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ENH: adds JoinedSequencesWithQuality #160

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merged 1 commit into from
Nov 16, 2017
Merged

ENH: adds JoinedSequencesWithQuality #160

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10 changes: 6 additions & 4 deletions q2_types/per_sample_sequences/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,8 @@
PairedEndFastqManifestPhred64,
QIIME1DemuxFormat, QIIME1DemuxDirFmt)
from ._type import (Sequences, SequencesWithQuality,
PairedEndSequencesWithQuality)
PairedEndSequencesWithQuality,
JoinedSequencesWithQuality)

__all__ = ['CasavaOneEightSingleLanePerSampleDirFmt',
'CasavaOneEightLanelessPerSampleDirFmt',
Expand All @@ -29,8 +30,9 @@
'SingleLanePerSampleSingleEndFastqDirFmt',
'SingleLanePerSamplePairedEndFastqDirFmt', 'Sequences',
'SequencesWithQuality', 'PairedEndSequencesWithQuality',
'SingleEndFastqManifestPhred33', 'SingleEndFastqManifestPhred64',
'PairedEndFastqManifestPhred33', 'PairedEndFastqManifestPhred64',
'QIIME1DemuxFormat', 'QIIME1DemuxDirFmt']
'JoinedSequencesWithQuality', 'SingleEndFastqManifestPhred33',
'SingleEndFastqManifestPhred64', 'PairedEndFastqManifestPhred33',
'PairedEndFastqManifestPhred64', 'QIIME1DemuxFormat',
'QIIME1DemuxDirFmt']

importlib.import_module('q2_types.per_sample_sequences._transformer')
9 changes: 8 additions & 1 deletion q2_types/per_sample_sequences/_type.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,12 @@
'SequencesWithQuality', variant_of=SampleData.field['type'])
PairedEndSequencesWithQuality = SemanticType(
'PairedEndSequencesWithQuality', variant_of=SampleData.field['type'])
JoinedSequencesWithQuality = SemanticType(
'JoinedSequencesWithQuality', variant_of=SampleData.field['type'])

plugin.register_semantic_types(Sequences, SequencesWithQuality,
PairedEndSequencesWithQuality)
PairedEndSequencesWithQuality,
JoinedSequencesWithQuality)

plugin.register_semantic_type_to_format(
SampleData[Sequences],
Expand All @@ -31,6 +34,10 @@
SampleData[SequencesWithQuality],
artifact_format=SingleLanePerSampleSingleEndFastqDirFmt
)
plugin.register_semantic_type_to_format(
SampleData[JoinedSequencesWithQuality],
artifact_format=SingleLanePerSampleSingleEndFastqDirFmt
)
plugin.register_semantic_type_to_format(
SampleData[PairedEndSequencesWithQuality],
artifact_format=SingleLanePerSamplePairedEndFastqDirFmt
Expand Down
12 changes: 11 additions & 1 deletion q2_types/per_sample_sequences/tests/test_type.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@
from q2_types.sample_data import SampleData
from q2_types.per_sample_sequences import (
Sequences, SequencesWithQuality, PairedEndSequencesWithQuality,
QIIME1DemuxDirFmt, SingleLanePerSampleSingleEndFastqDirFmt,
JoinedSequencesWithQuality, QIIME1DemuxDirFmt,
SingleLanePerSampleSingleEndFastqDirFmt,
SingleLanePerSamplePairedEndFastqDirFmt
)
from qiime2.plugin.testing import TestPluginBase
Expand All @@ -29,6 +30,9 @@ def test_sequences_with_quality_semantic_type_registration(self):
def test_paired_end_sequences_with_qual_semantic_type_registration(self):
self.assertRegisteredSemanticType(PairedEndSequencesWithQuality)

def test_joined_sequences_with_qual_semantic_type_registration(self):
self.assertRegisteredSemanticType(JoinedSequencesWithQuality)

def test_sequences_semantic_type_to_format_registration(self):
self.assertSemanticTypeRegisteredToFormat(
SampleData[Sequences],
Expand All @@ -47,6 +51,12 @@ def test_paired_end_sequences_semantic_type_to_format_registration(self):
SingleLanePerSamplePairedEndFastqDirFmt
)

def test_joined_sequences_with_quality_semantic_type_to_format_reg(self):
self.assertSemanticTypeRegisteredToFormat(
SampleData[JoinedSequencesWithQuality],
SingleLanePerSampleSingleEndFastqDirFmt
)


if __name__ == '__main__':
unittest.main()