroups; + +--- a/t/00_requires_external.t ++++ b/t/00_requires_external.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + + use Test::Most; + use FindBin; +--- a/t/Bio/Roary/AccessoryBinaryFasta.t ++++ b/t/Bio/Roary/AccessoryBinaryFasta.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/AccessoryClustering.t ++++ b/t/Bio/Roary/AccessoryClustering.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/AnalyseGroups.t ++++ b/t/Bio/Roary/AnalyseGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/AnnotateGroups.t ++++ b/t/Bio/Roary/AnnotateGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/AssemblyStatistics.t ++++ b/t/Bio/Roary/AssemblyStatistics.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ChunkFastaFile.t ++++ b/t/Bio/Roary/ChunkFastaFile.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/CombinedProteome.t ++++ b/t/Bio/Roary/CombinedProteome.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t ++++ b/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t ++++ b/t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t ++++ b/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/QueryRoary.t ++++ b/t/Bio/Roary/CommandLine/QueryRoary.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/Roary.t ++++ b/t/Bio/Roary/CommandLine/Roary.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use File::Path qw( remove_tree); +--- a/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t ++++ b/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t ++++ b/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use File::Path qw( remove_tree); +--- a/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t ++++ b/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t ++++ b/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Data::Dumper; + use Cwd; +--- a/t/Bio/Roary/ContigsToGeneIDsFromGFF.t ++++ b/t/Bio/Roary/ContigsToGeneIDsFromGFF.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/EmblGroups.t ++++ b/t/Bio/Roary/EmblGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Blastp.t ++++ b/t/Bio/Roary/External/Blastp.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Cdhit.t ++++ b/t/Bio/Roary/External/Cdhit.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/CheckTools.t ++++ b/t/Bio/Roary/External/CheckTools.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Mafft.t ++++ b/t/Bio/Roary/External/Mafft.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Makeblastdb.t ++++ b/t/Bio/Roary/External/Makeblastdb.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Mcl.t ++++ b/t/Bio/Roary/External/Mcl.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/External/Prank.t ++++ b/t/Bio/Roary/External/Prank.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t ++++ b/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ExtractProteomeFromGFFs.t ++++ b/t/Bio/Roary/ExtractProteomeFromGFFs.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/FilterFullClusters.t ++++ b/t/Bio/Roary/FilterFullClusters.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/GeneNamesFromGFF.t ++++ b/t/Bio/Roary/GeneNamesFromGFF.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/GroupLabels.t ++++ b/t/Bio/Roary/GroupLabels.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/GroupStatistics.t ++++ b/t/Bio/Roary/GroupStatistics.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/InflateClusters.t ++++ b/t/Bio/Roary/InflateClusters.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/OrderGenes.t ++++ b/t/Bio/Roary/OrderGenes.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t ++++ b/t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/DifferenceBetweenSets.t ++++ b/t/Bio/Roary/Output/DifferenceBetweenSets.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/GroupsMultifastaProtein.t ++++ b/t/Bio/Roary/Output/GroupsMultifastaProtein.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/GroupsMultifastas.t ++++ b/t/Bio/Roary/Output/GroupsMultifastas.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t ++++ b/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use File::Path qw( remove_tree); +--- a/t/Bio/Roary/Output/NumberOfGroups.t ++++ b/t/Bio/Roary/Output/NumberOfGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/Output/QueryGroups.t ++++ b/t/Bio/Roary/Output/QueryGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ParallelAllAgainstAllBlast.t ++++ b/t/Bio/Roary/ParallelAllAgainstAllBlast.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/PrepareInputFiles.t ++++ b/t/Bio/Roary/PrepareInputFiles.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/PresenceAbsenceMatrix.t ++++ b/t/Bio/Roary/PresenceAbsenceMatrix.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/QC/Report.t ++++ b/t/Bio/Roary/QC/Report.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ReformatInputGFFs.t ++++ b/t/Bio/Roary/ReformatInputGFFs.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/ReorderSpreadsheet.t ++++ b/t/Bio/Roary/ReorderSpreadsheet.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/SampleOrder.t ++++ b/t/Bio/Roary/SampleOrder.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/SequenceLengths.t ++++ b/t/Bio/Roary/SequenceLengths.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/SortFasta.t ++++ b/t/Bio/Roary/SortFasta.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/SplitGroups.t ++++ b/t/Bio/Roary/SplitGroups.