-
Notifications
You must be signed in to change notification settings - Fork 28
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
8 changed files
with
303 additions
and
282 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,215 @@ | ||
| #!/usr/bin/env python3 | ||
| # -*- coding: utf-8 -*- | ||
| """ | ||
| Purpose | ||
| ------- | ||
| This module contains variables used to test chewBBACA modules with pytest. | ||
| Code documentation | ||
| ------------------ | ||
| """ | ||
|
|
||
| # Test variables used by pytest | ||
| # AlleleCall default test command | ||
| ALLELECALL_TEST_GENOME_TEMPLATE = ['chewBBACA.py', 'AlleleCall', | ||
| '-i', 'data/allelecall_data/test_genome', | ||
| '-g', 'data/allelecall_data/sagalactiae_schema', | ||
| '-o', 'allelecall_results'] | ||
|
|
||
| ALLELECALL_TEST_DEFAULT = ALLELECALL_TEST_GENOME_TEMPLATE[:] | ||
| ALLELECALL_TEST_MODE1 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '1'] | ||
| ALLELECALL_TEST_MODE2 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '2'] | ||
| ALLELECALL_TEST_MODE3 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '3'] | ||
| ALLELECALL_TEST_MODE4 = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--mode', '4'] | ||
|
|
||
| ALLELECALL_TEST_CDS_TEMPLATE = ['chewBBACA.py', 'AlleleCall', | ||
| '-i', 'data/allelecall_data/test_cds_input', | ||
| '-g', 'data/allelecall_data/sagalactiae_schema', | ||
| '-o', 'allelecall_results', | ||
| '--cds-input'] | ||
|
|
||
| ALLELECALL_TEST_CDS_DEFAULT = ALLELECALL_TEST_CDS_TEMPLATE[:] | ||
| ALLELECALL_TEST_CDS_MODE1 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '1'] | ||
| ALLELECALL_TEST_CDS_MODE2 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '2'] | ||
| ALLELECALL_TEST_CDS_MODE3 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '3'] | ||
| ALLELECALL_TEST_CDS_MODE4 = ALLELECALL_TEST_CDS_TEMPLATE[:]+['--mode', '4'] | ||
|
|
||
| ALLELECALL_TEST_GENOME_LIST = ['chewBBACA.py', 'AlleleCall', | ||
| '-i', 'data/allelecall_data/test_genomes_list/test_genomes.txt', | ||
| '-g', 'data/allelecall_data/sagalactiae_schema', | ||
| '-o', 'allelecall_results'] | ||
|
|
||
| ALLELECALL_TEST_LOCI_IDS_EXTENSION = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--gl', 'data/allelecall_data/test_genes_list/test_genes_extension.txt'] | ||
| ALLELECALL_TEST_LOCI_IDS_NOEXTENSION = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--gl', 'data/allelecall_data/test_genes_list/test_genes_no_extension.txt'] | ||
| ALLELECALL_TEST_LOCI_PATHS = ALLELECALL_TEST_GENOME_TEMPLATE[:]+['--gl', 'data/allelecall_data/test_genes_list/test_genes_path.txt'] | ||
|
|
||
| ALLELECALL_TEST_EMPTY_DIR = ['chewBBACA.py', 'AlleleCall', | ||
| '-i', 'empty_dir', | ||
| '-g', 'data/allelecall_data/sagalactiae_schema', | ||
| '-o', 'allelecall_results'] | ||
|
|
||
| ALLELECALL_TEST_EMPTY_FILES = ['chewBBACA.py', 'AlleleCall', | ||
| '-i', 'data/createschema_data/genome_dir_with_empty_genomes', | ||
| '-g', 'data/allelecall_data/sagalactiae_schema', | ||
| '-o', 'allelecall_results'] | ||
|
|
||
| ALLELECALL_TEST_ZERO_BYTES = ['chewBBACA.py', 'AlleleCall', | ||
| '-i', 'data/createschema_data/zero_bytes_pair', | ||
| '-g', 'data/allelecall_data/sagalactiae_schema', | ||
| '-o', 'allelecall_results'] | ||
|
|
||
| ALLELECALL_TEST_FAKE_PATH = ['chewBBACA.py', 'AlleleCall', | ||
| '-i', 'this/path/aint/real', | ||
| '-g', 'data/allelecall_data/sagalactiae_schema', | ||
| '-o', 'allelecall_results'] | ||
|
|
||
| CREATESCHEMA_TEST_GENOME_TEMPLATE = ['chewBBACA.py', 'CreateSchema', | ||
| '-i', 'data/createschema_data/mock_genome_dir', | ||
