def annotate_sequence(seqrecord, features=['gene', 'RNA structure', 'other']):
'''Annotate a consensus with the genes and stuff (in place)'''
from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
from hivwholeseq.utils.genome_info import gene_edges, RNA_structure_edges, \
other_edges, find_region_edges, find_region_edges_multiple
from hivwholeseq.data.primers import primers_PCR as primers_PCR_edges
edge_dict = {'gene': gene_edges,
'RNA structure': RNA_structure_edges,
'PCR primers': primers_PCR_edges,
'other': other_edges}
smat = np.array(seqrecord)
for feature_type in features:
edges_all = edge_dict[feature_type]
for name, edges in edges_all.iteritems():
# Skip a feature if it's present already
if name in map(lambda x: x.id, seqrecord.features):
continue
# Behave differently for unsplit regions and split ones
if len(edges) == 2:
# LTR problems with F6
if 'F6' in name:
pos_edge = find_region_edges(smat[::-1], [edges[1][::-1], edges[0][::-1]])
pos_edge = [len(smat) - 1 - pos_edge[1], len(smat) - 1 - pos_edge[0]]
else:
pos_edge = find_region_edges(smat, edges)
location = FeatureLocation(*pos_edge)
else:
pos_edges = find_region_edges_multiple(smat, edges)
locations = [FeatureLocation(*pos_edge) for pos_edge in pos_edges]
location = CompoundLocation(locations)
feature = SeqFeature(location, type=feature_type, id=name, strand=1)
seqrecord.features.append(feature)
def annotate_sequence(seqrecord, features=['gene', 'RNA structure', 'other']):
'''Annotate a consensus with the genes and stuff (in place)'''
from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
from hivwholeseq.utils.genome_info import gene_edges, RNA_structure_edges, \
other_edges, find_region_edges, find_region_edges_multiple
from hivwholeseq.data.primers import primers_PCR as primers_PCR_edges
edge_dict = {
'gene': gene_edges,
'RNA structure': RNA_structure_edges,
'PCR primers': primers_PCR_edges,
'other': other_edges
}
smat = np.array(seqrecord)
for feature_type in features:
edges_all = edge_dict[feature_type]
for name, edges in edges_all.iteritems():
# Skip a feature if it's present already
if name in map(lambda x: x.id, seqrecord.features):
continue
# Behave differently for unsplit regions and split ones
if len(edges) == 2:
# LTR problems with F6
if 'F6' in name:
pos_edge = find_region_edges(
smat[::-1], [edges[1][::-1], edges[0][::-1]])
pos_edge = [
len(smat) - 1 - pos_edge[1],
len(smat) - 1 - pos_edge[0]
]
else:
pos_edge = find_region_edges(smat, edges)
location = FeatureLocation(*pos_edge)
else:
pos_edges = find_region_edges_multiple(smat, edges)
locations = [
FeatureLocation(*pos_edge) for pos_edge in pos_edges
]
location = CompoundLocation(locations)
feature = SeqFeature(location,
type=feature_type,
id=name,
strand=1)
seqrecord.features.append(feature)
def annotate_sequence(seqrecord, additional_edges={}, additional_features=['chunk'], VERBOSE=0):
'''Annotate a consensus with the genes and stuff (in place)'''
# TODO: what do we do with genes that do not start/end where they are
# supposed to? Do we follow biology and track their new locations?
from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
from hivwholeseq.utils.genome_info import gene_edges, RNA_structure_edges, \
other_edges, find_region_edges, find_region_edges_multiple, \
locate_gene
edge_dict = {'gene': gene_edges,
'RNA structure': RNA_structure_edges,
'other': other_edges}
edge_dict.update(additional_edges)
additional_features = ['protein'] + additional_features
features = edge_dict.keys() + additional_features
if VERBOSE:
print 'Features:', ', '.join(features)
smat = np.array(seqrecord)
for feature_type in edge_dict:
edges_all = edge_dict[feature_type]
print feature_type, edge_dict[feature_type].keys()
for name, edges in edges_all.iteritems():
if VERBOSE >= 2:
print name,
# Skip a feature if it's present already
if name in map(lambda x: x.id, seqrecord.features):
if VERBOSE >= 2:
print 'already present.'