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Data::Dumper; +--- a/t/Bio/Roary/UniqueGenesPerSample.t ++++ b/t/Bio/Roary/UniqueGenesPerSample.t +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use strict; + use warnings; + use Test::Files; +--- a/t/bin/dummy_blastp ++++ b/t/bin/dummy_blastp +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Getopt::Long; + my ($output_filename,$query,$db,$evalue,$num_threads,$outfmt,$max_target_seqs) ; +--- a/t/bin/dummy_cd-hit ++++ b/t/bin/dummy_cd-hit +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + system("touch output"); + system("touch output.clstr"); + system("touch output.bak.clstr"); +--- a/t/bin/dummy_makeblastdb ++++ b/t/bin/dummy_makeblastdb +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Getopt::Long; + my($output_filename,$dbtype,$in,$logfile,$parse_seqids,$mask_data); +--- a/t/bin/dummy_mcl ++++ b/t/bin/dummy_mcl +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Getopt::Long; + my ($output_filename,$abc_format,$inflation); +--- a/t/bin/dummy_mcxdeblast ++++ b/t/bin/dummy_mcxdeblast +@@ -1,2 +1,2 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + 1; +\ No newline at end of file +--- a/t/bin/dummy_segmasker ++++ b/t/bin/dummy_segmasker +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + use Moose; + use Getopt::Long; + my($output_filename,$dbtype,$in,$logfile,$parse_seqids,$mask_data,$infmt,$outfmt); +--- a/t/dummy_blastp ++++ b/t/dummy_blastp +@@ -1,3 +1,3 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + system("touch results.out"); + 1; +\ No newline at end of file +--- a/t/dummy_cd-hit ++++ b/t/dummy_cd-hit +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + system("touch output"); + system("touch output.clstr"); + system("touch output.bak.clstr"); +--- a/t/dummy_makeblastdb ++++ b/t/dummy_makeblastdb +@@ -1,4 +1,4 @@ +-#!/usr/bin/env perl ++#!/usr/bin/perl + system("touch output_contigs.phr"); + system("touch output_contigs.pin"); + system("touch output_contigs.psq"); diff -Nru roary-3.11.0+dfsg/dist.ini roary-3.12.0+dfsg/dist.ini --- roary-3.11.0+dfsg/dist.ini 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/dist.ini 2018-01-23 13:46:41.000000000 +0000 @@ -3,7 +3,7 @@ license = GPL_3 copyright_holder = Wellcome Trust Sanger Institute copyright_year = 2013 -version = 3.11.0 +version = 3.12.0 main_module = lib/Bio/Roary.pm [MetaResources] diff -Nru roary-3.11.0+dfsg/install_dependencies.sh roary-3.12.0+dfsg/install_dependencies.sh --- roary-3.11.0+dfsg/install_dependencies.sh 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/install_dependencies.sh 2018-01-23 13:46:41.000000000 +0000 @@ -11,7 +11,7 @@ PARALLEL_DOWNLOAD_FILENAME="parallel-${PARALLEL_VERSION}.tar.bz2" PARALLEL_URL="http://ftp.gnu.org/gnu/parallel/${PARALLEL_DOWNLOAD_FILENAME}" -BEDTOOLS_VERSION="2.26.0" +BEDTOOLS_VERSION="2.27.1" BEDTOOLS_DOWNLOAD_FILENAME="bedtools-${BEDTOOLS_VERSION}.tar.gz" BEDTOOLS_URL="https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/${BEDTOOLS_DOWNLOAD_FILENAME}" diff -Nru roary-3.11.0+dfsg/lib/Bio/Roary/BedFromGFFRole.pm roary-3.12.0+dfsg/lib/Bio/Roary/BedFromGFFRole.pm --- roary-3.11.0+dfsg/lib/Bio/Roary/BedFromGFFRole.pm 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/lib/Bio/Roary/BedFromGFFRole.pm 2018-01-23 13:46:41.000000000 +0000 @@ -13,7 +13,7 @@ use Bio::Tools::GFF; has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => '(CDS|ncRNA|tRNA|tmRNA|rRNA)' ); -has 'min_gene_size_in_nucleotides' => ( is => 'ro', isa => 'Int', default => 120 ); +has 'min_gene_size_in_nucleotides' => ( is => 'ro', isa => 'Int', default => 18 ); has 'output_directory' => ( is => 'ro', isa => 'Str', default => '.' ); sub _bed_output_filename { diff -Nru roary-3.11.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm roary-3.12.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm --- roary-3.11.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/lib/Bio/Roary/CommandLine/Roary.pm 2018-01-23 13:46:41.000000000 +0000 @@ -21,6 +21,7 @@ use File::Path qw(make_path); use Cwd qw(abs_path getcwd); use File::Temp; +use File::Basename; extends 'Bio::Roary::CommandLine::Common'; has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 ); @@ -41,6 +42,7 @@ has 'output_multifasta_files' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'perc_identity' => ( is => 'rw', isa => 'Num', default => 95 ); has 'dont_delete_files' => ( is => 'rw', isa => 'Bool', default => 0 ); +has 'check_dependancies' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'dont_create_rplots' => ( is => 'rw', isa => 'Bool', default => 1 ); has 'dont_run_qc' => ( is => 'rw', isa => 'Bool', default => 0 ); has 'dont_split_groups' => ( is => 'rw', isa => 'Bool', default => 0 ); @@ -120,21 +122,39 @@ Pubmed: 26198102\n\n"; $self->help($help) if ( defined($help) ); - if( $self->help ) + if( $self->help ) { print $self->usage_text; return; } + + if ( defined($verbose) ) { + $self->verbose($verbose); + $self->logger->level(10000); + } - if ($check_dependancies) { + $self->check_dependancies($check_dependancies) if ( defined($check_dependancies) ); + if ($self->check_dependancies) { my $check_tools = Bio::Roary::External::CheckTools->new(); $check_tools->check_all_tools; $self->logger->error( "Roary version " . $self->_version() ); + + if( @{ $self->args } < 1 ) + { + return; + } } - if ( defined($verbose) ) { - $self->verbose($verbose); - $self->logger->level(10000); + if ( @{ $self->args } < 2 ) { + $self->logger->error("Error: You need to provide at least 2 files to build a pan genome"); + die $self->usage_text; + } + my %basenames; + foreach my $string (@{$self->args}) { + my($base, $path, $suf) = fileparse($string); + next unless $basenames{$base}++; + $self->logger->error("Error: GFF files must have unique basenames."); + die $self->usage_text; } if ( @{ $self->args } < 2 ) { @@ -246,8 +266,8 @@ sub run { my ($self) = @_; - - return if($self->version || $self->help); + + return if($self->version || $self->help || ($self->check_dependancies && @{$self->fasta_files} < 1) ); $self->_setup_output_directory; diff -Nru roary-3.11.0+dfsg/lib/Bio/Roary/External/CheckTools.pm roary-3.12.0+dfsg/lib/Bio/Roary/External/CheckTools.pm --- roary-3.11.0+dfsg/lib/Bio/Roary/External/CheckTools.pm 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/lib/Bio/Roary/External/CheckTools.pm 2018-01-23 13:46:41.000000000 +0000 @@ -57,28 +57,30 @@ }, 'mafft' => { GETVER => "mafft --version < /dev/null 2>&1", - REGEXP => qr/(\d+\.\d+) /, + REGEXP => qr/(\d+\.\d+)/, NEEDED => 1, }, 'kraken' => { - GETVER => "kraken --version | head -n 1", - REGEXP => qr/(\d+\.\d+\.\d+.*)/, + GETVER => "kraken -v | head -n 1", + REGEXP => qr/(\d+\.\d+\.*\d*.*)/, NEEDED => 0, }, 'kraken-report' => { - GETVER => "kraken-report --version | head -n 1", - REGEXP => qr/(\d+\.