| '-o', 'createschema_results', | ||
| '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] | ||
|
|
||
| CREATESCHEMA_TEST_GENOME_LIST = ['chewBBACA.py', 'CreateSchema', | ||
| '-i', 'data/createschema_data/mock_genome_list/mock_genomes.txt', | ||
| '-o', 'createschema_results', | ||
| '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] | ||
|
|
||
| CREATESCHEMA_TEST_CDS = ['chewBBACA.py', 'CreateSchema', | ||
| '-i', 'data/createschema_data/mock_cds_dir', | ||
| '-o', 'createschema_results', | ||
| '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn', | ||
| '--cds-input'] | ||
|
|
||
| CREATESCHEMA_TEST_EMPTY_FILES = ['chewBBACA.py', 'CreateSchema', | ||
| '-i', 'data/createschema_data/genome_dir_with_empty_genomes', | ||
| '-o', 'createschema_results', | ||
| '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] | ||
|
|
||
| CREATESCHEMA_TEST_ZERO_BYTES = ['chewBBACA.py', 'CreateSchema', | ||
| '-i', 'data/createschema_data/zero_bytes_pair', | ||
| '-o', 'createschema_results', | ||
| '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] | ||
|
|
||
| CREATESCHEMA_INVALID_PTF_PATH = ['chewBBACA.py', 'CreateSchema', | ||
| '-i', 'data/createschema_data/mock_schema_dir', | ||
| '-o', 'createschema_results', | ||
| '--ptf', 'path/does/not/exist'] | ||
|
|
||
| CREATESCHEMA_TEST_HEADER_ONLY = ['chewBBACA.py', 'CreateSchema', | ||
| '-i', 'data/createschema_data/genome_dir_with_header_fasta_only', | ||
| '-o', 'createschema_results', | ||
| '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] | ||
|
|
||
| CREATESCHEMA_TEST_INVALID_GENOME = ['chewBBACA.py', 'CreateSchema', | ||
| '-i', 'data/createschema_data/invalid_genome_dir', | ||
| '-o', 'createschema_results', | ||
| '--ptf', 'data/createschema_data/Streptococcus_agalactiae.trn'] | ||
|
|
||
| ALLELECALL_EVALUATOR_INVALID_PATH = ['chewBBACA.py', 'AlleleCallEvaluator', | ||
| '-i', 'data/allelecall_data/fake_results', | ||
| '-g', 'data/allelecall_data/sagalactiae_schema', | ||
| '-o', 'results_report'] | ||
|
|
||
| ALLELECALL_EVALUATOR_VALID = ['chewBBACA.py', 'AlleleCallEvaluator', | ||
| '-i', 'data/allelecall_data/test_results/mode4', | ||
| '-g', 'data/allelecall_data/sagalactiae_schema', | ||
| '-o', 'results_report'] | ||
|
|
||
|
|
||
| CHEWIE_TEST_H = ['chewBBACA.py', '-h'] | ||
| CHEWIE_TEST_HELP = ['chewBBACA.py', '--help'] | ||
| CHEWIE_TEST_V = ['chewBBACA.py', '-v'] | ||
| CHEWIE_TEST_VERSION = ['chewBBACA.py', '--version'] | ||
| CREATESCHEMA_TEST_H = ['chewBBACA.py', 'CreateSchema', '-h'] | ||
| CREATESCHEMA_TEST_HELP = ['chewBBACA.py', 'CreateSchema', '--help'] | ||
| ALLELECALL_TEST_H = ['chewBBACA.py', 'AlleleCall', '-h'] | ||
| ALLELECALL_TEST_HELP = ['chewBBACA.py', 'AlleleCall', '--help'] | ||
| SCHEMAEVALUATOR_TEST_H = ['chewBBACA.py', 'SchemaEvaluator', '-h'] | ||
| SCHEMAEVALUATOR_TEST_HELP = ['chewBBACA.py', 'SchemaEvaluator', '--help'] | ||
| ALLELECALL_EVALUATOR_TEST_H = ['chewBBACA.py', 'AlleleCallEvaluator', '-h'] | ||
| ALLELECALL_EVALUATOR_TEST_HELP = ['chewBBACA.py', 'AlleleCallEvaluator', '--help'] | ||
| EXTRACTCGMLST_TEST_H = ['chewBBACA.py', 'ExtractCgMLST', '-h'] | ||
| EXTRACTCGMLST_TEST_HELP = ['chewBBACA.py', 'ExtractCgMLST', '--help'] | ||
| REMOVEGENES_TEST_H = ['chewBBACA.py', 'RemoveGenes', '-h'] | ||
| REMOVEGENES_TEST_HELP = ['chewBBACA.py', 'RemoveGenes', '--help'] | ||
| PREPEXTERNALSCHEMA_TEST_H = ['chewBBACA.py', 'PrepExternalSchema', '-h'] | ||
| PREPEXTERNALSCHEMA_TEST_HELP = ['chewBBACA.py', 'PrepExternalSchema', '--help'] | ||
| JOINPROFILES_TEST_H = ['chewBBACA.py', 'JoinProfiles', '-h'] | ||
