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| starting phase `check' | |
| t/00_requires_external.t | |
| 1..8 | |
| ok 1 - blastp in PATH | |
| ok 2 - makeblastdb in PATH | |
| ok 3 - mcl in PATH | |
| ok 4 - mcxdeblast in PATH | |
| ok 5 - bedtools in PATH | |
| ok 6 - prank in PATH | |
| ok 7 - parallel in PATH | |
| ok 8 - mafft in PATH | |
| t/Bio/Roary/AccessoryBinaryFasta.t | |
| ok 1 - use Bio::Roary::AccessoryBinaryFasta; | |
| ok 2 - initialise accessory binary fasta file | |
| ok 3 - create output file | |
| ok 4 - binary accessory fasta file created | |
| ok 5 - initialise accessory binary fasta file bounded | |
| ok 6 - lower bound value | |
| ok 7 - upper bound value | |
| ok 8 - create output file bounded | |
| ok 9 - binary accessory fasta file created bounded | |
| 1..9 | |
| t/Bio/Roary/AccessoryClustering.t | |
| ok 1 - use Bio::Roary::AccessoryClustering; | |
| ok 2 - initialise object with identity of 1 | |
| ok 3 - build the clusters for 1 | |
| ok 4 - build samples weights for 1 | |
| ok 5 - build samples to clusters for 1 | |
| ok 6 - check number of clusters as expected, allowing for some variation for 1 | |
| ok 7 - initialise object with identity of 0.90 | |
| ok 8 - build the clusters for 0.90 | |
| ok 9 - build samples weights for 0.90 | |
| ok 10 - build samples to clusters for 0.90 | |
| ok 11 - check number of clusters as expected, allowing for some variation for 0.90 | |
| ok 12 - initialise object with identity of 0.95 | |
| ok 13 - build the clusters for 0.95 | |
| ok 14 - build samples weights for 0.95 | |
| ok 15 - build samples to clusters for 0.95 | |
| ok 16 - check number of clusters as expected, allowing for some variation for 0.95 | |
| ok 17 - initialise object with identity of 0.99 | |
| ok 18 - build the clusters for 0.99 | |
| ok 19 - build samples weights for 0.99 | |
| ok 20 - build samples to clusters for 0.99 | |
| ok 21 - check number of clusters as expected, allowing for some variation for 0.99 | |
| ok 22 - samples to clusters | |
| ok 23 - sample weights | |
| ok 24 - samples to clusters | |
| ok 25 - sample weights | |
| ok 26 - build the clusters for large_accessory_binary_genes.fa | |
| ok 27 - build samples weights for large_accessory_binary_genes.fa | |
| ok 28 - build samples to clusters for large_accessory_binary_genes.fa | |
| ok 29 - check number of clusters as expected, allowing for some variation for large_accessory_binary_genes.fa | |
| 1..29 | |
| t/Bio/Roary/AnalyseGroups.t | |
| ok 1 - use Bio::Roary::AnalyseGroups; | |
| ok 2 - initialise with two fasta files | |
| ok 3 - Number of isolates | |
| ok 4 - genes map to the correct files | |
| ok 5 - Groups to genes hash | |
| ok 6 - genes to groups hash | |
| 1..6 | |
| t/Bio/Roary/AnnotateGroups.t | |
| ok 1 - use Bio::Roary::AnnotateGroups; | |
| ok 2 - initalise | |
| ok 3 - reannotate | |
| ok 4 - gene lengths as expected | |
| ok 5 - group lengths | |
| ok 6 - groups reannotated as expected | |
| 1..6 | |
| t/Bio/Roary/AssemblyStatistics.t | |
| ok 1 - use Bio::Roary::AssemblyStatistics; | |
| ok 2 - initialise spreadsheet | |
| ok 3 - all gene rows available | |
| ok 4 - ordered genes | |
| ok 5 - sample names to column index | |
| ok 6 - one block | |
| ok 7 - one block reversed | |
| ok 8 - one block where there are gaps everywhere | |
| ok 9 - no contiguous blocks | |
| ok 10 - three blocks | |
| ok 11 - three blocks with an inversion in the middle | |
| ok 12 - Gene category counts | |
| ok 13 - initialise spreadsheet with variable numbers of genes in samples | |
| ok 14 - Categories as expected | |
| All arguments to easy_init should be either an integer log level or a hash reference. at lib/Bio/Roary/AssemblyStatistics.pm line 42. | |
| ok 15 - create output file | |
| ok 16 - summary statistics as expected | |
| ok 17 - initialise spreadsheet with core of 96.67% | |
| ok 18 - Categories as expected with cd of 96.67% | |
| ok 19 - initialise spreadsheet with core of 96.66% | |
| ok 20 - Categories as expected with cd of 96.66% | |
| 1..20 | |
| t/Bio/Roary/ChunkFastaFile.t | |
| ok 1 - use Bio::Roary::ChunkFastaFile; | |
| ok 2 - initalise object to produce a single sequence file | |
| ok 3 - a single sequence file is created | |
| ok 4 - input and output file should be the same | |
| ok 5 - initalise object to produce one file per sequence | |
| ok 6 - a sequence file per sequence is created | |
| ok 7 - the first sequence file is as expected | |
| ok 8 - the last sequence file is as expected | |
| 1..8 | |
| t/Bio/Roary/CombinedProteome.t | |
| ok 1 - use Bio::Roary::CombinedProteome; | |
| ok 2 - initalise object with two files | |
| ok 3 - Create a combined file | |
| ok 4 - Combined file is as expected | |
| ok 5 - non existant files should throw an error | |
| 1..5 | |
| t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t | |
| ok 1 - use Bio::Roary::CommandLine::ExtractProteomeFromGff; | |
| ok 2 - Actual output file exists empty_file -h | |
| ok 3 - Actual and expected output match for '-h' | |
| ok 4 - Actual output file exists example_annotation.gff.proteome.faa -t 1 t/data/example_annotation.gff | |
| ok 5 - Actual and expected output match for '-t 1 t/data/example_annotation.gff' | |
| ok 6 - Actual output file exists example_annotation.gff.proteome.faa t/data/example_annotation.gff | |
| ok 7 - Actual and expected output match for 't/data/example_annotation.gff' | |
| 1..7 | |
| t/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.t | |
| ok 1 - use Bio::Roary::CommandLine::GeneAlignmentFromNucleotides; | |
| ok 2 - Actual output file exists empty_file -h | |
| ok 3 - Actual and expected output match for '-h' | |
| ok 4 - Actual output file exists t/data/f.fa.aln t/data/f.fa | |
| ok 5 - Actual and expected output match for 't/data/f.fa' | |
| ok 6 - Actual output file exists t/data/f.fa.aln --mafft t/data/f.fa | |
| ok 7 - Actual and expected output match for '--mafft t/data/f.fa' | |
| 1..7 | |
| t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t | |
| ok 1 - use Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp; | |
| ok 2 - Actual output file exists empty_file -h | |
| ok 3 - Actual and expected output match for '-h' | |
| ok 4 - Actual output file exists blast_results -m /tmp/guix-build-roary-3.6.4.drv-0/source/t/bin/dummy_makeblastdb -b /tmp/guix-build-roary-3.6.4.drv-0/source/t/bin/dummy_blastp -j Local t/data/example_1.faa | |
| ok 5 - Actual and expected output match for '-m /tmp/guix-build-roary-3.6.4.drv-0/source/t/bin/dummy_makeblastdb -b /tmp/guix-build-roary-3.6.4.drv-0/source/t/bin/dummy_blastp -j Local t/data/example_1.faa' | |
| ok 6 - Actual output file exists different_output_filename -o different_output_filename -m /tmp/guix-build-roary-3.6.4.drv-0/source/t/bin/dummy_makeblastdb -b /tmp/guix-build-roary-3.6.4.drv-0/source/t/bin/dummy_blastp -j Local t/data/example_1.faa | |
| ok 7 - Actual and expected output match for '-o different_output_filename -m /tmp/guix-build-roary-3.6.4.drv-0/source/t/bin/dummy_makeblastdb -b /tmp/guix-build-roary-3.6.4.drv-0/source/t/bin/dummy_blastp -j Local t/data/example_1.faa' | |
| 1..7 | |
| t/Bio/Roary/CommandLine/QueryRoary.t | |
| ok 1 - use Bio::Roary::CommandLine::QueryRoary; | |
| ok 2 - Actual output file exists pan_genome_results_group_2.fa -g t/data/example_groups -a gene_multifasta -n group_2 t/data/example_1.faa t/data/example_2.faa | |
| ok 3 - Actual and expected sorted output match for '-g t/data/example_groups -a gene_multifasta -n group_2 t/data/example_1.faa t/data/example_2.faa' | |
| ok 4 - Actual output file exists pan_genome_results_group_5.fa -g t/data/example_groups -a gene_multifasta -n group_2,group_5 t/data/example_1.faa t/data/example_2.faa | |
| ok 5 - Actual and expected sorted output match for '-g t/data/example_groups -a gene_multifasta -n group_2,group_5 t/data/example_1.faa t/data/example_2.faa' | |
| ok 6 - Actual output file exists pan_genome_results_group_2.fa -g t/data/example_groups -a gene_multifasta -n group_2,group_5 t/data/example_1.faa t/data/example_2.faa | |
| ok 7 - Actual and expected sorted output match for '-g t/data/example_groups -a gene_multifasta -n group_2,group_5 t/data/example_1.faa t/data/example_2.faa ' | |
| ok 8 - Actual output file exists pan_genome_results_group_5.fa -g t/data/example_groups -a gene_multifasta -n group_5 t/data/example_1.faa t/data/example_2.faa | |
| ok 9 - Actual and expected sorted output match for '-g t/data/example_groups -a gene_multifasta -n group_5 t/data/example_1.faa t/data/example_2.faa ' | |
| ok 10 - Actual output file exists pan_genome_results_group_5.fa -g t/data/example_groups -a gene_multifasta -n group_5,group_2 t/data/example_1.faa t/data/example_2.faa | |