\d+\.\d+.*)/, + GETVER => "kraken-report -v | head -n 1", + REGEXP => qr/(\d+\.\d+\.*\d*.*)/, NEEDED => 0, - }, + }, 'Rscript' => { GETVER => "Rscript --version 2>&1 | head -n 1", REGEXP => qr/R scripting front-end version ($BIDEC)/, MINVER => "3", NEEDED => 0, }, - - # prank version also performs an update check so cant use it - 'prank' => { NEEDED => 0 }, + 'prank' => { + GETVER => "prank | grep -m 1 ^prank", + REGEXP => qr/prank v.(\d+)/, + NEEDED => 0, + }, # now just the standard unix tools we need 'grep' => { NEEDED => 1 }, diff -Nru roary-3.11.0+dfsg/lib/Bio/Roary/ExtractProteomeFromGFF.pm roary-3.12.0+dfsg/lib/Bio/Roary/ExtractProteomeFromGFF.pm --- roary-3.11.0+dfsg/lib/Bio/Roary/ExtractProteomeFromGFF.pm 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/lib/Bio/Roary/ExtractProteomeFromGFF.pm 2018-01-23 13:46:41.000000000 +0000 @@ -132,8 +132,13 @@ open( my $in, '<', $infile ); open( my $out, '>', $outfile ); while ( my $line = <$in> ) { - chomp $line; - $line =~ s/"//g if ( $line =~ /^>/ ); + chomp $line; + if ( $line =~ /^>/ ) + { + $line =~ s/"//g; + # newer versions of Bedtools add (-) or (+) to the end of the sequence name, remove them + $line =~ s!\([-+]\)!!; + } if($line =~ /^(>[^:]+)/) { diff -Nru roary-3.11.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm roary-3.12.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm --- roary-3.11.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm 2018-01-23 13:46:41.000000000 +0000 @@ -177,7 +177,12 @@ open( my $out, '>', $outfile ); while ( my $line = <$in> ) { chomp $line; - $line =~ s/"//g if ( $line =~ /^>/ ); + if ( $line =~ /^>/ ) + { + $line =~ s/"//g ; + # newer versions of Bedtools add (-) or (+) to the end of the sequence name, remove them + $line =~ s!\([-+]\)!!; + } if($line =~ /^(>[^:]+)/) { diff -Nru roary-3.11.0+dfsg/README.md roary-3.12.0+dfsg/README.md --- roary-3.11.0+dfsg/README.md 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/README.md 2018-01-23 13:46:41.000000000 +0000 @@ -17,7 +17,6 @@ * CentOS/RedHat * Bioconda - OSX/Linux * Galaxy -* Homebrew/Linuxbrew - OSX/Linux * Guix - Linux * Virtual Machine - OSX/Linux/Windows * Docker - OSX/Linux/Windows/Cloud @@ -40,10 +39,7 @@ ``` ### Ubuntu 12.04 -Some of the software versions in apt are quite old so follow the instructions for [LinuxBrew](http://brew.sh/linuxbrew/) below. - -## CentOS/RedHat -To install the dependancies, the easiest way is to install [LinuxBrew](http://brew.sh/linuxbrew/) using the steps for Fedora, then follow the steps below for installing Roary on LinuxBrew. +Some of the software versions in apt are quite old so follow the instructions for Bioconda below. ## Bioconda - OSX/Linux Install conda. Then install bioconda and roary: @@ -57,21 +53,11 @@ ``` ## Galaxy -Roary is available from the Galaxy toolshed ( as is Prokka). - -## Homebrew/Linuxbrew - OSX/Linux -Assuming you have [homebrew](http://brew.sh/) (OSX) or [linuxbrew](http://brew.sh/linuxbrew/) (Linux) setup and installed on your system: - -``` -brew tap homebrew/science -brew install bedtools cd-hit blast mcl parallel prank mafft fasttree cpanm -sudo cpanm -f Bio::Roary -``` +Roary is available from the Galaxy toolshed ( as is Prokka ). ## GNU Guix -Roary is not included in version in [Guix](https://www.gnu.org/software/guix) 0.11.0 so `guix pull` is currently required before installation. +Roary is included in [Guix](https://www.gnu.org/software/guix) and can be installed in the usual way: ``` -guix pull guix package --install roary ``` @@ -123,14 +109,14 @@ ``` ## Ancient systems and versions of perl -The code will not work with perl 5.8 or below (pre-modern perl). We no longer test against 5.10 (released 2007). If you're running a very old verison of Linux, you're also in trouble. +The code will not work with perl 5.8 or below (pre-modern perl). We no longer test against 5.10 (released 2007) or 5.12 (released 2010). If you're running a very old verison of Linux, you're also in trouble. # Versions of software we test against -* Perl 5.14, 5.16, 5.20, 5.24 -* cdhit 4.6.1 -* ncbi blast+ 2.4.0 +* Perl 5.14, 5.26 +* cdhit 4.6.8 +* ncbi blast+ 2.6.0 * mcl 14-137 -* bedtools 2.26.0 -* prank 130410 -* GNU parallel 20130922, 20160722, 20150122 +* bedtools 2.27.1 +* prank 140603 +* GNU parallel 20170822, 20160722 * FastTree 2.1.9 diff -Nru roary-3.11.0+dfsg/t/data/example_annotation_2.gff roary-3.12.0+dfsg/t/data/example_annotation_2.gff --- roary-3.11.0+dfsg/t/data/example_annotation_2.gff 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/example_annotation_2.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 ID=abc_00010;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 ID=abc_00011;inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 ID=abc_00012;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 ID=abc_00014;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 ID=abc_00015;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 ID=abc_00016;eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=abc_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.0+dfsg/t/data/example_annotation.gff roary-3.12.0+dfsg/t/data/example_annotation.gff --- roary-3.11.0+dfsg/t/data/example_annotation.gff 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/example_annotation.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 ID=abc_00010;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 ID=abc_00011;inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 ID=abc_00012;inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 ID=abc_00013;inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 ID=abc_00014;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 ID=abc_00015;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 ID=abc_00016;eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=abc_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.0+dfsg/t/data/genbank_gbff/genbank2.gff roary-3.12.0+dfsg/t/data/genbank_gbff/genbank2.gff --- roary-3.11.0+dfsg/t/data/genbank_gbff/genbank2.gff 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/genbank_gbff/genbank2.gff 2018-01-23 13:46:41.000000000 +0000 @@ -17,9 +17,9 @@ CVBR01000001 GenBank mRNA 4176 6542 . + 1 ID=ERS325340_00004.t01;Parent=ERS325340_00004 CVBR01000001 GenBank CDS 4176 6542 . + 1 ID=ERS325340_00004.p01;Parent=ERS325340_00004.t01;Dbxref=GI:804333229;eC_number=6.3.2.