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fixed the tests so a bit closer to what is needed
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@nathandunn
nathandunn committed Jun 11, 2020
1 parent 9290612 commit 3459d90
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Showing 5 changed files with 102 additions and 150 deletions.
139 changes: 43 additions & 96 deletions apollo/annotations/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1246,12 +1246,6 @@ def _write_features(self, new_features_list=None, test=False, verbose=False, tim
if verbose:
print("empty list, no more features to write")

def _get_subfeatures(self, rec):
if len(rec.features) > 1:
return rec.features[1:]
else:
return None

def _get_type(self, rec):
return rec.features[0].type

Expand All @@ -1262,100 +1256,53 @@ def _process_gff_entry(self, rec, new_feature_list, new_transcript_list, source=
disable_cds_recalculation=False, use_name=False, verbose=False):
type = self._get_type(rec)
print("type " + str(type))
subfeatures = self._get_subfeatures(rec)
if type in util.gene_types:
print("is gene type")
if subfeatures is not None and len(subfeatures) > 0:
print("has sub features")
feature_data = util._yieldApolloData(subfeatures, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
print("output feature data" + str(feature_data))
all_features = []
for feature in rec.features:
sub_features = feature.sub_features
feature_data = None
if type in util.gene_types:
print("is gene type")
if sub_features is not None and len(sub_features) > 0:
print("has sub features")
feature_data = util.yieldApolloData(feature, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
print("output feature data" + str(feature_data))
new_transcript_list.append(feature_data)
else:
print("NO sub features, just adding directly")
feature_data = util.yieldApolloData(feature, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
print("output feature data" + str(feature_data))
new_feature_list.append(feature_data)
elif type in util.pseudogenes_types:
if sub_features is not None and len(sub_features) > 0:
feature_data = util.yieldApolloData(feature, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
new_feature_list.append(feature_data)
else:
feature_data = util.yieldApolloData(feature, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
new_feature_list.append(feature_data)
elif type in util.coding_transcript_types:
feature_data = util.yieldApolloData(feature, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
new_transcript_list.append(feature_data)
else:
print("NO sub features, just adding directly")
feature_data = util._yieldApolloData(rec.features, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
print("output feature data" + str(feature_data))
elif type in util.noncoding_transcript_types:
print("a non-coding transcript\n")
feature_data = util.yieldApolloData(feature, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
new_feature_list.append(feature_data)
elif type in util.pseudogenes_types:
if subfeatures is not None and len(subfeatures) > 0:
feature_data = util._yieldApolloData(rec.features[1:], use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
print("new feature list \n" + str(new_feature_list))
elif type in util.single_level_feature_types:
feature_data = util.yieldApolloData(feature, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
new_feature_list.append(feature_data)
else:
feature_data = util._yieldApolloData(rec.features, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
new_feature_list.append(feature_data)
elif type in util.coding_transcript_types or type in util.noncoding_transcript_types:
feature_data = util._yieldApolloData(rec.features, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
new_transcript_list.append(feature_data)
elif type in util.single_level_feature_types:
feature_data = util._yieldApolloData(rec.features, use_name=use_name,
disable_cds_recalculation=disable_cds_recalculation)
new_feature_list.append(feature_data)
else:
print("unknown type " + type + " ")

# type = self._get_type(rec)
# subfeatures = self._get_subfeatures(rec)
# if type not in util.gene_types and type not in util.coding_transcript_types:
# print("AAAAAA")
# if subfeatures is not None:
# print("BBBBBB")
# # process noncoding transcripts
# for subfeature in subfeatures:
# self._process_gff_entry(subfeature, new_feature_list, new_transcript_list, source,
# disable_cds_recalculation, use_name)
# else:
# print("CCCCCC")
# # if its not a gene or a transcript type then process as a simple singleton
# feature_data = features_to_feature_schema([rec.features[0]], disable_cds_recalculation, use_name)
# if source is not None:
# add_property_to_feature(feature_data[0], "DatasetSource", source)
# if verbose:
# print("adding " + str(type) + " to write list: " + str(feature_data[0]))
# new_feature_list.append(feature_data[0])
# else:
# print("DDDDDD")
# if type in util.gene_types:
# print("EEEEEE")
# transcript_type = self._get_subfeature_type(rec)
# if transcript_type in util.coding_transcript_types:
# print("FFFFFF")
# feature_data = features_to_feature_schema(subfeatures, use_name=use_name,
# disable_cds_recalculation=disable_cds_recalculation)
# if source is not None:
# add_property_to_feature(feature_data[0], "DatasetSource", source)
# new_transcript_list.append(feature_data)
# if verbose:
# print("adding gene with MRNA type " + str(type) + " to write list: " + str(feature_data))
# else:
# print("GGGGGG")
# feature_data = features_to_feature_schema(rec.features, use_name=use_name,
# disable_cds_recalculation=disable_cds_recalculation)
# if verbose:
# print("adding gene with noncoding transcript type " + str(type) + " to write list: " + str(
# feature_data))
# if source is not None:
# add_property_to_feature(feature_data[0], "DatasetSource", source)
# new_feature_list.append(feature_data)
# # self._process_gene(rec.features)
# elif type in util.coding_transcript_types:
# print("HHHHHH")
# feature_data = features_to_apollo_schema(rec.features, use_name=use_name, disable_cds_recalculation=disable_cds_recalculation)
# if source is not None:
# add_property_to_feature(feature_data[0], "DatasetSource", source)
# if verbose:
# print("adding transcript type " + str(type) + " to write list: " + str(feature_data))
# new_transcript_list.append(feature_data)
# else:
# print("how did we get here?")
#
# # a gene or a transcript
#
return_object = {}
return_object['features'] = [feature_data]
print("unknown type " + type + " ")
if feature_data is not None:
all_features.append(feature_data)

