Files

• AUTHORS
• CITATIONS.md
• Dockerfile
• GPL-LICENSE
• LICENSE
• MANIFEST
• META.json
• META.yml
• Makefile.PL
• README
• README.md
• bin/download_fasta_database
• bin/download_mlst_databases
• bin/get_emm_sequence_type
• bin/get_sequence_type
• dist.ini
• example/README.md
• example/expected_output_data/concatenated_alleles.fa
• example/expected_output_data/mlst_results.allele.csv
• example/expected_output_data/mlst_results.genomic.csv
• example/input_data/Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18_v1.fa
• example/input_data/Salmonella_enterica_subsp_enterica_serovar_Typhimurium_DT104_v1.fa
• example/input_data/Salmonella_enterica_subsp_enterica_serovar_Weltevreden_str_10259_v0.2.fa
• example/mlst_databases/Salmonella_enterica/alleles/aroC.tfa
• example/mlst_databases/Salmonella_enterica/alleles/dnaN.tfa
• example/mlst_databases/Salmonella_enterica/alleles/hemD.tfa
• example/mlst_databases/Salmonella_enterica/alleles/hisD.tfa
• example/mlst_databases/Salmonella_enterica/alleles/purE.tfa
• example/mlst_databases/Salmonella_enterica/alleles/sucA.tfa
• example/mlst_databases/Salmonella_enterica/alleles/thrA.tfa
• example/mlst_databases/Salmonella_enterica/profiles/senterica.txt
• install_dependencies.sh
• lib/Bio/MLST/Blast/BlastN.pm
• lib/Bio/MLST/Blast/Database.pm
• lib/Bio/MLST/CDC/Convert.pm
• lib/Bio/MLST/Check.pm
• lib/Bio/MLST/CheckMultipleSpecies.pm
• lib/Bio/MLST/CompareAlleles.pm
• lib/Bio/MLST/DatabaseSettings.pm
• lib/Bio/MLST/Databases.pm
• lib/Bio/MLST/Download/Database.pm
• lib/Bio/MLST/Download/Databases.pm
• lib/Bio/MLST/Download/Downloadable.pm
• lib/Bio/MLST/FilterAlleles.pm
• lib/Bio/MLST/NormaliseFasta.pm
• lib/Bio/MLST/OutputFasta.pm
• lib/Bio/MLST/ProcessFasta.pm
• lib/Bio/MLST/SearchForFiles.pm
• lib/Bio/MLST/SequenceType.pm
• lib/Bio/MLST/Spreadsheet/File.pm
• lib/Bio/MLST/Spreadsheet/Row.pm
• lib/Bio/MLST/Types.pm
• lib/Bio/MLST/Validate/Executable.pm
• lib/Bio/MLST/Validate/File.pm
• lib/Bio/MLST/Validate/Resource.pm
• paper.bib
• paper.md
• t/00-report-prereqs.dd
• t/00-report-prereqs.t
• t/Blast/BlastN.t
• t/Blast/Database.t
• t/CDC/Convert.t
• t/Download/Database.t
• t/Download/Database_fails.t
• t/Download/Database_succeeds.t
• t/Download/Databases.t
• t/FilterAlleles.t
• t/Input/NormaliseFasta.t
• t/Output/Databases.t
• t/Output/MultipleFastas.t
• t/Output/MultipleSpecies.t
• t/Output/OutputFasta.t
• t/Output/SpreadsheetRow.t
• t/Overall/CheckAllModulesCompile.t
• t/SequenceTypes/CompareAlleles.t
• t/SequenceTypes/SearchForFiles.t
• t/SequenceTypes/SequenceType.t
• t/Settings/DatabaseSettings.t
• t/Validate/Executable.t
• t/data/CDC_emmST_partial.tfa
• t/data/Pediococcus_pentosaceus_filtering.xml
• t/data/Streptococcus_pyogenes_emmST_contigs.fa
• t/data/Streptococcus_pyogenes_emmST_unknown.fa
• t/data/abc.fas
• t/data/adk.tfa
• t/data/adk_99_percent.tfa