-;Name=sspH2;codon_start=1;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002244314.1;locus_tag=ERS325340_00004;product=secreted effector protein;protein_id=CQU31395.1;transl_table=11;translation=length.788 CVBR01000001 GenBank exon 4176 6542 . + 1 Parent=ERS325340_00004.t01 -CVBR01000001 GenBank gene 7163 7239 . - 1 ID=ERS325340_00005;Name=ERS325340_00005 -CVBR01000001 GenBank tRNA 7163 7239 . - 1 ID=ERS325340_00005.r01;Parent=ERS325340_00005;Name=ERS325340_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro -CVBR01000001 GenBank exon 7163 7239 . - 1 Parent=ERS325340_00005.r01;Name=ERS325340_00005 +CVBR01000001 GenBank gene 7163 7180 . - 1 ID=ERS325340_00005;Name=ERS325340_00005 +CVBR01000001 GenBank tRNA 7163 7180 . - 1 ID=ERS325340_00005.r01;Parent=ERS325340_00005;Name=ERS325340_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro +CVBR01000001 GenBank exon 7163 7180 . - 1 Parent=ERS325340_00005.r01;Name=ERS325340_00005 ##FASTA >CVBR01000001 TAGAGCGCAGTATCCGGCTGGCGCAGGAGAAATAAGACCCTGACGGCCCGGTGGCGTGGC diff -Nru roary-3.11.0+dfsg/t/data/genbank_gbff/genbank3.gff roary-3.12.0+dfsg/t/data/genbank_gbff/genbank3.gff --- roary-3.11.0+dfsg/t/data/genbank_gbff/genbank3.gff 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/genbank_gbff/genbank3.gff 2018-01-23 13:46:41.000000000 +0000 @@ -17,9 +17,9 @@ CVBT01000001 GenBank mRNA 4180 6546 . + 1 ID=ERS325326_00004.t01;Parent=ERS325326_00004 CVBT01000001 GenBank CDS 4180 6546 . + 1 ID=ERS325326_00004.p01;Parent=ERS325326_00004.t01;Dbxref=GI:804342842;eC_number=6.3.2.-;Name=sspH2;codon_start=1;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002244314.1;locus_tag=ERS325326_00004;product=secreted effector protein;protein_id=CQU32561.1;transl_table=11;translation=length.788 CVBT01000001 GenBank exon 4180 6546 . + 1 Parent=ERS325326_00004.t01 -CVBT01000001 GenBank gene 7167 7243 . - 1 ID=ERS325326_00005;Name=ERS325326_00005 -CVBT01000001 GenBank tRNA 7167 7243 . - 1 ID=ERS325326_00005.r01;Parent=ERS325326_00005;Name=ERS325326_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro -CVBT01000001 GenBank exon 7167 7243 . - 1 Parent=ERS325326_00005.r01;Name=ERS325326_00005 +CVBT01000001 GenBank gene 7167 7184 . - 1 ID=ERS325326_00005;Name=ERS325326_00005 +CVBT01000001 GenBank tRNA 7167 7184 . - 1 ID=ERS325326_00005.r01;Parent=ERS325326_00005;Name=ERS325326_00005;inference=COORDINATES: profile:Aragorn:1.2.36;product=tRNA-Pro +CVBT01000001 GenBank exon 7167 7184 . - 1 Parent=ERS325326_00005.r01;Name=ERS325326_00005 ##FASTA >CVBT01000001 GTGATAGAGCGCAGTATCCGGCTGGCGCAGGAGAAATAAGACCCTGACGGCCCGGTGGCG diff -Nru roary-3.11.0+dfsg/t/data/locus_tag_gffs/query_1.gff roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_1.gff --- roary-3.11.0+dfsg/t/data/locus_tag_gffs/query_1.gff 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_1.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=abc_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=abc_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=abc_00013;product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=abc_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=abc_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.0+dfsg/t/data/locus_tag_gffs/query_2.gff roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_2.gff --- roary-3.11.0+dfsg/t/data/locus_tag_gffs/query_2.gff 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_2.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag="zzz_00010";product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag="zzz_00011";product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag="zzz_00012";product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag="zzz_00013";product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag="zzz_00013";product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag="zzz_00014";product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag="zzz_00015";product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag="zzz_00016";product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.0+dfsg/t/data/locus_tag_gffs/query_3.gff roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_3.gff --- roary-3.11.0+dfsg/t/data/locus_tag_gffs/query_3.gff 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/locus_tag_gffs/query_3.gff 2018-01-23 13:46:41.000000000 +0000 @@ -12,7 +12,7 @@ abc|SC|contig000001 Prodigal:2.60 CDS 9419 9646 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=xxx_00010;product=hypothetical protein;protein_id=gnl|SC|abc_00010 abc|SC|contig000001 Prodigal:2.60 CDS 9952 10899 . - 0 inference=ab initio prediction:Prodigal:2.60,protein motif:Pfam:PF03595.11;locus_tag=xxx_00011;product=C4-dicarboxylate transporter/malic acid transport protein;protein_id=gnl|SC|abc_00011 abc|SC|contig000001 Prodigal:2.60 CDS 11148 11336 . + 0 inference=ab initio prediction:Prodigal:2.60;locus_tag=xxx_00012;product=hypothetical protein;protein_id=gnl|SC|abc_00012 -abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11878 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=xxx_00013;product=tRNA-Arg(tct) +abc|SC|contig000001 Aragorn:1.2.34 tRNA 11803 11820 . - 0 inference=COORDINATES:profile:Aragorn:1.2.34;locus_tag=xxx_00013;product=tRNA-Arg(tct) abc|SC|contig000001 Prodigal:2.60 CDS 12241 12375 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=xxx_00014;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00014 abc|SC|contig000001 Prodigal:2.60 CDS 12432 12566 . + 0 inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:P11699,protein motif:Pfam:PF05480.5;locus_tag=xxx_00015;product=Gonococcal growth inhibitor III,Staphylococcus haemolytic protein;protein_id=gnl|SC|abc_00015 abc|SC|contig000001 Prodigal:2.60 CDS 12699 13385 . + 0 eC_number=3.-.-.