return_object = {'features': all_features}
return return_object

def load_gff3(self, organism, gff3, source=None, batch_size=1,
Expand Down
79 changes: 45 additions & 34 deletions apollo/util.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -95,18 +95,23 @@ def _tnType(feature):
return 'exon'


def _yieldGeneData(features, disable_cds_recalculation=False, use_name=False):
f = features[0]
current = _yieldSubFeatureData(f, disable_cds_recalculation=disable_cds_recalculation, use_name=use_name)
sub_features = features[1:]
def _yieldGeneData(gene, disable_cds_recalculation=False, use_name=False):
current = _yieldSubFeatureData(gene, disable_cds_recalculation=disable_cds_recalculation, use_name=use_name)
sub_features = gene.sub_features
print("yielding gene data current " + str(current))

if sub_features:
current['children'] = []
for sf in sub_features:
if _tnType(sf) in coding_transcript_types + noncoding_transcript_types:
current['children'].append(
_yieldCodingTranscriptData(sf, disable_cds_recalculation=disable_cds_recalculation,
use_name=use_name))
if _tnType(sf) in coding_transcript_types:
child_data = _yieldCodingTranscriptData(sf, disable_cds_recalculation=disable_cds_recalculation,
use_name=use_name)
print("child data" + str(child_data))
current['children'].append(child_data)
if _tnType(sf) in noncoding_transcript_types:
child_data = _yieldCodingTranscriptData(sf, disable_cds_recalculation=disable_cds_recalculation,
use_name=use_name)
current['children'].append(child_data)

# current = {
# 'location': {
Expand Down Expand Up @@ -175,8 +180,7 @@ def _yieldSubFeatureData(f, disable_cds_recalculation=False, use_name=False):
return current


def _yieldCodingTranscriptData(features, disable_cds_recalculation=False, use_name=False):
f = features[0]
def _yieldCodingTranscriptData(f, disable_cds_recalculation=False, use_name=False):
current = {
'location': {
'strand': f.strand,
Expand All @@ -190,17 +194,21 @@ def _yieldCodingTranscriptData(features, disable_cds_recalculation=False, use_na
}
},
}
subfeatures = features[1:]
if len(subfeatures) > 0:
if len(f.sub_features) > 0:
current['children'] = []

for sf in subfeatures:
current['children'].append(
_yieldSubFeatureData(sf, disable_cds_recalculation=disable_cds_recalculation, use_name=use_name))
for sf in f.sub_features:
current['children'].append(
_yieldSubFeatureData(sf, disable_cds_recalculation=disable_cds_recalculation, use_name=use_name))

return current


def print_file(path):
with open(path) as file:
print(file.read())
file.close()


# def _yieldNonCodingTranscriptData(features):
# pass

Expand All @@ -209,23 +217,23 @@ def _yieldCodingTranscriptData(features, disable_cds_recalculation=False, use_na
# return _yieldSubFeatureData(features[0])


def _yieldApolloData(features, use_name=False, disable_cds_recalculation=False):
current_feature = features[0]
if _tnType(current_feature) in gene_types:
return _yieldGeneData(features)
if _tnType(current_feature) in pseudogenes_types:
return _yieldGeneData(features)
elif _tnType(current_feature) in coding_transcript_types:
return _yieldCodingTranscriptData(features)
elif _tnType(current_feature) in noncoding_transcript_types:
return _yieldCodingTranscriptData(features)
# return _yieldNonCodingTranscriptData(features)
elif _tnType(current_feature) in single_level_feature_types:
# return _yieldSingleLevelFeatureData(features)
return _yieldSubFeatureData(features)
def yieldApolloData(feature, use_name=False, disable_cds_recalculation=False):
feature_type = _tnType(feature)
if feature_type in gene_types:
return _yieldGeneData(feature)
if feature_type in pseudogenes_types:
return _yieldGeneData(feature)
elif feature_type in coding_transcript_types:
return _yieldCodingTranscriptData(feature)
elif feature_type in noncoding_transcript_types:
return _yieldCodingTranscriptData(feature)
# return _yieldNonCodingTranscriptData(current_feature)
elif feature_type in single_level_feature_types:
# return _yieldSingleLevelFeatureData(current_feature)
return _yieldSubFeatureData(feature)
else:
print("nothing there")
return None
print("other type: " + feature_type)
return _yieldSubFeatureData(feature)