continue
# Behave differently for unsplit regions and split ones
if len(edges) == 2:
# LTR problems with F6
if 'F6' in name:
pos_edge = find_region_edges(smat[6000::], [edges[0], None])
pos_edge[0] += 6000
elif feature_type == 'genes':
pos_edge = locate_gene(smat, name, output_compact=True)
else:
pos_edge = find_region_edges(smat, edges)
# Cut the primers for some features
if (None not in pos_edge) and name in ['V1', 'V3', 'V4', 'V5']:
pos_edge[0] += len(edges[0])
pos_edge[1] -= len(edges[1])
# Cut only the right primer for V2
if (None not in pos_edge) and name in ['V2']:
pos_edge[1] -= len(edges[1])
if pos_edge[0] is None:
if name not in ['F1', "LTR5'"]:
print 'WARNING: start not found'
pos_edge[0] = 0
if pos_edge[1] is None:
if name not in ['F6', "LTR3'"]:
print 'WARNING: end not found'
pos_edge[1] = len(smat)
location = FeatureLocation(*pos_edge)
else:
if feature_type == 'genes':
pos_edges = [locate_gene(smat, name+suff, output_compact=True)
for suff in ('1', '2')]
else:
pos_edges = find_region_edges_multiple(smat, edges, min_distance=1)
locations = [FeatureLocation(*pos_edge) for pos_edge in pos_edges]
location = CompoundLocation(locations)
if VERBOSE >= 2:
print 'found:', location
feature = SeqFeature(location, type=feature_type, id=name, strand=1)
seqrecord.features.append(feature)
# Add proteins and other features from HXB2
from operator import attrgetter
from seqanpy import align_overlap
from hivwholeseq.utils.genome_info import proteins, chunks
from hivwholeseq.reference import load_custom_reference
additional_features_dict = {}
if 'protein' in additional_features:
additional_features_dict['protein'] = proteins
if 'chunk' in additional_features:
additional_features_dict['chunk'] = chunks
ref_ann = load_custom_reference('HXB2', 'gb')
for feagroup, additional_features_grp in additional_features_dict.iteritems():
for feaname in additional_features_grp:
if VERBOSE >= 2:
print feaname,
fea = ref_ann.features[map(attrgetter('id'), ref_ann.features).index(feaname)]
seq = fea.extract(ref_ann)
(score, ali1, ali2) = align_overlap(seqrecord, seq, score_gapopen=-20)
start = len(ali2) - len(ali2.lstrip('-'))
end = len(ali2.rstrip('-'))
end -= ali1[start: end].count('-')
location = FeatureLocation(start, end)
if VERBOSE >= 2:
print 'found:', location
feature = SeqFeature(location, type=feagroup, id=feaname, strand=1)
seqrecord.features.append(feature)
def annotate_sequence(seqrecord,
additional_edges={},
additional_features=['chunk'],
VERBOSE=0):
'''Annotate a consensus with the genes and stuff (in place)'''
# TODO: what do we do with genes that do not start/end where they are
# supposed to? Do we follow biology and track their new locations?
from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
from hivwholeseq.utils.genome_info import gene_edges, RNA_structure_edges, \
other_edges, find_region_edges, find_region_edges_multiple, \
locate_gene
edge_dict = {
'gene': gene_edges,
'RNA structure': RNA_structure_edges,
'other': other_edges
}
edge_dict.update(additional_edges)
additional_features = ['protein'] + additional_features
features = edge_dict.keys() + additional_features
if VERBOSE:
print 'Features:', ', '.join(features)
smat = np.array(seqrecord)
for feature_type in edge_dict:
edges_all = edge_dict[feature_type]
print feature_type, edge_dict[feature_type].keys()
for name, edges in edges_all.iteritems():
if VERBOSE >= 2:
print name,
# Skip a feature if it's present already
if name in map(lambda x: x.id, seqrecord.features):
if VERBOSE >= 2:
print 'already present.'
continue
# Behave differently for unsplit regions and split ones
if len(edges) == 2:
# LTR problems with F6
if 'F6' in name:
pos_edge = find_region_edges(smat[6000::],
[edges[0], None])
pos_edge[0] += 6000
elif feature_type == 'genes':
pos_edge = locate_gene(smat, name, output_compact=True)
else:
pos_edge = find_region_edges(smat, edges)
# Cut the primers for some features
if (None not in pos_edge) and name in ['V1', 'V3', 'V4', 'V5']:
pos_edge[0] += len(edges[0])
pos_edge[1] -= len(edges[1])
# Cut only the right primer for V2
if (None not in pos_edge) and name in ['V2']:
pos_edge[1] -= len(edges[1])
if pos_edge[0] is None:
if name not in ['F1', "LTR5'"]:
print 'WARNING: start not found'
pos_edge[0] = 0
if pos_edge[1] is None:
if name not in ['F6', "LTR3'"]:
print 'WARNING: end not found'
pos_edge[1] = len(smat)
location = FeatureLocation(*pos_edge)
else:
if feature_type == 'genes':
pos_edges = [
locate_gene(smat, name + suff, output_compact=True)
for suff in ('1', '2')
]
else:
pos_edges = find_region_edges_multiple(smat,
edges,
min_distance=1)
locations = [
FeatureLocation(*pos_edge) for pos_edge in pos_edges
]
location = CompoundLocation(locations)
if VERBOSE >= 2:
print 'found:', location
feature = SeqFeature(location,
type=feature_type,
id=name,
strand=1)
seqrecord.features.append(feature)
# Add proteins and other features from HXB2
from operator import attrgetter
from seqanpy import align_overlap
from hivwholeseq.utils.genome_info import proteins, chunks
from hivwholeseq.reference import load_custom_reference
additional_features_dict = {}
if 'protein' in additional_features:
additional_features_dict['protein'] = proteins
if 'chunk' in additional_features:
additional_features_dict['chunk'] = chunks
ref_ann = load_custom_reference('HXB2', 'gb')
for feagroup, additional_features_grp in additional_features_dict.iteritems(
):
for feaname in additional_features_grp:
if VERBOSE >= 2:
print feaname,
fea = ref_ann.features[map(attrgetter('id'),
ref_ann.features).index(feaname)]
seq = fea.extract(ref_ann)
(score, ali1, ali2) = align_overlap(seqrecord,
seq,
score_gapopen=-20)
start = len(ali2) - len(ali2.lstrip('-'))
end = len(ali2.rstrip('-'))
end -= ali1[start:end].count('-')
location = FeatureLocation(start, end)
if VERBOSE >= 2:
print 'found:', location
feature = SeqFeature(location, type=feagroup, id=feaname, strand=1)
seqrecord.features.append(feature)