-;gene=yfnB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:UniProtKB:O06480,protein motif:CLUSTERS:PRK09449,protein motif:TIGRFAMs:TIGR02254,protein motif:Pfam:PF00702.1;locus_tag=xxx_00016;product=Putative HAD-hydrolase yfnB,dUMP phosphatase,HAD hydrolase,haloacid dehalogenase-like hydrolase;protein_id=gnl|SC|abc_00016 diff -Nru roary-3.11.0+dfsg/t/data/real_data_1.gff roary-3.12.0+dfsg/t/data/real_data_1.gff --- roary-3.11.0+dfsg/t/data/real_data_1.gff 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/real_data_1.gff 2018-01-23 13:46:41.000000000 +0000 @@ -2,7 +2,7 @@ ##sequence-region ERS111111|SC|contig000020 1 92255 ERS111111|SC|contig000020 Prodigal:2.60 CDS 241 921 . - 0 ID=11111_1#11_04055;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145956.2,protein motif:Pfam:PF07108.5;locus_tag=11111_1#11_04055;product=pathogenicity island-encoded protein A,PipA protein;protein_id=gnl|SC|11111_1#11_04055 ERS111111|SC|contig000020 Prodigal:2.60 CDS 1144 2019 . - 0 ID=11111_1#11_04056;gene=pipB2_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145957.1,similar to AA sequence:UniProtKB:Q8ZMM8,protein motif:CLUSTERS:PRK15197,protein motif:Cdd:COG5351,protein motif:Pfam:PF00805.16;locus_tag=11111_1#11_04056;product=secreted effector protein,Type III effector pipB2,secreted effector protein PipB,Uncharacterized protein conserved in bacteria,Pentapeptide repeats (8 copies);protein_id=gnl|SC|11111_1#11_04056 -ERS111111|SC|contig000020 Infernal:1.1 ncRNA 2139 2237 . + 0 ID=11111_1#11_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04057;product=isrI +ERS111111|SC|contig000020 Infernal:1.1 ncRNA 2139 2156 . + 0 ID=11111_1#11_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04057;product=isrI ERS111111|SC|contig000020 Prodigal:2.60 CDS 2567 2908 . - 0 ID=11111_1#11_04058;gene=sigE;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145959.1,similar to AA sequence:UniProtKB:O30917,protein motif:CLUSTERS:PRK15202,protein motif:Pfam:PF07824.6;locus_tag=11111_1#11_04058;product=chaperone protein SigE,Chaperone protein sigE,type III secretion chaperone protein SigE,Type III secretion chaperone domain;protein_id=gnl|SC|11111_1#11_04058 ERS111111|SC|contig000020 Prodigal:2.60 CDS 2925 4610 . - 0 ID=11111_1#11_04059;eC_number=3.1.3.-,3.1.3.-;gene=sopB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145960.1,similar to AA sequence:UniProtKB:O30916,protein motif:CLUSTERS:PRK15378,protein motif:Pfam:PF05925.6;locus_tag=11111_1#11_04059;product=inositol phosphate phosphatase SopB,Inositol phosphate phosphatase sopB,inositol phosphate phosphatase SopB,Enterobacterial virulence protein IpgD;protein_id=gnl|SC|11111_1#11_04059 ERS111111|SC|contig000020 Prodigal:2.60 CDS 5332 6801 . - 0 ID=11111_1#11_04060;eC_number=3.4.-.-;gene=pepD_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002215025.1,similar to AA sequence:UniProtKB:Q8G6Z9,protein motif:Pfam:PF03577.9;locus_tag=11111_1#11_04060;product=peptidase family C69,Dipeptidase,Peptidase family C69;protein_id=gnl|SC|11111_1#11_04060 @@ -47,7 +47,7 @@ ERS111111|SC|contig000020 Prodigal:2.60 CDS 44992 45684 . + 0 ID=11111_1#11_04099;gene=yiiy;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216068.1,similar to AA sequence:UniProtKB:Q934G3,protein motif:CLUSTERS:PRK09980,protein motif:Cdd:COG3203,protein motif:Pfam:PF06178.7;locus_tag=11111_1#11_04099;product=outer membrane protein,Oligogalacturonate-specific porin kdgM precursor,outer membrane porin L,Outer membrane protein (porin),Oligogalacturonate-specific porin protein (KdgM);protein_id=gnl|SC|11111_1#11_04099 ERS111111|SC|contig000020 Prodigal:2.60 CDS 45967 47247 . + 0 ID=11111_1#11_04100;gene=nanT_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570893.1,similar to AA sequence:UniProtKB:P41036,protein motif:CLUSTERS:PRK12307,protein motif:Cdd:COG2814,protein motif:TIGRFAMs:TIGR00891,protein motif:Pfam:PF00083.18;locus_tag=11111_1#11_04100;product=putative sialic acid transporter,Sialic acid permease,putative sialic acid transporter,Arabinose efflux permease,MFS transporter%2C sialate:H+ symporter (SHS) family,Sugar (and other) transporter;protein_id=gnl|SC|11111_1#11_04100 ERS111111|SC|contig000020 Prodigal:2.60 CDS 47261 48364 . + 0 ID=11111_1#11_04101;eC_number=1.1.1.292;gene=yjhC;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216069.1,similar to AA sequence:UniProtKB:Q2I8V6,protein motif:CLUSTERS:PRK11579,protein motif:Pfam:PF01408.16;locus_tag=11111_1#11_04101;product=dehydrogenase-like protein,1%2C5-anhydro-D-fructose reductase,putative oxidoreductase,Oxidoreductase family%2C NAD-binding Rossmann fold;protein_id=gnl|SC|11111_1#11_04101 -ERS111111|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48788 . - 0 ID=11111_1#11_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=11111_1#11_04102;product=tRNA-Ser(gga) +ERS111111|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48718 . - 0 ID=11111_1#11_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=11111_1#11_04102;product=tRNA-Ser(gga) ERS111111|SC|contig000020 Prodigal:2.60 CDS 49024 49962 . + 0 ID=11111_1#11_04103;eC_number=1.1.1.79;gene=ghrA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729856.1,similar to AA sequence:UniProtKB:Q8ZQ30,protein motif:CLUSTERS:PRK15469,protein motif:Cdd:COG1932,protein motif:TIGRFAMs:TIGR01327,protein motif:Pfam:PF02826.13;locus_tag=11111_1#11_04103;product=2-hydroxyacid dehydrogenase,Glyoxylate/hydroxypyruvate reductase A,bifunctional glyoxylate/hydroxypyruvate reductase A,Phosphoserine aminotransferase,phosphoglycerate dehydrogenase,D-isomer specific 2-hydroxyacid dehydrogenase%2C NAD binding domain;protein_id=gnl|SC|11111_1#11_04103 ERS111111|SC|contig000020 Prodigal:2.60 CDS 50047 50784 . + 0 ID=11111_1#11_04104;eC_number=3.1.3.