| ok 11 - Actual and expected sorted output match for '-g t/data/example_groups -a gene_multifasta -n group_5,group_2 t/data/example_1.faa t/data/example_2.faa ' | |
| ok 12 - Actual output file exists pan_genome_results_group_2.fa -g t/data/example_groups -a gene_multifasta -n group_5,group_2 t/data/example_1.faa t/data/example_2.faa | |
| ok 13 - Actual and expected sorted output match for '-g t/data/example_groups -a gene_multifasta -n group_5,group_2 t/data/example_1.faa t/data/example_2.faa ' | |
| ok 14 - Actual output file exists empty_file -g t/data/example_groups -n group_which_doesnt_exist t/data/example_1.faa t/data/example_2.faa | |
| ok 15 - Actual and expected sorted output match for '-g t/data/example_groups -n group_which_doesnt_exist t/data/example_1.faa t/data/example_2.faa' | |
| ok 16 - Actual output file exists pan_genome_results -g t/data/query_groups -a complement t/data/query_1.fa t/data/query_2.fa t/data/query_3.fa | |
| ok 17 - Actual and expected sorted output match for '-g t/data/query_groups -a complement t/data/query_1.fa t/data/query_2.fa t/data/query_3.fa' | |
| ok 18 - Actual output file exists set_difference_common_set -g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa | |
| ok 19 - Actual and expected sorted output match for '-g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa' | |
| ok 20 - Actual output file exists set_difference_unique_set_two_statistics.csv -g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa | |
| ok 21 - Actual and expected sorted output match for '-g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa ' | |
| ok 22 - Actual output file exists set_difference_common_set_statistics.csv -g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa | |
| ok 23 - Actual and expected sorted output match for '-g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa ' | |
| ok 24 - Actual output file exists set_difference_unique_set_one_statistics.csv -g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa | |
| ok 25 - Actual and expected sorted output match for '-g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa ' | |
| ok 26 - Actual output file exists set_difference_common_set_statistics.csv -g t/data/query_groups -a difference -i t/data/query_1.gff -t t/data/query_2.gff,t/data/query_3.gff | |
| ok 27 - Actual and expected sorted output match for '-g t/data/query_groups -a difference -i t/data/query_1.gff -t t/data/query_2.gff,t/data/query_3.gff' | |
| ok 28 - Actual output file exists set_difference_unique_set_two -g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa | |
| ok 29 - Actual and expected sorted output match for '-g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa' | |
| ok 30 - Actual output file exists set_difference_unique_set_one -g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa | |
| ok 31 - Actual and expected sorted output match for '-g t/data/query_groups -a difference -i t/data/query_1.fa -t t/data/query_2.fa,t/data/query_3.fa' | |
| ok 32 - Actual output file exists pan_genome_results -g t/data/query_groups -a intersection t/data/query_1.fa t/data/query_2.fa t/data/query_3.fa | |
| ok 33 - Actual and expected sorted output match for '-g t/data/query_groups -a intersection t/data/query_1.fa t/data/query_2.fa t/data/query_3.fa' | |
| ok 34 - Actual output file exists pan_genome_results -g t/data/query_groups -a union t/data/query_1.fa t/data/query_2.fa t/data/query_3.fa | |
| ok 35 - Actual and expected sorted output match for '-g t/data/query_groups -a union t/data/query_1.fa t/data/query_2.fa t/data/query_3.fa' | |
| ok 36 - Actual output file exists empty_file2 -h | |
| ok 37 - Actual and expected sorted output match for '-h' | |
| 1..37 | |
| t/Bio/Roary/CommandLine/Roary.t | |
| ok 1 - use Bio::Roary::CommandLine::Roary; | |
| ok 2 - use Bio::Roary::CommandLine::CreatePanGenome; | |
| ok 3 - Actual output file exists gene_presence_absence.csv --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff | |
| ok 4 - Actual and expected match output excluding variable columns | |
| ok 5 - Actual output file exists gene_presence_absence.csv -j Local --dont_split_groups t/data/genbank_gbff/genbank1.gff t/data/genbank_gbff/genbank2.gff t/data/genbank_gbff/genbank3.gff | |
| ok 6 - Actual and expected match output excluding variable columns | |
| ok 7 - Actual output file exists gene_presence_absence.csv -j Local -t 1 --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff | |
| ok 8 - Actual and expected match output excluding variable columns | |
| ok 9 - Actual output file exists gene_presence_absence.csv -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff | |
| ok 10 - Actual and expected match output excluding variable columns | |
| ok 11 - Actual output file exists gene_presence_absence.csv -t 1 -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff | |
| ok 12 - Actual and expected match output excluding variable columns | |
| ok 13 - Actual output file exists empty_file -h | |
| ok 14 - Actual and expected match output excluding variable columns | |
| ok 15 - Actual output file exists clustered_proteins -j Local --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff | |
| ok 16 - Actual and expected match output excluding variable columns | |
| ok 17 - Actual output file exists clustered_proteins -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff | |
| ok 18 - Actual and expected match output excluding variable columns | |
| ok 19 - Check protein query_1.gff.proteome.faa is cleaned up | |
| ok 20 - Check protein query_2.gff.proteome.faa is cleaned up | |
| ok 21 - Check protein query_5.gff.proteome.faa is cleaned up | |
| ok 22 - got expected text Looking for for -a | |
| ok 23 - got expected text Output directory created for -v --output_directory t/data/directory_which_doesnt_exist t/data/real_data_1.gff t/data/real_data_2.gff | |
| ok 24 - pan genome files should be in directory | |
| ok 25 - current working directory should not have changed after script is finished | |
| --------------------- WARNING --------------------- | |
| MSG: Got a sequence without letters. Could not guess alphabet | |
| --------------------------------------------------- | |
| --------------------- WARNING --------------------- | |
| MSG: Got a sequence without letters. Could not guess alphabet | |
| --------------------------------------------------- | |
| Core gene file missing: pan_genome_sequences/sigE.fa.aln | |
| Core gene file missing: pan_genome_sequences/sopB.fa.aln | |
| Core gene file missing: pan_genome_sequences/pepD_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/yedV.fa.aln | |
| Core gene file missing: pan_genome_sequences/copR.fa.aln | |
| Core gene file missing: pan_genome_sequences/uraH.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaC.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaB.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaR.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaG.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcC_1.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcC_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcB.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcD.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcG.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaI.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaX.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaA.fa.aln | |
| Core gene file missing: pan_genome_sequences/rnz.fa.aln | |
| Core gene file missing: pan_genome_sequences/cbpM.fa.aln | |
| Core gene file missing: pan_genome_sequences/cbpA.fa.aln | |
| Core gene file missing: pan_genome_sequences/scsA.fa.aln | |
| Core gene file missing: pan_genome_sequences/scsB.fa.aln | |
| Core gene file missing: pan_genome_sequences/scsC.fa.aln | |
| Core gene file missing: pan_genome_sequences/resA.fa.aln | |
| Core gene file missing: pan_genome_sequences/agp.fa.aln | |
| Core gene file missing: pan_genome_sequences/yccJ.fa.aln | |
| Core gene file missing: pan_genome_sequences/wrbA.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_61.fa.aln | |
| Core gene file missing: pan_genome_sequences/rutR.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_77.fa.aln | |
| Core gene file missing: pan_genome_sequences/putA.fa.aln | |
| Core gene file missing: pan_genome_sequences/putP.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_62.fa.aln | |
| Core gene file missing: pan_genome_sequences/phoH.fa.aln | |
| Core gene file missing: pan_genome_sequences/ybbH_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/yidK.fa.aln | |
