Reference¶
Utilities¶
Test helper functions.
-
class
resolwe_bio.utils.test.
BioProcessTestCase
(methodName='runTest')[source]¶ Base class for writing bioinformatics process tests.
It is a subclass of Resolwe’s
ProcessTestCase
with some specific functions used for testing bioinformatics processes.-
prepare_amplicon_master_file
(mfile='56G_masterfile_test.txt', pname='56G panel, v2')[source]¶ Prepare amplicon master file.
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prepare_annotation
(fn='sp_test.gtf', source='DICTYBASE', species='Dictyostelium discoideum', build='dd-05-2009')[source]¶ Prepare annotation GTF.
-
prepare_annotation_gff
(fn='annotation dicty.gff.gz', source='DICTYBASE', species='Dictyostelium discoideum', build='dd-05-2009')[source]¶ Prepare annotation GFF3.
-
prepare_bam
(fn='sp_test.bam', species='Dictyostelium discoideum', build='dd-05-2009')[source]¶ Prepare alignment BAM.
-
prepare_expression
(f_rc='exp_1_rc.tab.gz', f_exp='exp_1_tpm.tab.gz', f_type='TPM', name='Expression', source='DICTYBASE', descriptor=None, feature_type='gene', species='Dictyostelium discoideum', build='dd-05-2009')[source]¶ Prepare expression.
-
-
class
resolwe_bio.utils.test.
KBBioProcessTestCase
(methodName='runTest')[source]¶ Class for bioinformatics process tests that use knowledge base.
It is based on
BioProcessTestCase
and Django’sLiveServerTestCase
. The latter launches a live Django server in a separate thread so that the tests may use it to query the knowledge base.