-;gene=ycdX;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570887.1,similar to AA sequence:UniProtKB:P75914,protein motif:CLUSTERS:PRK09248,protein motif:Cdd:COG1387,protein motif:TIGRFAMs:TIGR01856,protein motif:Pfam:PF02811.13;locus_tag=11111_1#11_04104;product=putative hydrolase,Probable phosphatase YcdX,putative hydrolase,Histidinol phosphatase and related hydrolases of the PHP family,histidinol phosphate phosphatase%2C HisJ family,PHP domain;protein_id=gnl|SC|11111_1#11_04104 ERS111111|SC|contig000020 Prodigal:2.60 CDS 50808 51362 . + 0 ID=11111_1#11_04105;gene=ycdY;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002146908.1,similar to AA sequence:UniProtKB:P75915,protein motif:CLUSTERS:PRK11621,protein motif:Cdd:COG3381,protein motif:Pfam:PF02613.9;locus_tag=11111_1#11_04105;product=chaperone%2C TorD family,Chaperone protein YcdY,twin-argninine leader-binding protein DmsD,Uncharacterized component of anaerobic dehydrogenases,Nitrate reductase delta subunit;protein_id=gnl|SC|11111_1#11_04105 @@ -72,7 +72,7 @@ ERS111111|SC|contig000020 Prodigal:2.60 CDS 67715 68767 . + 0 ID=11111_1#11_04124;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087420.1,protein motif:CLUSTERS:PRK00142,protein motif:Cdd:COG2210,protein motif:Pfam:PF00581.14;locus_tag=11111_1#11_04124;product=Rhodanese-like sulfurtransferase,putative rhodanese-related sulfurtransferase,Uncharacterized conserved protein,Rhodanese-like domain;protein_id=gnl|SC|11111_1#11_04124 ERS111111|SC|contig000020 Prodigal:2.60 CDS 68819 69394 . - 0 ID=11111_1#11_04125;gene=yceI_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087865.1,similar to AA sequence:UniProtKB:P0A8X2,protein motif:CLUSTERS:PRK03757,protein motif:Cdd:COG2353,protein motif:Pfam:PF04264.7;locus_tag=11111_1#11_04125;product=YceI protein,hypothetical protein,hypothetical protein,Uncharacterized conserved protein,YceI-like domain;protein_id=gnl|SC|11111_1#11_04125 ERS111111|SC|contig000020 Prodigal:2.60 CDS 69391 69795 . - 0 ID=11111_1#11_04126;gene=yceJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_005212184.1,similar to AA sequence:UniProtKB:P75925,protein motif:CLUSTERS:PRK11513,protein motif:Pfam:PF00033.13;locus_tag=11111_1#11_04126;product=cytochrome b561-like protein 2,Cytochrome b561 homolog 2,cytochrome b561,Cytochrome b(N-terminal)/b6/petB;protein_id=gnl|SC|11111_1#11_04126 -ERS111111|SC|contig000020 Prodigal:2.60 CDS 70226 70339 . - 0 ID=11111_1#11_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=11111_1#11_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|11111_1#11_04127 +ERS111111|SC|contig000020 Prodigal:2.60 CDS 70226 70243 . - 0 ID=11111_1#11_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=11111_1#11_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|11111_1#11_04127 ERS111111|SC|contig000020 Prodigal:2.60 CDS 70380 71498 . - 0 ID=11111_1#11_04128;eC_number=1.5.3.1,1.5.3.-;gene=solA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729880.1,similar to AA sequence:UniProtKB:P40874,protein motif:CLUSTERS:PRK11259,protein motif:Cdd:COG4121,protein motif:TIGRFAMs:TIGR01377,protein motif:Pfam:PF01266.18;locus_tag=11111_1#11_04128;product=sarcosine oxidase,N-methyl-L-tryptophan oxidase,N-methyltryptophan oxidase,Uncharacterized conserved protein,sarcosine oxidase%2C monomeric form,FAD dependent oxidoreductase;protein_id=gnl|SC|11111_1#11_04128 ERS111111|SC|contig000020 Prodigal:2.60 CDS 71611 71865 . - 0 ID=11111_1#11_04129;gene=bssS;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570863.1,protein motif:CLUSTERS:PRK12301;locus_tag=11111_1#11_04129;product=biofilm formation regulatory protein BssS,biofilm formation regulatory protein BssS;protein_id=gnl|SC|11111_1#11_04129 ERS111111|SC|contig000020 Prodigal:2.60 CDS 72155 72418 . - 0 ID=11111_1#11_04130;gene=dinI_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729882.1,similar to AA sequence:UniProtKB:P0ABR1,protein motif:CLUSTERS:PRK10597,protein motif:Pfam:PF06183.7;locus_tag=11111_1#11_04130;product=damage-inducible protein,DNA-damage-inducible protein I,DNA damage-inducible protein I,DinI-like family;protein_id=gnl|SC|11111_1#11_04130 @@ -98,7 +98,7 @@ ERS111111|SC|contig000020 Prodigal:2.60 CDS 88429 89379 . + 0 ID=11111_1#11_04150;eC_number=3.2.1.-;gene=flgJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729902.1,similar to AA sequence:UniProtKB:P15931,protein motif:CLUSTERS:PRK05684,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02541,protein motif:Pfam:PF01832.14;locus_tag=11111_1#11_04150;product=flagellar protein FlgJ,Peptidoglycan hydrolase flgJ,flagellar rod assembly protein/muramidase FlgJ,Rod binding protein,flagellar rod assembly protein/muramidase FlgJ,Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase;protein_id=gnl|SC|11111_1#11_04150 ERS111111|SC|contig000020 Prodigal:2.60 CDS 89444 91105 . + 0 ID=11111_1#11_04151;gene=flgK;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729903.1,similar to AA sequence:UniProtKB:P0A1J5,protein motif:CLUSTERS:PRK08147,protein motif:Cdd:COG1749,protein motif:TIGRFAMs:TIGR02492,protein motif:Pfam:PF06429.7;locus_tag=11111_1#11_04151;product=flagellar hook-associated protein 1,Flagellar hook-associated protein 1,flagellar hook-associated protein FlgK,Flagellar hook protein FlgE,flagellar hook-associated protein FlgK,Domain of unknown function (DUF1078);protein_id=gnl|SC|11111_1#11_04151 ERS111111|SC|contig000020 Prodigal:2.60 CDS 91120 92073 . + 0 ID=11111_1#11_04152;gene=flgL;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729904.1,similar to AA sequence:UniProtKB:P16326,protein motif:CLUSTERS:PRK08027,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02550,protein motif:Pfam:PF00669.14;locus_tag=11111_1#11_04152;product=flagellar hook-associated protein 3,Hook-filament junction protein,flagellar hook-associated protein FlgL,Rod binding protein,flagellar hook-associated protein 3,Bacterial flagellin N-terminal helical region;protein_id=gnl|SC|11111_1#11_04152 -ERS111111|SC|contig000020 Infernal:1.1 ncRNA 92162 92255 . + 0 ID=11111_1#11_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04153;product=STnc490k +ERS111111|SC|contig000020 Infernal:1.1 ncRNA 92162 92179 . + 0 ID=11111_1#11_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=11111_1#11_04153;product=STnc490k ##FASTA >ERS111111|SC|contig000020 