| Core gene file missing: pan_genome_sequences/sglT.fa.aln | |
| Core gene file missing: pan_genome_sequences/nanE.fa.aln | |
| Core gene file missing: pan_genome_sequences/nanM.fa.aln | |
| Core gene file missing: pan_genome_sequences/yiiy.fa.aln | |
| Core gene file missing: pan_genome_sequences/nanT_3.fa.aln | |
| Core gene file missing: pan_genome_sequences/yjhC.fa.aln | |
| Core gene file missing: pan_genome_sequences/ghrA.fa.aln | |
| Core gene file missing: pan_genome_sequences/ycdX.fa.aln | |
| Core gene file missing: pan_genome_sequences/ycdY.fa.aln | |
| Core gene file missing: pan_genome_sequences/ycdZ.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgL.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgK.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgJ.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgI.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgH.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgG.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgF.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgE.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgD.fa.aln | |
| Core gene file missing: pan_genome_sequences/mdtH.fa.aln | |
| Core gene file missing: pan_genome_sequences/bssS.fa.aln | |
| Core gene file missing: pan_genome_sequences/solA.fa.aln | |
| Core gene file missing: pan_genome_sequences/yceJ.fa.aln | |
| Core gene file missing: pan_genome_sequences/yceI_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/msyB.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_93.fa.aln | |
| Core gene file missing: pan_genome_sequences/mdoH.fa.aln | |
| Core gene file missing: pan_genome_sequences/mdoG.fa.aln | |
| Core gene file missing: pan_genome_sequences/mdoC.fa.aln | |
| Core gene file missing: pan_genome_sequences/ybhO_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/ymdB.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_70.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgC.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgB.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgD.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgE.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgF.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgG.fa.aln | |
| not ok 26 - Actual output file exists pan_genome_sequences/mdoH.fa.aln -j Local --dont_delete_files --dont_split_groups --output_multifasta_files t/data/real_data_1.gff t/data/real_data_2.gff | |
| # Failed test 'Actual output file exists pan_genome_sequences/mdoH.fa.aln -j Local --dont_delete_files --dont_split_groups --output_multifasta_files t/data/real_data_1.gff t/data/real_data_2.gff' | |
| # at /tmp/guix-build-roary-3.6.4.drv-0/source/t/lib/TestHelper.pm line 139. | |
| not ok 27 - Actual and expected output match for '-j Local --dont_delete_files --dont_split_groups --output_multifasta_files t/data/real_data_1.gff t/data/real_data_2.gff' | |
| # Failed test 'Actual and expected output match for '-j Local --dont_delete_files --dont_split_groups --output_multifasta_files t/data/real_data_1.gff t/data/real_data_2.gff'' | |
| # at /tmp/guix-build-roary-3.6.4.drv-0/source/t/lib/TestHelper.pm line 148. | |
| # pan_genome_sequences/mdoH.fa.aln absent | |
| ok 28 - Core gene alignment exists | |
| ok 29 - Check size of the core_gene_alignment.aln init | |
| not ok 30 - length of first sequence | |
| # Failed test 'length of first sequence' | |
| # at t/Bio/Roary/CommandLine/Roary.t line 93. | |
| # got: '0' | |
| # expected: '64983' | |
| ok 31 - Core gene alignment header exists | |
| ok 32 | |
| ok 33 | |
| ok 34 | |
| ok 35 | |
| ok 36 | |
| ok 37 | |
| ok 38 | |
| --------------------- WARNING --------------------- | |
| MSG: Got a sequence without letters. Could not guess alphabet | |
| --------------------------------------------------- | |
| --------------------- WARNING --------------------- | |
| MSG: Got a sequence without letters. Could not guess alphabet | |
| --------------------------------------------------- | |
| --------------------- WARNING --------------------- | |
| MSG: Got a sequence without letters. Could not guess alphabet | |
| --------------------------------------------------- | |
| Core gene file missing: pan_genome_sequences/group_1.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_3.fa.aln | |
| ok 39 - Actual output file exists core_gene_alignment.aln -j Local --output_multifasta_files t/data/core_alignment_gene_lookup/query_1.gff t/data/core_alignment_gene_lookup/query_2.gff t/data/core_alignment_gene_lookup/query_3.gff | |
| not ok 40 - Actual and expected output match for '-j Local --output_multifasta_files t/data/core_alignment_gene_lookup/query_1.gff t/data/core_alignment_gene_lookup/query_2.gff t/data/core_alignment_gene_lookup/query_3.gff' | |
| # Failed test 'Actual and expected output match for '-j Local --output_multifasta_files t/data/core_alignment_gene_lookup/query_1.gff t/data/core_alignment_gene_lookup/query_2.gff t/data/core_alignment_gene_lookup/query_3.gff'' | |
| # at /tmp/guix-build-roary-3.6.4.drv-0/source/t/lib/TestHelper.pm line 148. | |
| # +---+----------+---+----------------------------------------------------------------+ | |
| # | |Got | |Expected | | |
| # | Ln| | Ln| | | |
| # +---+----------+---+----------------------------------------------------------------+ | |
| # | 1|>query_1 | 1|>query_1 | | |
| # * 2|\n * 2|ATGAATCTACCTTTACCTGATAATTATGAATTTGTGTTTTTATCTGGTGGATTATCTGGG\n * | |
| # | | * 3|CATGCTGCAATGATGTCATTTTTTAATGTTTGTGGCATTGGATATTTGTATCATCATATG * | |
| # | | * 4|GATTTAATGAAAAATAGATATATAGATTATTACCATTTTTCTAGGATTGAAAATTTATAT * | |
| # | | * 5|TCAATTATAACATATGGACAATACAGTTTAACGCAAGGAATGAATAATATAGGTAAATAT * | |
| # | | * 6|TTGACTTTAATTAATAAAATTCCAATTCTTTTTTTGGTAAGAGATCCCATATCAAGACTA * | |
| # | | * 7|AAAACCGGAGTAAATCATCCTATTCTAAATCCAAAAAGTATGAAGGAGATATGTTTAAAC * | |
| # | | * 8|AATGATTATAGTGATGTGTTTAAGAATAAAATGTATGTTGGCGATATTGGAAAAAATTTT * | |
| # | | * 9|TACTATTCAGAAAAGCCAAGCATGAAATATTTACCTAGATTGAAATATGAAAATTTGGGA * | |
| # | | * 10|ATATTTTTAAAACCACAAGAATTTGAGCGTTTAAAGCAAGATTCTAAGCTATTTGATGTT * | |
| # | | * 11|GCTAAAAGATATTTGAATAATTTTATTGAAGCTTTAGAAGAGAGAATAGACCTAGAAAAA * | |
| # | | * 12|GCTAAATTATTTAAAGAAAAAGACGTGTTAAACTATTTAAAAGAAAATAAAGAATTAAGA * | |
| # | | * 13|GTTAAGTTAAAAAACATATTAGATAAAGAACTTGTTCATATTAAACAACATCGTCCAGAT * | |
| # | | * 14|ATAGTAGCTTCTTGGAAATACTATCAAGAATTTGAACAAATGTGCAAGGAGTTGAATGGT * | |
| # | | * 15|AATATTTAG * | |
| # | 3|>query_2 | 16|>query_2 | | |
| # * 4|\n * 17|ATGAATCTACCTTTACCTGATAATTATGAATTTGTGTTTTTATCTGGTGGATTATCTGGG\n * | |
| # | | * 18|CATGCTGCAATGATGTCATTTTTTAATGTTTGTGGCATTGGATATTTGTATCATCATATG * | |
| # | | * 19|GATTTAATGAAAAATAGATATATAGATTATTACCATTTTTCTAGGATTGAAAATTTATAT * | |
| # | | * 20|TCAATTATAACATATGGACAATACAGTTTAACGCAAGGAATGAATAATATAGGTAAATAT * | |
| # | | * 21|TTGACTTTAATTAATNNNNNNNNNATTCTTTTTTTGGTAAGAGATCCCATATCAAGACTA * | |
| # | | * 22|AAAACCGGAGTAAATCATCCTATTCTAAATCCAAAAAGTATGAAGGAGATATGTTTAAAC * | |
| # | | * 23|AATGATTATAGTGATNNNNNNNNNAATAAAATGTATGTTGGCGATATTGGAAAAAATTTT * | |
| # | | * 24|TACTATTCAGAAAAGCCAAGCATGAAATATTTACCTAGATTGAAATATGAAAATTTGGGA * | |
| # | | * 25|ATATTTTTAAAACCACAAGAATTTGAGCGTTTAAAGCAAGATTCTAAGCTATTTGATGTT * | |
| # | | * 26|GCTAAAAGATATTTGAATAATTTTATTGAAGCTTTAGAAGAGAGAATAGACCTAGAAAAA * | |
| # | | * 27|GCTAAATTATTTAAAGAAAAAGACGTGTTAAACTATTTAAAAGAAAATAAAGAATTAAGA * | |
| # | | * 28|GTTAAGTTAAAAAACATATTAGATAAAGAACTTGTTCATATTAAACAACATCGTCCAGAT * | |
| # | | * 29|ATAGTAGCTTCTTGGAAATACTATCAAGAATTTGAACAAATGTGCAAGGAGTTGAATGGT * | |
| # | | * 30|AATATTTAG * | |
| # | 5|>query_3 | 31|>query_3 | | |
| # * 6|\n * 32|ATGAATCTACCTTTACCTGATAATTATGAATTTGTGTTTTTATCTGGTGGATTATCTGGG\n * | |
| # | | * 33|CATGCTGCAATGATGTCATTTTTTAATGTTTGTGGCATTGGATATTTGTATCATCATATG * | |
| # | | * 34|GATTTAATGAAAAATAGATATATAGATTATTACCATTTTTCTAGGATTGAAAATTTATAT * | |
| # | | * 35|TCAATTATAACATATGGACAATACAGTTTAACGCAAGGAATGAATAATATAGGTAAATAT * | |
| # | | * 36|TTGACTTTAATTAATAAAATTCCAATTCTTTTTTTGGTAAGAGATCCCATATCAAGACTA * | |
| # | | * 37|AAAACCGGAGTAAATCATCCTATTCTAAATCCAAAAAGTATGAAGGAGATATGTTTAAAC * | |
| # | | * 38|AATGATTATAGTGATGTGTTTAAGAATAAAATGTATGTTGGCGATATTGGAAAAAATTTT * | |
| # | | * 39|TACTATTCAGAAAAGCCAAGCATGAAATATTTACCTAGATTGAAATATGAAAATTTGGGA * | |
| # | | * 40|ATATTTTTAAAACCACAAGAATTCGAGCGTTTAAAGCAAGATTCTAAGCTATTTGATGTT * | |
| # | | * 41|GCTAAAAGATATTTGAATAATTTTATTGAAGCTTTAGAAGAGAGAATAGACCTAGAAAAA * | |
| # | | * 42|GCTAAATTATTTAAAGAAAAAGACGTGTTAAACTATTTAAAAGAAAATAAAGAATTAAGA * | |
| # | | * 43|GTTAAGTTAAAAAACATATTAGATAAAGAACTTGTTCATATTAAACAACATCGTCCAGAT * | |
| # | | * 44|ATAGTAGCTTCTTGGAAATACTATCAAGAATTTGAACAAATGTGCAAGGAGTTGAATGGT * | |