| JOINPROFILES_TEST_HELP = ['chewBBACA.py', 'JoinProfiles', '--help'] | ||
| UNIPROTFINDER_TEST_H = ['chewBBACA.py', 'UniprotFinder', '-h'] | ||
| UNIPROTFINDER_TEST_HELP = ['chewBBACA.py', 'UniprotFinder', '--help'] | ||
| DOWNLOADSCHEMA_TEST_H = ['chewBBACA.py', 'DownloadSchema', '-h'] | ||
| DOWNLOADSCHEMA_TEST_HELP = ['chewBBACA.py', 'DownloadSchema', '--help'] | ||
| LOADSCHEMA_TEST_H = ['chewBBACA.py', 'LoadSchema', '-h'] | ||
| LOADSCHEMA_TEST_HELP = ['chewBBACA.py', 'LoadSchema', '--help'] | ||
| SYNCSCHEMA_TEST_H = ['chewBBACA.py', 'SyncSchema', '-h'] | ||
| SYNCSCHEMA_TEST_HELP = ['chewBBACA.py', 'SyncSchema', '--help'] | ||
| NSSTATS_TEST_H = ['chewBBACA.py', 'NSStats', '-h'] | ||
| NSSTATS_TEST_HELP = ['chewBBACA.py', 'NSStats', '--help'] | ||
| FAKEMODULE_TEST_H = ['chewBBACA.py', 'FakeModule', '-h'] | ||
| FAKEMODULE_TEST_HELP = ['chewBBACA.py', 'FakeModule', '--help'] | ||
|
|
||
| PREPEXTERNALSCHEMA_TEST_EMPTY_DIR = ['chewBBACA.py', 'PrepExternalSchema', | ||
| '-g', 'empty_dir', | ||
| '-o', 'adapted_schema'] | ||
|
|
||
| PREPEXTERNALSCHEMA_TEST_EMPTY_FILES = ['chewBBACA.py', 'PrepExternalSchema', | ||
| '-g', 'data/prep_data/empty_files', | ||
| '-o', 'adapted_schema'] | ||
|
|
||
| PREPEXTERNALSCHEMA_TEST_ZERO_BYTES = ['chewBBACA.py', 'PrepExternalSchema', | ||
| '-g', 'data/prep_data/zero_bytes_pair', | ||
| '-o', 'adapted_schema'] | ||
|
|
||
| PREPEXTERNALSCHEMA_TEST_INVALID_PATH = ['chewBBACA.py', 'PrepExternalSchema', | ||
| '-g', 'this/path/aint/real', | ||
| '-o', 'adapted_schema'] | ||
|
|
||
| PREPEXTERNALSCHEMA_TEST_VALID_INPUT = ['chewBBACA.py', 'PrepExternalSchema', | ||
| '-g', 'data/prep_data/valid_input', | ||
| '-o', 'preped_schema'] | ||
|
|
||
| PREPEXTERNALSCHEMA_TEST_EXTENSIONS = ['chewBBACA.py', 'PrepExternalSchema', | ||
| '-g', 'data/prep_data/file_extensions', | ||
| '-o', 'preped_schema'] | ||
|
|
||
| PREPEXTERNALSCHEMA_TEST_GENE_LIST = ['chewBBACA.py', 'PrepExternalSchema', | ||
| '-g', 'data/prep_data/file_extensions', | ||
| '-o', 'preped_schema', | ||
| '--gl', 'data/prep_data/test_genes_list/test_genes_extension.txt'] | ||
|
|
||
| SCHEMAEVALUATOR_TEST_EMPTY_FILES = ['chewBBACA.py', 'SchemaEvaluator', | ||
| '-g', 'data/schemaevaluator_data/empty_files', | ||
| '-o', 'schema_report'] | ||
|
|
||
| SCHEMAEVALUATOR_TEST_ZERO_BYTES = ['chewBBACA.py', 'SchemaEvaluator', | ||
| '-g', 'data/schemaevaluator_data/zero_bytes_pair', | ||
| '-o', 'schema_report'] | ||
|
|
||
| SCHEMAEVALUATOR_TEST_FAKE_PATH = ['chewBBACA.py', 'SchemaEvaluator', | ||
| '-g', 'this/path/aint/real', | ||
| '-o', 'schema_report'] | ||
|
|
||
| SCHEMAEVALUATOR_TEST_VALID_INPUT = ['chewBBACA.py', 'SchemaEvaluator', | ||
| '-g', 'data/schemaevaluator_data/test_schema', | ||
| '-o', 'schema_report', | ||
| '--loci-reports', '--add-sequences'] | ||
|
|
||
| SCHEMAEVALUATOR_TEST_SINGLE_ALLELE = ['chewBBACA.py', 'SchemaEvaluator', | ||
| '-g', 'data/schemaevaluator_data/single_allele', | ||
| '-o', 'schema_report', | ||
| '--loci-reports', '--add-sequences'] | ||
|
|
||
| SCHEMAEVALUATOR_TEST_SINGLE_INVALID_ALLELE = ['chewBBACA.py', 'SchemaEvaluator', | ||
| '-g', 'data/schemaevaluator_data/single_invalid_allele', | ||
| '-o', 'schema_report', | ||
| '--loci-reports', '--add-sequences'] | ||
|
|
||
| SCHEMAEVALUATOR_TEST_SEVERAL_INVALID_ALLELES = ['chewBBACA.py', 'SchemaEvaluator', | ||
| '-g', 'data/schemaevaluator_data/several_invalid_alleles', | ||
| '-o', 'schema_report', | ||
| '--loci-reports', '--add-sequences'] | ||
|
|
||
|
|
||
|
|
||
|
|
Oops, something went wrong.