TATCCGGGCAGCCCGTTTACGGGCCGTAAGTAACGAAGTTTGATGCAAATGTCAGATCGT diff -Nru roary-3.11.0+dfsg/t/data/real_data_2.gff roary-3.12.0+dfsg/t/data/real_data_2.gff --- roary-3.11.0+dfsg/t/data/real_data_2.gff 2017-10-10 16:03:00.000000000 +0000 +++ roary-3.12.0+dfsg/t/data/real_data_2.gff 2018-01-23 13:46:41.000000000 +0000 @@ -2,7 +2,7 @@ ##sequence-region ERS222222|SC|contig000020 1 92255 ERS222222|SC|contig000020 Prodigal:2.60 CDS 241 921 . - 0 ID=22222_2#22_04055;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145956.2,protein motif:Pfam:PF07108.5;locus_tag=22222_2#22_04055;product=pathogenicity island-encoded protein A,PipA protein;protein_id=gnl|SC|22222_2#22_04055 ERS222222|SC|contig000020 Prodigal:2.60 CDS 1144 2019 . - 0 ID=22222_2#22_04056;gene=pipB2_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145957.1,similar to AA sequence:UniProtKB:Q8ZMM8,protein motif:CLUSTERS:PRK15197,protein motif:Cdd:COG5351,protein motif:Pfam:PF00805.16;locus_tag=22222_2#22_04056;product=secreted effector protein,Type III effector pipB2,secreted effector protein PipB,Uncharacterized protein conserved in bacteria,Pentapeptide repeats (8 copies);protein_id=gnl|SC|22222_2#22_04056 -ERS222222|SC|contig000020 Infernal:1.1 ncRNA 2139 2237 . + 0 ID=22222_2#22_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=22222_2#22_04057;product=isrI +ERS222222|SC|contig000020 Infernal:1.1 ncRNA 2139 2156 . + 0 ID=22222_2#22_04057;inference=COORDINATES:profile:Infernal:1.1;locus_tag=22222_2#22_04057;product=isrI ERS222222|SC|contig000020 Prodigal:2.60 CDS 2567 2908 . - 0 ID=22222_2#22_04058;gene=sigE;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145959.1,similar to AA sequence:UniProtKB:O30917,protein motif:CLUSTERS:PRK15202,protein motif:Pfam:PF07824.6;locus_tag=22222_2#22_04058;product=chaperone protein SigE,Chaperone protein sigE,type III secretion chaperone protein SigE,Type III secretion chaperone domain;protein_id=gnl|SC|22222_2#22_04058 ERS222222|SC|contig000020 Prodigal:2.60 CDS 2925 4610 . - 0 ID=22222_2#22_04059;eC_number=3.1.3.-,3.1.3.-;gene=sopB;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002145960.1,similar to AA sequence:UniProtKB:O30916,protein motif:CLUSTERS:PRK15378,protein motif:Pfam:PF05925.6;locus_tag=22222_2#22_04059;product=inositol phosphate phosphatase SopB,Inositol phosphate phosphatase sopB,inositol phosphate phosphatase SopB,Enterobacterial virulence protein IpgD;protein_id=gnl|SC|22222_2#22_04059 ERS222222|SC|contig000020 Prodigal:2.60 CDS 5332 6801 . - 0 ID=22222_2#22_04060;eC_number=3.4.-.-;gene=pepD_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002215025.1,similar to AA sequence:UniProtKB:Q8G6Z9,protein motif:Pfam:PF03577.9;locus_tag=22222_2#22_04060;product=peptidase family C69,Dipeptidase,Peptidase family C69;protein_id=gnl|SC|22222_2#22_04060 @@ -47,7 +47,7 @@ ERS222222|SC|contig000020 Prodigal:2.60 CDS 44992 45684 . + 0 ID=22222_2#22_04099;gene=yiiy;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216068.1,similar to AA sequence:UniProtKB:Q934G3,protein motif:CLUSTERS:PRK09980,protein motif:Cdd:COG3203,protein motif:Pfam:PF06178.7;locus_tag=22222_2#22_04099;product=outer membrane protein,Oligogalacturonate-specific porin kdgM precursor,outer membrane porin L,Outer membrane protein (porin),Oligogalacturonate-specific porin protein (KdgM);protein_id=gnl|SC|22222_2#22_04099 ERS222222|SC|contig000020 Prodigal:2.60 CDS 45967 47247 . + 0 ID=22222_2#22_04100;gene=nanT_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570893.1,similar to AA sequence:UniProtKB:P41036,protein motif:CLUSTERS:PRK12307,protein motif:Cdd:COG2814,protein motif:TIGRFAMs:TIGR00891,protein motif:Pfam:PF00083.18;locus_tag=22222_2#22_04100;product=putative sialic acid transporter,Sialic acid permease,putative sialic acid transporter,Arabinose efflux permease,MFS transporter%2C sialate:H+ symporter (SHS) family,Sugar (and other) transporter;protein_id=gnl|SC|22222_2#22_04100 ERS222222|SC|contig000020 Prodigal:2.60 CDS 47261 48364 . + 0 ID=22222_2#22_04101;eC_number=1.1.1.292;gene=yjhC;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216069.1,similar to AA sequence:UniProtKB:Q2I8V6,protein motif:CLUSTERS:PRK11579,protein motif:Pfam:PF01408.16;locus_tag=22222_2#22_04101;product=dehydrogenase-like protein,1%2C5-anhydro-D-fructose reductase,putative oxidoreductase,Oxidoreductase family%2C NAD-binding Rossmann fold;protein_id=gnl|SC|22222_2#22_04101 -ERS222222|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48788 . - 0 ID=22222_2#22_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=22222_2#22_04102;product=tRNA-Ser(gga) +ERS222222|SC|contig000020 Aragorn:1.2.36 tRNA 48701 48718 . - 0 ID=22222_2#22_04102;inference=COORDINATES:profile:Aragorn:1.2.36;locus_tag=22222_2#22_04102;product=tRNA-Ser(gga) ERS222222|SC|contig000020 Prodigal:2.60 CDS 49024 49962 . + 0 ID=22222_2#22_04103;eC_number=1.1.1.79;gene=ghrA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729856.1,similar to AA sequence:UniProtKB:Q8ZQ30,protein motif:CLUSTERS:PRK15469,protein motif:Cdd:COG1932,protein motif:TIGRFAMs:TIGR01327,protein motif:Pfam:PF02826.13;locus_tag=22222_2#22_04103;product=2-hydroxyacid dehydrogenase,Glyoxylate/hydroxypyruvate reductase A,bifunctional glyoxylate/hydroxypyruvate reductase A,Phosphoserine aminotransferase,phosphoglycerate dehydrogenase,D-isomer specific 2-hydroxyacid dehydrogenase%2C NAD binding domain;protein_id=gnl|SC|22222_2#22_04103 ERS222222|SC|contig000020 Prodigal:2.60 CDS 50047 50784 . + 0 ID=22222_2#22_04104;eC_number=3.1.3.