| # | | * 45|AATATTTAG * | |
| # +---+----------+---+----------------------------------------------------------------+ | |
| --------------------- WARNING --------------------- | |
| MSG: Got a sequence without letters. Could not guess alphabet | |
| --------------------------------------------------- | |
| --------------------- WARNING --------------------- | |
| MSG: Got a sequence without letters. Could not guess alphabet | |
| --------------------------------------------------- | |
| Core gene file missing: pan_genome_sequences/flgL.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgK.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgJ.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgI.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgH.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgG.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgF.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgE.fa.aln | |
| Core gene file missing: pan_genome_sequences/flgD.fa.aln | |
| Core gene file missing: pan_genome_sequences/mdtH.fa.aln | |
| Core gene file missing: pan_genome_sequences/bssS.fa.aln | |
| Core gene file missing: pan_genome_sequences/solA.fa.aln | |
| Core gene file missing: pan_genome_sequences/yceJ.fa.aln | |
| Core gene file missing: pan_genome_sequences/yceI_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/msyB.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_93.fa.aln | |
| Core gene file missing: pan_genome_sequences/mdoH.fa.aln | |
| Core gene file missing: pan_genome_sequences/mdoG.fa.aln | |
| Core gene file missing: pan_genome_sequences/mdoC.fa.aln | |
| Core gene file missing: pan_genome_sequences/ybhO_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/ymdB.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_59.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgC.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgB.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgD.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgE.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgF.fa.aln | |
| Core gene file missing: pan_genome_sequences/csgG.fa.aln | |
| Core gene file missing: pan_genome_sequences/ycdZ.fa.aln | |
| Core gene file missing: pan_genome_sequences/ycdY.fa.aln | |
| Core gene file missing: pan_genome_sequences/ycdX.fa.aln | |
| Core gene file missing: pan_genome_sequences/ghrA.fa.aln | |
| Core gene file missing: pan_genome_sequences/yjhC.fa.aln | |
| Core gene file missing: pan_genome_sequences/nanT_3.fa.aln | |
| Core gene file missing: pan_genome_sequences/yiiy.fa.aln | |
| Core gene file missing: pan_genome_sequences/nanM.fa.aln | |
| Core gene file missing: pan_genome_sequences/nanE.fa.aln | |
| Core gene file missing: pan_genome_sequences/sglT.fa.aln | |
| Core gene file missing: pan_genome_sequences/yidK.fa.aln | |
| Core gene file missing: pan_genome_sequences/ybbH_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/phoH.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_51.fa.aln | |
| Core gene file missing: pan_genome_sequences/putP.fa.aln | |
| Core gene file missing: pan_genome_sequences/putA.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_82.fa.aln | |
| Core gene file missing: pan_genome_sequences/rutR.fa.aln | |
| Core gene file missing: pan_genome_sequences/group_48.fa.aln | |
| Core gene file missing: pan_genome_sequences/wrbA.fa.aln | |
| Core gene file missing: pan_genome_sequences/yccJ.fa.aln | |
| Core gene file missing: pan_genome_sequences/agp.fa.aln | |
| Core gene file missing: pan_genome_sequences/resA.fa.aln | |
| Core gene file missing: pan_genome_sequences/scsC.fa.aln | |
| Core gene file missing: pan_genome_sequences/scsB.fa.aln | |
| Core gene file missing: pan_genome_sequences/scsA.fa.aln | |
| Core gene file missing: pan_genome_sequences/cbpA.fa.aln | |
| Core gene file missing: pan_genome_sequences/cbpM.fa.aln | |
| Core gene file missing: pan_genome_sequences/rnz.fa.aln | |
| Core gene file missing: pan_genome_sequences/sigE.fa.aln | |
| Core gene file missing: pan_genome_sequences/sopB.fa.aln | |
| Core gene file missing: pan_genome_sequences/pepD_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/yedV.fa.aln | |
| Core gene file missing: pan_genome_sequences/copR.fa.aln | |
| Core gene file missing: pan_genome_sequences/uraH.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaC.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaB.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaR.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaG.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcC_1.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcC_2.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcB.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcD.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpcG.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaI.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaX.fa.aln | |
| Core gene file missing: pan_genome_sequences/hpaA.fa.aln | |
| not ok 41 - Actual output file exists pan_genome_sequences/mdoH.fa.aln -j Local --dont_delete_files --dont_split_groups --output_multifasta_files --mafft t/data/real_data_1.gff t/data/real_data_2.gff | |
| # Failed test 'Actual output file exists pan_genome_sequences/mdoH.fa.aln -j Local --dont_delete_files --dont_split_groups --output_multifasta_files --mafft t/data/real_data_1.gff t/data/real_data_2.gff' | |
| # at /tmp/guix-build-roary-3.6.4.drv-0/source/t/lib/TestHelper.pm line 139. | |
| not ok 42 - Actual and expected output match for '-j Local --dont_delete_files --dont_split_groups --output_multifasta_files --mafft t/data/real_data_1.gff t/data/real_data_2.gff' | |
| # Failed test 'Actual and expected output match for '-j Local --dont_delete_files --dont_split_groups --output_multifasta_files --mafft t/data/real_data_1.gff t/data/real_data_2.gff'' | |
| # at /tmp/guix-build-roary-3.6.4.drv-0/source/t/lib/TestHelper.pm line 148. | |
| # pan_genome_sequences/mdoH.fa.aln absent | |
| ok 43 - Core gene alignment exists | |
| ok 44 # skip extended tests not run | |
| ok 45 # skip extended tests not run | |
| ok 46 # skip extended tests not run | |
| ok 47 # skip extended tests not run | |
| ok 48 # skip extended tests not run | |
| ok 49 # skip extended tests not run | |
| ok 50 # skip extended tests not run | |
| ok 51 # skip extended tests not run | |
| ok 52 # skip extended tests not run | |
| ok 53 # skip extended tests not run | |
| ok 54 # skip extended tests not run | |
| ok 55 # skip extended tests not run | |
| ok 56 # skip extended tests not run | |
| ok 57 # skip extended tests not run | |
| ok 58 # skip extended tests not run | |
| ok 59 # skip extended tests not run | |
| ok 60 # skip extended tests not run | |
| ok 61 # skip extended tests not run | |
| ok 62 # skip extended tests not run | |
| ok 63 # skip extended tests not run | |
| ok 64 # skip extended tests not run | |
| ok 65 # skip extended tests not run | |
| ok 66 # skip extended tests not run | |
| ok 67 # skip extended tests not run | |
| ok 68 # skip extended tests not run | |
| ok 69 # skip extended tests not run | |
| ok 70 # skip extended tests not run | |
| ok 71 # skip extended tests not run | |
| ok 72 # skip extended tests not run | |
| ok 73 # skip extended tests not run | |
| ok 74 # skip extended tests not run | |
| ok 75 # skip extended tests not run | |
| ok 76 # skip extended tests not run | |
| ok 77 # skip extended tests not run | |
| ok 78 # skip extended tests not run | |
| ok 79 # skip extended tests not run | |
| ok 80 # skip extended tests not run | |
| ok 81 # skip extended tests not run | |
| ok 82 # skip extended tests not run | |
| ok 83 # skip extended tests not run | |
| 1..83 | |
| # Looks like you failed 6 tests of 83. | |
| t/Bio/Roary/CommandLine/RoaryCoreAlignment.t | |
| ok 1 - use Bio::Roary::CommandLine::RoaryCoreAlignment; | |
| ok 2 - Actual output file exists empty_file -h | |
| ok 3 - Actual and expected output match for '-h' | |
| ok 4 - Actual output file exists core_gene_alignment.aln -m t/data/core_alignment -s t/data/core_alignment.csv | |
| ok 5 - Actual and expected output match for '-m t/data/core_alignment -s t/data/core_alignment.csv' | |
| ok 6 - Actual output file exists core_gene_alignment.aln -m t/data/core_alignment -s t/data/core_alignment_core0.66.csv --core_definition 0.66 | |
| ok 7 - Actual and expected output match for '-m t/data/core_alignment -s t/data/core_alignment_core0.66.csv --core_definition 0.66' | |
| 1..7 | |
| t/Bio/Roary/CommandLine/RoaryPostAnalysis.t | |
| ok 1 - use Bio::Roary::CommandLine::RoaryPostAnalysis; | |