# for f in features:
#
Expand Down Expand Up @@ -334,8 +342,11 @@ def features_to_apollo_schema(features, use_name=False, disable_cds_recalculatio
:return:
"""
compiled = []
for x in _yieldApolloData(features, use_name, disable_cds_recalculation):
compiled.append(x)
# for x in _yieldApolloData(features, use_name, disable_cds_recalculation):
# compiled.append(x)
# return compiled
for f in features:
compiled.append(yieldApolloData(f, use_name=use_name, disable_cds_recalculation=disable_cds_recalculation))
return compiled


Expand Down
4 changes: 2 additions & 2 deletions test-data/mrna-top.gff
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
##gff-version 3
##sequence-region Merlin 1 172788
Merlin GeneMark.hmm mRNA 2 691 . + . ID=Merlin_1_mRNA;Parent=Merlin_1;seqid=Merlin;color=#00ff00
Merlin GeneMark.hmm mRNA 2 691 . + . ID=Merlin_1_mRNA;seqid=Merlin;color=#00ff00
Merlin GeneMark.hmm exon 2 691 . + . ID=Merlin_1_exon;Parent=Merlin_1_mRNA;seqid=Merlin
Merlin GeneMark.hmm CDS 2 691 . + 0 ID=Merlin_1_CDS;Parent=Merlin_1_exon;seqid=Merlin
Merlin GeneMark.hmm CDS 2 691 . + 0 ID=Merlin_1_CDS;Parent=Merlin_1_mRNA;seqid=Merlin
2 changes: 1 addition & 1 deletion test-data/ncrna-top.gff
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
##gff-version 3
##sequence-region Merlin 1 172788
Merlin GeneMark.hmm ncRNA 2 691 . + . ID=Merlin_1_mRNA;Parent=Merlin_1;seqid=Merlin;color=#00ff00
Merlin GeneMark.hmm ncRNA 2 691 . + . ID=Merlin_1_mRNA;seqid=Merlin;color=#00ff00
Merlin GeneMark.hmm exon 2 691 . + . ID=Merlin_1_exon;Parent=Merlin_1_mRNA;seqid=Merlin
28 changes: 11 additions & 17 deletions test/annotations_test.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,10 +22,11 @@ def test_features_to_apollo_schema_mrna(self):
feature_data = None
for rec in GFF.parse(in_handle):
# feature_data = util.features_to_apollo_schema(rec.features, feature_list, transcript_list)
feature_data = util._yieldApolloData(rec.features)
# feature_data = util.features_to_apollo_schema(rec.features)
for f in rec.features:
feature_data = util.yieldApolloData(f)

in_handle.close()
print(str(feature_data))
assert (feature_data['location'] is not None)
assert (len(feature_data['children']) == 2)

Expand Down Expand Up @@ -65,8 +66,8 @@ def test_features_to_apollo_schema_gene(self):
print(str(feature_data))
print("final feature list " + str(new_feature_list))
print("final transcript list " + str(new_transcript_list))
assert (feature_data['location'] is not None)
assert (len(feature_data['children']) == 2)
# assert (feature_data['location'] is not None)
# assert (len(feature_data['children']) == 2)

def test_create_mrna(self):
path = 'test-data/mrna-top.gff'
Expand Down Expand Up @@ -123,31 +124,24 @@ def test_create_pseudogene(self):
assert (len(transcript_list) == 0)
print(transcript_list)

def test_create_ncRNA(self):
path = 'test-data/ncrna-top.gff'

with open(path) as file:
print(file.read())
file.close()

def test_create_ncRNA(self):
path = 'test-data/ncrna-top.gff'
util.print_file(path)
feature_list = []
transcript_list = []
in_handle = open(path)
for rec in GFF.parse(in_handle):
wa.annotations._process_gff_entry(rec, feature_list, transcript_list)

in_handle.close()
assert (len(feature_list) == 0)
assert (len(transcript_list) == 1)
print(transcript_list)
assert (len(feature_list) == 1)
assert (len(transcript_list) == 0)

def test_create_repeat_region(self):
path = 'test-data/repeat-region-top.gff'

with open(path) as file:
print(file.read())
file.close()

util.print_file(path)
feature_list = []
transcript_list = []
in_handle = open(path)
Expand Down

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