-;gene=ycdX;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570887.1,similar to AA sequence:UniProtKB:P75914,protein motif:CLUSTERS:PRK09248,protein motif:Cdd:COG1387,protein motif:TIGRFAMs:TIGR01856,protein motif:Pfam:PF02811.13;locus_tag=22222_2#22_04104;product=putative hydrolase,Probable phosphatase YcdX,putative hydrolase,Histidinol phosphatase and related hydrolases of the PHP family,histidinol phosphate phosphatase%2C HisJ family,PHP domain;protein_id=gnl|SC|22222_2#22_04104 ERS222222|SC|contig000020 Prodigal:2.60 CDS 50808 51362 . + 0 ID=22222_2#22_04105;gene=ycdY;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_002146908.1,similar to AA sequence:UniProtKB:P75915,protein motif:CLUSTERS:PRK11621,protein motif:Cdd:COG3381,protein motif:Pfam:PF02613.9;locus_tag=22222_2#22_04105;product=chaperone%2C TorD family,Chaperone protein YcdY,twin-argninine leader-binding protein DmsD,Uncharacterized component of anaerobic dehydrogenases,Nitrate reductase delta subunit;protein_id=gnl|SC|22222_2#22_04105 @@ -72,7 +72,7 @@ ERS222222|SC|contig000020 Prodigal:2.60 CDS 67715 68767 . + 0 ID=22222_2#22_04124;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087420.1,protein motif:CLUSTERS:PRK00142,protein motif:Cdd:COG2210,protein motif:Pfam:PF00581.14;locus_tag=22222_2#22_04124;product=Rhodanese-like sulfurtransferase,putative rhodanese-related sulfurtransferase,Uncharacterized conserved protein,Rhodanese-like domain;protein_id=gnl|SC|22222_2#22_04124 ERS222222|SC|contig000020 Prodigal:2.60 CDS 68819 69394 . - 0 ID=22222_2#22_04125;gene=yceI_2;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_006087865.1,similar to AA sequence:UniProtKB:P0A8X2,protein motif:CLUSTERS:PRK03757,protein motif:Cdd:COG2353,protein motif:Pfam:PF04264.7;locus_tag=22222_2#22_04125;product=YceI protein,hypothetical protein,hypothetical protein,Uncharacterized conserved protein,YceI-like domain;protein_id=gnl|SC|22222_2#22_04125 ERS222222|SC|contig000020 Prodigal:2.60 CDS 69391 69795 . - 0 ID=22222_2#22_04126;gene=yceJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_005212184.1,similar to AA sequence:UniProtKB:P75925,protein motif:CLUSTERS:PRK11513,protein motif:Pfam:PF00033.13;locus_tag=22222_2#22_04126;product=cytochrome b561-like protein 2,Cytochrome b561 homolog 2,cytochrome b561,Cytochrome b(N-terminal)/b6/petB;protein_id=gnl|SC|22222_2#22_04126 -ERS222222|SC|contig000020 Prodigal:2.60 CDS 70226 70339 . - 0 ID=22222_2#22_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=22222_2#22_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|22222_2#22_04127 +ERS222222|SC|contig000020 Prodigal:2.60 CDS 70226 70243 . - 0 ID=22222_2#22_04127;gene=yceO;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_216094.1,similar to AA sequence:UniProtKB:P64442,protein motif:Pfam:PF10968.2;locus_tag=22222_2#22_04127;product=inner membrane protein,hypothetical protein,Protein of unknown function (DUF2770);protein_id=gnl|SC|22222_2#22_04127 ERS222222|SC|contig000020 Prodigal:2.60 CDS 70380 71498 . - 0 ID=22222_2#22_04128;eC_number=1.5.3.1,1.5.3.-;gene=solA;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729880.1,similar to AA sequence:UniProtKB:P40874,protein motif:CLUSTERS:PRK11259,protein motif:Cdd:COG4121,protein motif:TIGRFAMs:TIGR01377,protein motif:Pfam:PF01266.18;locus_tag=22222_2#22_04128;product=sarcosine oxidase,N-methyl-L-tryptophan oxidase,N-methyltryptophan oxidase,Uncharacterized conserved protein,sarcosine oxidase%2C monomeric form,FAD dependent oxidoreductase;protein_id=gnl|SC|22222_2#22_04128 ERS222222|SC|contig000020 Prodigal:2.60 CDS 71611 71865 . - 0 ID=22222_2#22_04129;gene=bssS;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_001570863.1,protein motif:CLUSTERS:PRK12301;locus_tag=22222_2#22_04129;product=biofilm formation regulatory protein BssS,biofilm formation regulatory protein BssS;protein_id=gnl|SC|22222_2#22_04129 ERS222222|SC|contig000020 Prodigal:2.60 CDS 72155 72418 . - 0 ID=22222_2#22_04130;gene=dinI_3;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729882.1,similar to AA sequence:UniProtKB:P0ABR1,protein motif:CLUSTERS:PRK10597,protein motif:Pfam:PF06183.7;locus_tag=22222_2#22_04130;product=damage-inducible protein,DNA-damage-inducible protein I,DNA damage-inducible protein I,DinI-like family;protein_id=gnl|SC|22222_2#22_04130 @@ -98,7 +98,7 @@ ERS222222|SC|contig000020 Prodigal:2.60 CDS 88429 89379 . + 0 ID=22222_2#22_04150;eC_number=3.2.1.-;gene=flgJ;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729902.1,similar to AA sequence:UniProtKB:P15931,protein motif:CLUSTERS:PRK05684,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02541,protein motif:Pfam:PF01832.14;locus_tag=22222_2#22_04150;product=flagellar protein FlgJ,Peptidoglycan hydrolase flgJ,flagellar rod assembly protein/muramidase FlgJ,Rod binding protein,flagellar rod assembly protein/muramidase FlgJ,Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase;protein_id=gnl|SC|22222_2#22_04150 ERS222222|SC|contig000020 Prodigal:2.60 CDS 89444 91105 . + 0 ID=22222_2#22_04151;gene=flgK;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729903.1,similar to AA sequence:UniProtKB:P0A1J5,protein motif:CLUSTERS:PRK08147,protein motif:Cdd:COG1749,protein motif:TIGRFAMs:TIGR02492,protein motif:Pfam:PF06429.7;locus_tag=22222_2#22_04151;product=flagellar hook-associated protein 1,Flagellar hook-associated protein 1,flagellar hook-associated protein FlgK,Flagellar hook protein FlgE,flagellar hook-associated protein FlgK,Domain of unknown function (DUF1078);protein_id=gnl|SC|22222_2#22_04151 ERS222222|SC|contig000020 Prodigal:2.60 CDS 91120 92073 . + 0 ID=22222_2#22_04152;gene=flgL;inference=ab initio prediction:Prodigal:2.60,similar to AA sequence:RefSeq:YP_004729904.1,similar to AA sequence:UniProtKB:P16326,protein motif:CLUSTERS:PRK08027,protein motif:Cdd:COG3951,protein motif:TIGRFAMs:TIGR02550,protein motif:Pfam:PF00669.14;locus_tag=22222_2#22_04152;product=flagellar hook-associated protein 3,Hook-filament junction protein,flagellar hook-associated protein FlgL,Rod binding protein,flagellar hook-associated protein 3,Bacterial flagellin N-terminal helical region;protein_id=gnl|SC|22222_2#22_04152 -ERS222222|SC|contig000020 Infernal:1.1 ncRNA 92162 92255 . + 0 ID=22222_2#22_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=22222_2#22_04153;product=STnc490k +ERS222222|SC|contig000020 Infernal:1.1 ncRNA 92162 92179 . + 0 ID=22222_2#22_04153;inference=COORDINATES:profile:Infernal:1.1;locus_tag=22222_2#22_04153;product=STnc490k ##FASTA >ERS222222|SC|contig000020 TATCCGGGCAGCCCGTTTACGGGCCGTAAGTAACGAAGTTTGATGCAAATGTCAGATCGT