| ok 2 # skip Tests dont take variablity into account | |
| ok 3 # skip Tests dont take variablity into account | |
| 1..3 | |
| t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t | |
| ok 1 - use Bio::Roary::CommandLine::RoaryReorderSpreadsheet; | |
| ok 2 - Actual output file exists empty_file -h | |
| ok 3 - Actual and expected output match for '-h' | |
| ok 4 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv | |
| ok 5 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv' | |
| ok 6 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth | |
| ok 7 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth' | |
| ok 8 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth -b alpha | |
| ok 9 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth -b alpha' | |
| ok 10 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth -b creation | |
| ok 11 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth -b creation' | |
| ok 12 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth -b height | |
| ok 13 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth -b height' | |
| ok 14 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth -b revalpha | |
| ok 15 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a breadth -b revalpha' | |
| ok 16 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth | |
| ok 17 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth' | |
| ok 18 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth -b alpha | |
| ok 19 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth -b alpha' | |
| ok 20 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth -b creation | |
| ok 21 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth -b creation' | |
| ok 22 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth -b height | |
| ok 23 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth -b height' | |
| ok 24 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth -b revalpha | |
| ok 25 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -a depth -b revalpha' | |
| ok 26 - Actual output file exists reordered_spreadsheet.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -f newick | |
| ok 27 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -f newick' | |
| ok 28 - Actual output file exists different_output_name.csv -t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -o different_output_name.csv | |
| ok 29 - Actual and expected output match for '-t t/data/reorder_isolates.tre -s t/data/reorder_isolates_input.csv -o different_output_name.csv' | |
| 1..29 | |
| t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t | |
| ok 1 - use Bio::Roary::CommandLine::TransferAnnotationToGroups; | |
| ok 2 - Actual output file exists reannotated_groups -g t/data/query_groups t/data/query_1.gff t/data/query_2.gff t/data/query_3.gff | |
| ok 3 - Actual and expected sorted output match for '-g t/data/query_groups t/data/query_1.gff t/data/query_2.gff t/data/query_3.gff' | |
| ok 4 - Actual output file exists empty_file -h | |
| ok 5 - Actual and expected sorted output match for '-h' | |
| 1..5 | |
| t/Bio/Roary/ContigsToGeneIDsFromGFF.t | |
| ok 1 - use Bio::Roary::ContigsToGeneIDsFromGFF; | |
| ok 2 - Initialise contigs to gene ids obj | |
| ok 3 - Contigs match expected with standard output | |
| ok 4 - Initialise contigs to gene ids obj with alternative ID patterns | |
| ok 5 - Contigs match expected with alternative output | |
| ok 6 - Product annotation with non standard format | |
| 1..6 | |
| t/Bio/Roary/EmblGroups.t | |
| ok 1 - use Bio::Roary::Output::EmblGroups; | |
| ok 2 - initialise embl groups | |
| ok 3 - heatmap colour | |
| ok 4 - heatmap colour | |
| ok 5 - heatmap colour | |
| ok 6 - heatmap colour | |
| ok 7 - heatmap colour loop over each colour 10 | |
| ok 8 - heatmap colour loop over each colour 9 | |
| ok 9 - heatmap colour loop over each colour 8 | |
| ok 10 - heatmap colour loop over each colour 7 | |
| ok 11 - heatmap colour loop over each colour 6 | |
| ok 12 - heatmap colour loop over each colour 5 | |
| ok 13 - heatmap colour loop over each colour 4 | |
| ok 14 - heatmap colour loop over each colour 3 | |
| ok 15 - heatmap colour loop over each colour 2 | |
| ok 16 - heatmap colour loop over each colour 1 | |
| 1..16 | |
| t/Bio/Roary/External/Blastp.t | |
| ok 1 - use Bio::Roary::External::Blastp; | |
| ok 2 - initialise object | |
| ok 3 - Command constructed as expected | |
| ok 4 - run dummy command | |
| 1..4 | |
| t/Bio/Roary/External/Cdhit.t | |
| ok 1 - use Bio::Roary::External::Cdhit; | |
| ok 2 - initialise object | |
| ok 3 - Command constructed as expected | |
| ok 4 - run dummy command | |
| ok 5 - initialise object with lots of threads | |
| ok 6 - number of threads capped at a lower level | |
| 1..6 | |
| t/Bio/Roary/External/CheckTools.t | |
| ok 1 - use Bio::Roary::External::CheckTools; | |
| ok 2 - initialise checking for tools | |
| ok 3 - Check for parallel | |
| ok 4 - Check for blastp | |
| ok 5 - Check for makeblastdb | |
| ok 6 - Check for mcl | |
| ok 7 - Check for bedtools | |
| ok 8 - Check for prank | |
| ok 9 - Check for mafft | |
| ok 10 - Check for grep | |
| ok 11 - Check for sed | |
| ok 12 - Check for awk | |
| ok 13 - Check for all tools | |
| 1..13 | |
| t/Bio/Roary/External/Mafft.t | |
| ok 1 - use Bio::Roary::External::Mafft; | |
| ok 2 - initialise mafft obj | |
| ok 3 - Command constructed as expected | |
| ok 4 - run mafft | |
| ok 5 - output file exists | |
| ok 6 - output for mafft matches | |
| 1..6 | |
| t/Bio/Roary/External/Makeblastdb.t | |
| ok 1 - use Bio::Roary::External::Makeblastdb; | |
| ok 2 - initialise object | |
| ok 3 - Command constructed as expected | |
| ok 4 - run dummy command | |
| 1..4 | |
| t/Bio/Roary/External/Mcl.t | |
| ok 1 - use Bio::Roary::External::Mcl; | |
| ok 2 - initialise object with dummy values | |
| ok 3 - Command constructed as expected | |
| ok 4 - run dummy command | |
| ok 5 - initialise object with real values | |
| ok 6 - run the real command | |
| ok 7 - outgroups as expected | |
| 1..7 | |
| t/Bio/Roary/External/Prank.t | |
| ok 1 - use Bio::Roary::External::Prank; | |
| ok 2 - initialise prank obj | |
| ok 3 - Command constructed as expected | |
| ok 4 - run prank | |
| ok 5 - output file exists | |
| ok 6 - output for prank matches | |
| 1..6 | |
| t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t | |
| ok 1 - use Bio::Roary::ExtractCoreGenesFromSpreadsheet; | |
| ok 2 - initalise obj | |
| ok 3 - Correct ordering | |
| ok 4 - Correct of sample names to genes is correct | |
| 1..4 | |
| t/Bio/Roary/ExtractProteomeFromGFFs.t | |
| ok 1 - use Bio::Roary::ExtractProteomeFromGFFs; | |
| ok 2 - initialise object | |
| ok 3 - one file created | |
| ok 4 - content of proteome 1 as expected | |
| ok 5 - initialise object where one GFF has no FASTA line | |
| ok 6 - content of proteome 1 as expected | |
| ok 7 - initialise object with genbank gff files | |
| ok 8 - GB files created output | |
| ok 9 - content of proteome /tmp/guix-build-roary-3.6.4.drv-0/source/2AKcKqq7N4/genbank1.gff.proteome.faa as expected | |
| ok 10 - content of proteome /tmp/guix-build-roary-3.6.4.drv-0/source/2AKcKqq7N4/genbank2.gff.proteome.faa as expected | |
| ok 11 - content of proteome /tmp/guix-build-roary-3.6.4.drv-0/source/2AKcKqq7N4/genbank3.gff.proteome.faa as expected | |
| ok 12 - initialise object with locus tag id gff files | |
| ok 13 - locus tag id files created output | |
| ok 14 - content of proteome /tmp/guix-build-roary-3.6.4.drv-0/source/pLyItSXe1A/query_1.gff.proteome.faa as expected | |
| ok 15 - content of proteome /tmp/guix-build-roary-3.6.4.drv-0/source/pLyItSXe1A/query_2.gff.proteome.faa as expected | |
| ok 16 - content of proteome /tmp/guix-build-roary-3.6.4.drv-0/source/pLyItSXe1A/query_3.gff.proteome.faa as expected | |
| 1..16 | |
| t/Bio/Roary/FilterFullClusters.t | |
| ok 1 - use Bio::Roary::FilterFullClusters; | |
| ok 2 - initialise object | |
| ok 3 - filter the clusters | |
| ok 4 - filter original input and save full groups | |
| ok 5 - content as expected | |
| ok 6 - content as expected | |
| ok 7 - content as expected | |
| 1..7 | |
| t/Bio/Roary/GeneNamesFromGFF.t | |
| ok 1 - use Bio::Roary::GeneNamesFromGFF; | |
| ok 2 - initialise reading GFF file | |
| ok 3 - ids to gene names as expected | |
| ok 4 - ids to gene lengths as expected | |
| ok 5 - initialise reading another GFF file | |
| ok 6 - ids to gene names as expected again | |
| ok 7 - initialise a GFF file with locus tags only | |
| ok 8 - ids to gene names with GFF file with locus tags only | |
| 1..8 | |
| t/Bio/Roary/GroupLabels.t | |