• t/data/adk_contamination.tfa
• t/data/adk_imperfect.tfa
• t/data/adk_imperfect_contamination.tfa
• t/data/adk_less_than_95_percent.tfa
• t/data/adk_top_hit_low_hit.tfa
• t/data/adk_truncation.tfa
• t/data/adk_two_imperfect_contamination.tfa
• t/data/bbb.fas
• t/data/bordetella.txt
• t/data/ccc.fas
• t/data/contigs.fa
• t/data/contigs_check_concat_allele_order.fa
• t/data/contigs_missing_locus.fa
• t/data/contigs_near_match.fa
• t/data/contigs_novel.fa
• t/data/contigs_one_unknown.tfa
• t/data/contigs_pipe_character_in_seq_name.fa
• t/data/databases/Escherichia_coli_1/alleles/adk.tfa
• t/data/databases/Escherichia_coli_1/alleles/purA.tfa
• t/data/databases/Escherichia_coli_1/alleles/recA.tfa
• t/data/databases/Escherichia_coli_1/profiles/escherichia_coli.txt
• t/data/databases/Helicobacter_pylori/alleles/atpA.tfa
• t/data/databases/Helicobacter_pylori/alleles/efp.tfa
• t/data/databases/Helicobacter_pylori/alleles/mutY.tfa
• t/data/databases/Helicobacter_pylori/profiles/hpylori.txt
• t/data/databases/Streptococcus_pyogenes/profiles/spyogenes.txt
• t/data/databases/Streptococcus_pyogenes_emmST/alleles/emmST.tfa
• t/data/databases/Streptococcus_pyogenes_emmST/profiles/Streptococcus_pyogenes_emmST.txt
• t/data/ddd.fas
• t/data/eee.fas
• t/data/efg.fas
• t/data/expected_Streptococcus_pyogenes_emmST.allele.csv
• t/data/expected_Streptococcus_pyogenes_emmST.genomic.csv
• t/data/expected_Streptococcus_pyogenes_emmST_alleles.fa
• t/data/expected_Streptococcus_pyogenes_emmST_alleles_with_unknown.fa
• t/data/expected_concatenated_alleles.fa
• t/data/expected_mlst_results.allele.csv
• t/data/expected_mlst_results.genomic.csv
• t/data/expected_multi_mlst_results.allele.csv
• t/data/expected_multi_mlst_results.genomic.csv
• t/data/expected_sorted_concatenated_alleles.fa
• t/data/expected_sorted_mlst_results.allele.csv
• t/data/expected_sorted_mlst_results.genomic.csv
• t/data/expected_three_concatenated_alleles.fa
• t/data/expected_three_concatenated_alleles.phylip
• t/data/expected_three_contigs_one_unknown.unknown_allele.adk-2~.fa
• t/data/expected_three_contigs_one_unknown.unknown_allele.recA-1~.fa
• t/data/expected_three_mlst_best_results.allele.csv
• t/data/expected_three_mlst_best_results.genomic.csv
• t/data/expected_three_mlst_results.allele.csv
• t/data/expected_three_mlst_results.genomic.csv
• t/data/expected_two_concatenated_alleles.fa
• t/data/expected_two_mlst_results.allele.csv
• t/data/expected_two_mlst_results.genomic.csv
• t/data/fake_executables/another_executable.sh
• t/data/fake_executables/executable.sh
• t/data/fake_executables/not_executable.sh
• t/data/gdh_fake_blast_output.sh
• t/data/homo_sapiens.txt
• t/data/missing_web_database.xml
• t/data/overall_databases.xml
• t/data/purA.tfa
• t/data/recA.tfa
• t/requires_external.t
• weaver.ini
• xt/author/00-compile.t
• xt/author/pod-syntax.t