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t/Output/MultipleFastas.t  view on Meta::CPAN

  makeblastdb_exec      => 'makeblastdb',
  blastn_exec           => 'blastn',
  output_directory      => $tmpdirectory,
  output_fasta_files    => 1,
  output_phylip_files   => 1,
  spreadsheet_basename  => 'mlst_results',
  parallel_processes    => 3,
  report_lowest_st      => 1
)),'Pass in 3 assemblies, 2 perfect and where 1 has partial matches.');
ok(($multiple_fastas->create_result_files),'Create all the results files for three assemblies.');
compare_files( $tmpdirectory.'/mlst_results.genomic.csv',    't/data/expected_three_mlst_results.genomic.csv', 'Create a spreadsheet with the 3 sets of assemblies combined and the sequences, and give one best guess ST.' );
compare_files( $tmpdirectory.'/mlst_results.allele.csv',     't/data/expected_three_mlst_results.allele.csv', 'Create a spreadsheet with the 3 sets of assemblies combined and the allele numbers, and give one best guess ST.' );
compare_files( $tmpdirectory.'/concatenated_alleles.fa',     't/data/expected_three_concatenated_alleles.fa', 'Create a multi-FASTA file containing the concatenated sequences.');
###
compare_phylip_files( $tmpdirectory.'/concatenated_alleles.phylip', 't/data/expected_three_concatenated_alleles.phylip', 'Output the alignment of the concatenated gene sequences in phylip format, which is used as input to some tree building applicati...
compare_files( $tmpdirectory.'/contigs_one_unknown.unknown_allele.adk-2~.fa',  't/data/expected_three_contigs_one_unknown.unknown_allele.adk-2~.fa', 'Create FASTA files for alleles which are not in the database, so that they can be added later.' );
compare_files( $tmpdirectory.'/contigs_one_unknown.unknown_allele.recA-1~.fa', 't/data/expected_three_contigs_one_unknown.unknown_allele.recA-1~.fa', 'Create FASTA files for alleles which are not in the database, so that they can be added later.' );


$tmpdirectory_obj = File::Temp->newdir(DIR => getcwd, CLEANUP => 1);
$tmpdirectory = $tmpdirectory_obj->dirname();
ok(($multiple_fastas = Bio::MLST::Check->new(