| ok 1 - use Bio::Roary::GroupLabels; | |
| ok 2 - initialise with a groups file | |
| ok 3 - Add labels to groups | |
| ok 4 - groups labeled as expected | |
| 1..4 | |
| t/Bio/Roary/GroupStatistics.t | |
| ok 1 - use Bio::Roary::GroupStatistics; | |
| ok 2 - Initialise group statistics object | |
| ok 3 - Create the CSV file | |
| ok 4 - CSV file exists | |
| ok 5 - Spreadsheet content as expected | |
| ok 6 - Create the Rtab file | |
| ok 7 - Rtab file exists | |
| ok 8 - Rtab matrix content as expected | |
| ok 9 - Initialise group statistics object where one isolate has only 1 gene | |
| ok 10 - Create the CSV file | |
| ok 11 - CSV file exists | |
| ok 12 - Spreadsheet content as expected with missing genes | |
| ok 13 - Initialise group statistics object | |
| ok 14 - Create the CSV file | |
| ok 15 - CSV file exists | |
| ok 16 - Verbose spreadsheet content as expected | |
| 1..16 | |
| t/Bio/Roary/InflateClusters.t | |
| ok 1 - use Bio::Roary::InflateClusters; | |
| ok 2 - initialise object | |
| ok 3 - inflate the results | |
| ok 4 - inflated results as expected | |
| ok 5 - initialise object | |
| ok 6 - inflate the results | |
| ok 7 - inflated results as expected | |
| 1..7 | |
| t/Bio/Roary/OrderGenes.t | |
| ok 1 - use Bio::Roary::OrderGenes; | |
| ok 2 - Initialise order genes object for t/data/accessory_graphs/no_accessory | |
| ok 3 - build the graph | |
| ok 4 - group group_A found in file t/data/accessory_graphs/no_accessory | |
| ok 5 - group group_A is core so shouldnt have any accessory labels | |
| ok 6 - group group_B found in file t/data/accessory_graphs/no_accessory | |
| ok 7 - group group_B is core so shouldnt have any accessory labels | |
| ok 8 - group group_C found in file t/data/accessory_graphs/no_accessory | |
| ok 9 - group group_C is core so shouldnt have any accessory labels | |
| ok 10 - core accessory graph created | |
| ok 11 - accessory graph created | |
| ok 12 - Initialise order genes object for t/data/accessory_graphs/no_accessory | |
| ok 13 - build the graph | |
| ok 14 - group group_A found in file t/data/accessory_graphs/no_accessory | |
| ok 15 - group group_A is core so shouldnt have any accessory labels | |
| ok 16 - group group_B found in file t/data/accessory_graphs/no_accessory | |
| ok 17 - group group_B is core so shouldnt have any accessory labels | |
| ok 18 - group group_C found in file t/data/accessory_graphs/no_accessory | |
| ok 19 - group group_C is core so shouldnt have any accessory labels | |
| ok 20 - core accessory graph created | |
| ok 21 - accessory graph created | |
| ok 22 - Initialise order genes object for t/data/accessory_graphs/one_bubble | |
| ok 23 - build the graph | |
| ok 24 - group group_C found in file t/data/accessory_graphs/one_bubble | |
| ok 25 - group group_C is core so shouldnt have any accessory labels | |
| ok 26 - group group_E found in file t/data/accessory_graphs/one_bubble | |
| ok 27 - group group_E is core so shouldnt have any accessory labels | |
| ok 28 - group group_bubble_1 found in file t/data/accessory_graphs/one_bubble | |
| ok 29 - group group_bubble_1 is accessory so should have accessory label | |
| ok 30 - group group_bubble_2 found in file t/data/accessory_graphs/one_bubble | |
| ok 31 - group group_bubble_2 is accessory so should have accessory label | |
| ok 32 - group group_F found in file t/data/accessory_graphs/one_bubble | |
| ok 33 - group group_F is accessory so should have accessory label | |
| ok 34 - group group_G found in file t/data/accessory_graphs/one_bubble | |
| ok 35 - group group_G is core so shouldnt have any accessory labels | |
| ok 36 - core accessory graph created | |
| ok 37 - accessory graph created | |
| ok 38 - Initialise order genes object for t/data/accessory_graphs/one_bubble | |
| ok 39 - build the graph | |
| ok 40 - group group_C found in file t/data/accessory_graphs/one_bubble | |
| ok 41 - group group_C is core so shouldnt have any accessory labels | |
| ok 42 - group group_E found in file t/data/accessory_graphs/one_bubble | |
| ok 43 - group group_E is core so shouldnt have any accessory labels | |
| ok 44 - group group_bubble_1 found in file t/data/accessory_graphs/one_bubble | |
| ok 45 - group group_bubble_1 is accessory so should have accessory label | |
| ok 46 - group group_bubble_2 found in file t/data/accessory_graphs/one_bubble | |
| ok 47 - group group_bubble_2 is accessory so should have accessory label | |
| ok 48 - group group_F found in file t/data/accessory_graphs/one_bubble | |
| ok 49 - group group_F is core so shouldnt have any accessory labels | |
| ok 50 - group group_G found in file t/data/accessory_graphs/one_bubble | |
| ok 51 - group group_G is core so shouldnt have any accessory labels | |
| ok 52 - core accessory graph created | |
| ok 53 - accessory graph created | |
| ok 54 - Initialise order genes object for t/data/accessory_graphs/one_branch | |
| ok 55 - build the graph | |
| ok 56 - group group_A found in file t/data/accessory_graphs/one_branch | |
| ok 57 - group group_A is core so shouldnt have any accessory labels | |
| ok 58 - group group_B1 found in file t/data/accessory_graphs/one_branch | |
| ok 59 - group group_B1 is accessory so should have accessory label | |
| ok 60 - group group_B2 found in file t/data/accessory_graphs/one_branch | |
| ok 61 - group group_B2 is accessory so should have accessory label | |
| ok 62 - group group_C found in file t/data/accessory_graphs/one_branch | |
| ok 63 - group group_C is core so shouldnt have any accessory labels | |
| ok 64 - group group_E found in file t/data/accessory_graphs/one_branch | |
| ok 65 - group group_E is core so shouldnt have any accessory labels | |
| ok 66 - core accessory graph created | |
| ok 67 - accessory graph created | |
| ok 68 - Initialise order genes object for t/data/accessory_graphs/one_branch | |
| ok 69 - build the graph | |
| ok 70 - group group_A found in file t/data/accessory_graphs/one_branch | |
| ok 71 - group group_A is core so shouldnt have any accessory labels | |
| ok 72 - group group_B1 found in file t/data/accessory_graphs/one_branch | |
| ok 73 - group group_B1 is accessory so should have accessory label | |
| ok 74 - group group_B2 found in file t/data/accessory_graphs/one_branch | |
| ok 75 - group group_B2 is core so shouldnt have any accessory labels | |
| ok 76 - group group_C found in file t/data/accessory_graphs/one_branch | |
| ok 77 - group group_C is core so shouldnt have any accessory labels | |
| ok 78 - group group_E found in file t/data/accessory_graphs/one_branch | |
| ok 79 - group group_E is core so shouldnt have any accessory labels | |
| ok 80 - core accessory graph created | |
| ok 81 - accessory graph created | |
| ok 82 - Initialise order genes object for t/data/accessory_graphs/two_graphs | |
| ok 83 - build the graph | |
| ok 84 - group group_A found in file t/data/accessory_graphs/two_graphs | |
| ok 85 - group group_A is core so shouldnt have any accessory labels | |
| ok 86 - group group_B found in file t/data/accessory_graphs/two_graphs | |
| ok 87 - group group_B is core so shouldnt have any accessory labels | |
| ok 88 - group group_G found in file t/data/accessory_graphs/two_graphs | |
| ok 89 - group group_G is core so shouldnt have any accessory labels | |
| ok 90 - group group_H found in file t/data/accessory_graphs/two_graphs | |
| ok 91 - group group_H is core so shouldnt have any accessory labels | |
| ok 92 - core accessory graph created | |
| ok 93 - accessory graph created | |
| ok 94 - Initialise order genes object for t/data/accessory_graphs/two_graphs | |
| ok 95 - build the graph | |
| ok 96 - group group_A found in file t/data/accessory_graphs/two_graphs | |
| ok 97 - group group_A is core so shouldnt have any accessory labels | |
| ok 98 - group group_B found in file t/data/accessory_graphs/two_graphs | |
| ok 99 - group group_B is core so shouldnt have any accessory labels | |
| ok 100 - group group_G found in file t/data/accessory_graphs/two_graphs | |
| ok 101 - group group_G is core so shouldnt have any accessory labels | |
| ok 102 - group group_H found in file t/data/accessory_graphs/two_graphs | |
| ok 103 - group group_H is core so shouldnt have any accessory labels | |
| ok 104 - core accessory graph created | |
| ok 105 - accessory graph created | |
| ok 106 - Initialise order genes object for t/data/accessory_graphs/single_gene_contig | |
| ok 107 - build the graph | |
| ok 108 - group group_A found in file t/data/accessory_graphs/single_gene_contig | |
| ok 109 - group group_A is core so shouldnt have any accessory labels | |
| ok 110 - core accessory graph created | |
| ok 111 - accessory graph created | |
| ok 112 - Initialise order genes object for t/data/accessory_graphs/single_gene_contig | |
| ok 113 - build the graph | |
| ok 114 - group group_A found in file t/data/accessory_graphs/single_gene_contig | |
| ok 115 - group group_A is core so shouldnt have any accessory labels | |
| ok 116 - core accessory graph created | |
| ok 117 - accessory graph created | |
| ok 118 - Initialise order genes object for t/data/accessory_graphs/core_deletion | |
| ok 119 - build the graph | |
| ok 120 - group group_A found in file t/data/accessory_graphs/core_deletion | |
| ok 121 - group group_A is core so shouldnt have any accessory labels | |
| ok 122 - group group_B found in file t/data/accessory_graphs/core_deletion | |
| ok 123 - group group_B is core so shouldnt have any accessory labels | |
| ok 124 - group group_C found in file t/data/accessory_graphs/core_deletion | |
| ok 125 - group group_C is core so shouldnt have any accessory labels | |
| ok 126 - group group_D found in file t/data/accessory_graphs/core_deletion | |
| ok 127 - group group_D is accessory so should have accessory label | |
| ok 128 - group group_E found in file t/data/accessory_graphs/core_deletion | |
| ok 129 - group group_E is accessory so should have accessory label | |
| ok 130 - group group_F found in file t/data/accessory_graphs/core_deletion | |
| ok 131 - group group_F is accessory so should have accessory label | |
| ok 132 - group group_G found in file t/data/accessory_graphs/core_deletion | |
| ok 133 - group group_G is core so shouldnt have any accessory labels | |
| ok 134 - group group_H found in file t/data/accessory_graphs/core_deletion | |
| ok 135 - group group_H is core so shouldnt have any accessory labels | |
| ok 136 - core accessory graph created | |
| ok 137 - accessory graph created | |
| ok 138 - Initialise order genes object for t/data/accessory_graphs/core_deletion | |
| ok 139 - build the graph | |
| ok 140 - group group_A found in file t/data/accessory_graphs/core_deletion | |
| ok 141 - group group_A is core so shouldnt have any accessory labels | |
| ok 142 - group group_B found in file t/data/accessory_graphs/core_deletion | |
| ok 143 - group group_B is core so shouldnt have any accessory labels | |
| ok 144 - group group_C found in file t/data/accessory_graphs/core_deletion | |
| ok 145 - group group_C is core so shouldnt have any accessory labels | |
| ok 146 - group group_D found in file t/data/accessory_graphs/core_deletion | |
| ok 147 - group group_D is accessory so should have accessory label | |
| ok 148 - group group_E found in file t/data/accessory_graphs/core_deletion | |
| ok 149 - group group_E is accessory so should have accessory label | |
| ok 150 - group group_F found in file t/data/accessory_graphs/core_deletion | |
| ok 151 - group group_F is accessory so should have accessory label | |
| ok 152 - group group_G found in file t/data/accessory_graphs/core_deletion | |
| ok 153 - group group_G is core so shouldnt have any accessory labels | |
| ok 154 - group group_H found in file t/data/accessory_graphs/core_deletion | |
| ok 155 - group group_H is core so shouldnt have any accessory labels | |
| ok 156 - core accessory graph created | |
| ok 157 - accessory graph created | |
| ok 158 - Initialise order genes object for t/data/accessory_graphs/core_island | |
| ok 159 - build the graph | |
| ok 160 - group group_A found in file t/data/accessory_graphs/core_island | |
| ok 161 - group group_A is accessory so should have accessory label | |
| ok 162 - group group_B found in file t/data/accessory_graphs/core_island | |
| ok 163 - group group_B is accessory so should have accessory label | |
| ok 164 - group group_C found in file t/data/accessory_graphs/core_island | |
| ok 165 - group group_C is accessory so should have accessory label | |
| ok 166 - group group_D found in file t/data/accessory_graphs/core_island | |
| ok 167 - group group_D is core so shouldnt have any accessory labels | |
| ok 168 - group group_E found in file t/data/accessory_graphs/core_island | |
| ok 169 - group group_E is core so shouldnt have any accessory labels | |
| ok 170 - group group_F found in file t/data/accessory_graphs/core_island | |
| ok 171 - group group_F is core so shouldnt have any accessory labels | |
| ok 172 - group group_G found in file t/data/accessory_graphs/core_island | |
| ok 173 - group group_G is accessory so should have accessory label | |
| ok 174 - group group_H found in file t/data/accessory_graphs/core_island | |
| ok 175 - group group_H is accessory so should have accessory label | |
| ok 176 - core accessory graph created | |
| ok 177 - accessory graph created | |
| ok 178 - Initialise order genes object for t/data/accessory_graphs/core_island | |
| ok 179 - build the graph | |
| ok 180 - group group_A found in file t/data/accessory_graphs/core_island | |
| ok 181 - group group_A is accessory so should have accessory label | |
| ok 182 - group group_B found in file t/data/accessory_graphs/core_island | |
| ok 183 - group group_B is accessory so should have accessory label | |
| ok 184 - group group_C found in file t/data/accessory_graphs/core_island | |
| ok 185 - group group_C is accessory so should have accessory label | |
| ok 186 - group group_D found in file t/data/accessory_graphs/core_island | |
| ok 187 - group group_D is core so shouldnt have any accessory labels | |
| ok 188 - group group_E found in file t/data/accessory_graphs/core_island | |
| ok 189 - group group_E is core so shouldnt have any accessory labels | |
| ok 190 - group group_F found in file t/data/accessory_graphs/core_island | |
| ok 191 - group group_F is core so shouldnt have any accessory labels | |
| ok 192 - group group_G found in file t/data/accessory_graphs/core_island | |
| ok 193 - group group_G is accessory so should have accessory label | |
| ok 194 - group group_H found in file t/data/accessory_graphs/core_island | |
| ok 195 - group group_H is accessory so should have accessory label | |
| ok 196 - core accessory graph created | |
| ok 197 - accessory graph created | |
| ok 198 - Initialise order genes object for sample weights | |
| ok 199 - build the graph for sample weights | |
| ok 200 - core accessory graph created for sample weights | |
| ok 201 - accessory graph created for sample weights | |
| ok 202 - graph weights changed | |
| ok 203 - graphs reordered as expected | |
| 1..203 | |
| t/Bio/Roary/Output/CoreGeneAlignmentCoorindatesEMBL.t | |
| ok 1 - use Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL; | |
| ok 2 - initialise core gene obj | |
| ok 3 - Get gene name with directory | |
| ok 4 - Get gene name with no directory | |
| ok 5 - Get gene name where theres no extension | |
| ok 6 - Get gene name with partial extension | |
| ok 7 - create the embl header file | |
| ok 8 - content of embl file as expected | |
| ok 9 - next coordinate | |
| 1..9 | |
| t/Bio/Roary/Output/DifferenceBetweenSets.t | |
| ok 1 - use Bio::Roary::Output::DifferenceBetweenSets; | |
| ok 2 - initialise set difference obj | |
| ok 3 - create set one unique | |
| ok 4 - create set two unique | |
| ok 5 - create common set unique | |
| ok 6 - set one file content as expected | |
| ok 7 - set two file content as expected | |
| ok 8 - common set file content as expected | |
| 1..8 | |
| t/Bio/Roary/Output/GroupsMultifastaProtein.t | |
| ok 1 - use Bio::Roary::Output::GroupsMultifastaProtein; | |
| ok 2 - initialise creating the nuc fasta obj | |
| ok 3 - perform the conversion | |
| ok 4 - File content as expected | |
| 1..4 | |
| t/Bio/Roary/Output/GroupsMultifastas.t | |
| ok 1 - use Bio::Roary::Output::GroupsMultifastas; | |
| ok 2 - initialise creating multiple fastas | |
| ok 3 - Create multiple fasta files | |
| ok 4 - output_groups_group_2.fa group created | |
| ok 5 - output_groups_group_2.fa group created | |
| ok 6 - group 2 contect as expected | |
| ok 7 - group 5 contect as expected | |
| 1..7 | |
| t/Bio/Roary/Output/GroupsMultifastasNucleotide.t | |
| ok 1 - use Bio::Roary::Output::GroupsMultifastasNucleotide; | |
| ok 2 | |
| ok 3 - initialise creating multiple fastas where you dont delete non core files | |
| ok 4 - Create multiple fasta files where you dont delete non core files | |
| not ok 5 - Check multifasta content is correct for 3-hly.fa | |
| # Failed test 'Check multifasta content is correct for 3-hly.fa' | |
| # at t/Bio/Roary/Output/GroupsMultifastasNucleotide.t line 42. | |
| # pan_genome_sequences/hly.fa absent | |
| not ok 6 - Check multifasta content is correct for 2-speH.fa | |
| # Failed test 'Check multifasta content is correct for 2-speH.fa' | |
| # at t/Bio/Roary/Output/GroupsMultifastasNucleotide.t line 43. | |
| # pan_genome_sequences/speH.fa absent | |
| not ok 7 - Check multifasta content is correct for 2-argF.fa | |
| # Failed test 'Check multifasta content is correct for 2-argF.fa' | |
| # at t/Bio/Roary/Output/GroupsMultifastasNucleotide.t line 44. | |
| # pan_genome_sequences/argF.fa absent | |
| not ok 8 - pan genome reference file created | |
| # Failed test 'pan genome reference file created' | |
| # at t/Bio/Roary/Output/GroupsMultifastasNucleotide.t line 45. | |
| not ok 9 - pan genome reference as expected | |
| # Failed test 'pan genome reference as expected' | |
| # at t/Bio/Roary/Output/GroupsMultifastasNucleotide.t line 46. | |
| # pan_genome_reference.fa absent | |
| ok 10 - initialise creating multiple fastas where you delete non core files | |
| ok 11 - Create multiple fasta files where you delete non core files | |
| not ok 12 - Check multifasta content is correct for 3-hly.fa | |
| # Failed test 'Check multifasta content is correct for 3-hly.fa ' | |
| # at t/Bio/Roary/Output/GroupsMultifastasNucleotide.t line 62. | |
| # pan_genome_sequences/hly.fa absent | |
| ok 13 - Check 2-speH.fa doesnt exist since its non core | |
| ok 14 - Check 2-argF.fa doesnt exist since its non core | |
| ok 15 - initialise creating multiple fastas | |
| ok 16 - multifasta creation fails when group limit exceeded | |
| 1..16 | |
| # Looks like you failed 6 tests of 16. | |
| t/Bio/Roary/Output/NumberOfGroups.t | |
| ok 1 - use Bio::Roary::Output::NumberOfGroups; | |
| ok 2 - initialise object | |
| ok 3 - create the raw output file | |
| ok 4 - check raw output file created | |
| ok 5 - Content of total groups tab file as expected | |
| ok 6 - check raw output file created | |
| ok 7 - | |
| ok 8 - check raw output file created | |
| ok 9 - Content of total groups tab file as expected | |
| ok 10 - check raw output file created | |
| ok 11 - Content of unique groups tab file as expected | |
| ok 12 - initialise object with 60 percent core definition | |
| ok 13 - create the raw output files for 60 percent core def | |
| ok 14 - Content of conserved genes with 60 percent core def | |
| 1..14 | |
| t/Bio/Roary/Output/QueryGroups.t | |
| ok 1 - use Bio::Roary::Output::QueryGroups; | |
| ok 2 - initialise groups query object | |
| ok 3 - create the union file | |
| ok 4 - create the intersection file | |
| ok 5 - create the complement file | |
| ok 6 - contents of the union groups as expected | |
| ok 7 - contents of the intersection groups as expected | |
| ok 8 - contents of the complement groups as expected | |
| ok 9 - initialise groups query object | |
| ok 10 - create the intersection file | |
| ok 11 - create the complement file | |
| ok 12 - contents of the intersection groups as expected | |
| ok 13 - contents of the complement groups as expected | |
| ok 14 - initialise groups query object with paralogs | |
| ok 15 - create the intersection file | |
| ok 16 - contents of the intersection groups with paralogs as expected | |
| 1..16 | |
| t/Bio/Roary/ParallelAllAgainstAllBlast.t | |
| ok 1 - use Bio::Roary::ParallelAllAgainstAllBlast; | |
| ok 2 - initialise obj with mocked external applications | |
| ok 3 - Run locally | |
| ok 4 - Combined blast results | |
| 1..4 | |
| t/Bio/Roary/PrepareInputFiles.t | |
| ok 1 - use Bio::Roary::PrepareInputFiles; | |
| ok 2 - initalise | |
| ok 3 - proteome extracted from gff files, input fasta files filtered | |
| ok 4 - previously created faa file looked up from gff filename | |
| 1..4 | |
| t/Bio/Roary/PresenceAbsenceMatrix.t | |
| ok 1 - use Bio::Roary::PresenceAbsenceMatrix; | |
| ok 2 - initialise object | |
| ok 3 - create matrix file | |
| ok 4 - matrix file exists | |
| ok 5 - Rtab matrix content as expected | |
| ok 6 - initialise object one gene one group | |
| ok 7 - create matrix file one gene one group | |
| ok 8 - Rtab matrix content as expected for one gene one group | |
| 1..8 | |
| t/Bio/Roary/QC/Report.t | |
| ok 1 - use Bio::Roary::QC::Report; | |
| ok 2 - QC report object created with no input gff files | |
| ok 3 - report generated | |
| ok 4 - report file exists | |
| ok 5 - report file correct | |
| ok 6 - QC report object created with data | |
| ok 7 - filename of nuc from gff | |
| ok 8 - extract nuc command | |
| ok 9 - extract nuc files from gffs | |
| ok 10 - check extracted nuc files from gffs list | |
| ok 11 - Check FASTA file 1 extracted as expected | |
| ok 12 - Check FASTA file 2 extracted as expected | |
| ok 13 # skip kraken not installed | |
| ok 14 # skip kraken not installed | |
| 1..14 | |
| t/Bio/Roary/ReformatInputGFFs.t | |
| ok 1 - use Bio::Roary::ReformatInputGFFs; | |
| ok 2 - initialise with one input gff | |
| ok 3 - fix duplicates with one input gff | |
| ok 4 - list of gff files with one input gff, nothing should change | |
| ok 5 - Directory shouldnt exist because there arent any fixed input files | |
| ok 6 - initialise with 2 input gffs | |
| ok 7 - Directory shouldnt exist before running | |
| ok 8 - extract ids | |
| ok 9 - extract ids | |
| All arguments to easy_init should be either an integer log level or a hash reference. at lib/Bio/Roary/ReformatInputGFFs.pm line 36. | |
| ok 10 - fix duplicates with 2 input gffs | |
| ok 11 - Directory should exist because there is one gff thats fixed | |
| ok 12 - list of gff files one in the fixed directory | |
| ok 13 - fixed file should exist | |
| ok 14 - fixed file should have expected changes | |
| ok 15 - initialise with 3 input gffs | |
| ok 16 - Directory shouldnt exist before running | |
| All arguments to easy_init should be either an integer log level or a hash reference. at lib/Bio/Roary/ReformatInputGFFs.pm line 36. | |
| ok 17 - fix duplicates with 3 input gffs | |
| ok 18 - Directory should exist because there is 2 gffs thats fixed | |
| ok 19 - list of gff files 2 in the fixed directory | |
| ok 20 - fixed file should exist | |
| ok 21 - fixed file should exist | |
| ok 22 - fixed file should have expected changes | |
| ok 23 - fixed file should have expected changes | |
| ok 24 - initialise with 1 gff that has shown to have a bug | |
| ok 25 - fix duplicates | |
| ok 26 - fixed file should exist | |
| ok 27 - fixed file should have expected changes | |
| 1..27 | |
| t/Bio/Roary/ReorderSpreadsheet.t | |
| ok 1 - use Bio::Roary::ReorderSpreadsheet; | |
| ok 2 - initialise reordering the spreadsheet | |
| ok 3 - Column mappings with fixed in same order and end columns ordered by tree file | |
| ok 4 - run the reorder method | |
| ok 5 - check the output file exists | |
| ok 6 - content of the spreadsheet as expected | |
| 1..6 | |
| t/Bio/Roary/SampleOrder.t | |
| ok 1 - use Bio::Roary::SampleOrder; | |
| ok 2 - initialise sample order object | |
| ok 3 - order of sample names matches the tree | |
| ok 4 - initialise sample order object with raxml tree | |
| ok 5 - order of sample names matches the raxml tree | |
| 1..5 | |
| t/Bio/Roary/SequenceLengths.t | |
| ok 1 - use Bio::Roary::SequenceLengths; | |
| ok 2 - Initialise object | |
| ok 3 - hash with lengths of each sequence | |
| 1..3 | |
| t/Bio/Roary/SortFasta.t | |
| ok 1 - use Bio::Roary::SortFasta; | |
| ok 2 - initalise object | |
| ok 3 - sort the fasta file | |
| ok 4 - the new file exists | |
| ok 5 - check order of sorted fasta | |
| ok 6 - initalise object with uneven sequences | |
| ok 7 - sort the fasta file | |
| ok 8 - output sequences are now divisible by three | |
| ok 9 - initalise object with alignment with nnn at end | |
| ok 10 - sort the fasta file and remove nnn at end | |
| ok 11 - output sequences are now divisible by three | |
| ok 12 - initalise object with uneven sequences and remove nnn from end but nothing to remove | |
| ok 13 - sort the fasta file | |
| ok 14 - output sequences are now divisible by three and no nnn removed | |
| ok 15 - totally different | |
| ok 16 - all the same | |
| ok 17 - half different | |
| ok 18 - first half the same | |
| 1..18 | |
| t/Bio/Roary/SplitGroups.t | |
| ok 1 - use Bio::Roary::SplitGroups; | |
| ok 2 - initalise object | |
| ok 3 - output file exists | |
| ok 4 - split group output correct for test 1 | |
| ok 5 - initalise object | |
| ok 6 - output file exists | |
| ok 7 - split group output correct for test 2 | |
| ok 8 - initalise object | |
| ok 9 - output file exists | |
| ok 10 - split group output correct for test 3 | |
| ok 11 - initalise object | |
| ok 12 - output file exists | |
| ok 13 - split group output correct for test 4 | |
| 1..13 | |
| phase `check' failed after 320.5 seconds |
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