def __init__(self,
seqrecord,
draw_type='simple',
gene_to_draw=None,
feature_class_qualifier='ft_description',
feature_name_qualifier='hit_name',
**kwargs):
self.seqrecord = seqrecord
self.panel = Panel(**kwargs)
self.feature_class_qualifier = feature_class_qualifier
self.feature_name_qualifier = feature_name_qualifier
if draw_type == 'simple':
ref_obj_track = tracks.BaseTrack(
features.Simple(
1,
len(self.seqrecord),
height=1.5,
name=seqrecord.name,
color_by_cm=True,
track_lines=3,
alpha=1,
))
self.panel.add_track(ref_obj_track)
self.draw_features()
elif draw_type == 'gene structure':
self.draw_features_ordered_by_gene_struct(gene_code=gene_to_draw)
def drawFeatures2(tks, highlight=[], filename=None, color=None, **kwargs):
from biograpy import Panel, tracks, features
panel = Panel(fig_width=500,
fig_height=150,
fig_dpi=100,
padding=10,
grid='both')
for feats in tks:
test_track = tracks.BaseTrack(name='X', height=.2)
for feat in feats:
if feat.location.strand == -1:
arr = "larrow,pad=0.6"
else:
arr = "rarrow,pad=0.6"
q = feat.qualifiers
tag = q['locus_tag'][0]
test_track.append(
features.GenericSeqFeature(
feat,
name=tag,
boxstyle=arr,
))
panel.add_track(test_track)
if filename == None:
filename = 'genediagram'
panel.save(filename + '.png')
panel.close()
return filename + '.png'
def doWork(args):
panel = Panel(fig_width=900, padding=25, grid=None, xmin=0)
seq_length = 0
for gff in args.gffs:
seqrecord = GFF.parse(gff).next()
if len(seqrecord) > seq_length:
seq_length = len(seqrecord)
#seqrecord = SeqIO.parse(args.infile, "genbank").next()
cds_track = tracks.BaseTrack(sort_by='collapse')
for feature in seqrecord.features:
if feature.type == 'CDS':
#print feature.qualifiers['product']
if feature.qualifiers['product'][0] == 'hypothetical protein':
col = '#BDBDBD'
else:
col = '#2B8CBE'
feat = features.GenericSeqFeature(feature,
color_by_cm=False,
fc=col)
cds_track.append(feat)
elif feature.type == 'source':
cds_track.append(
features.GenericSeqFeature(feature,
color_by_cm=False,
alpha=0.0,
fc='1.0',
ec='1.0'))
else:
cds_track.append(
features.GenericSeqFeature(feature,
color_by_cm=False,
fc='0.0',
ec='0.0'))
panel.add_track(cds_track)
panel.save(args.outfile, xmin=0, xmax=seq_length)
def test_simple_features(self):
panel=Panel(fig_width=1000)#initialize a drawer
test_track = tracks.BaseTrack(features.Simple(name='feat1',start=100,end=756,),
features.Simple(name='feat2',start=300,end=1056,),
features.Simple(name='feat3',start=600,end=1356,),
features.Simple(name='feat4',start=800,end=1356,),
features.Simple(name='feat5',start= 1357,end=1806,),
name = 'test')
panel.add_track(test_track)
fh = tempfile.TemporaryFile()
panel.save(fh, format='png')
fh.seek(0)
img = Image.open(fh)
#self.assertEqual(img.size, (1000, 220))
self.assertEqual(img.format, 'PNG')
if is_gene_name_replace_protein_name:
m = re.search('([^.]+)', seq_title)
seq_title = m.group(1)
else:
pass
print seq_title
for domain_obj in domain_objs:
print domain_obj.start
# draw domain structure using BioGraPy
panel = Panel(fig_dpi=100)
#if not test_track:
test_track = tracks.BaseTrack(name=seq_title, sort_by=None)
for index, domain_obj in enumerate(domain_objs):
dfeat = None
feat = SeqFeature.SeqFeature()
start, stop = domain_obj.start, domain_obj.stop
#feat.location = SeqFeature.FeatureLocation(start, stop)
feat.location = SeqFeature.FeatureLocation(1, 100)
feats.append(feat)
domain_names.append(domain_obj.short_name)
if is_domain_on_same_line:
continue
if is_domain_on_diff_line:
colors_4_this_domain = [domain_colors[domain_obj.short_name]]
colors_4_this_domain = 'y'
if index == 0:
def draw_features(self):
tracks2draw = dict()
feat_collector = {
} #store complex feature grouping. drawing for witch it is called later
for feature in self.seqrecord.features:
if feature.type not in tracks2draw:
tracks2draw[feature.type] = tracks.BaseTrack(name=feature.type)
feature_name = ''
if feature.id != '<unknown id>':
feature_name = feature.id
if self.feature_name_qualifier in feature.qualifiers:
if isinstance(feature.qualifiers[self.feature_name_qualifier],
list):
feature_name = feature.qualifiers[
self.feature_name_qualifier][0]
elif isinstance(
feature.qualifiers[self.feature_name_qualifier], str):
feature_name = feature.qualifiers[
self.feature_name_qualifier]
'''draw segmented features '''
drawn = False
if feature.sub_features:
for sub_feature in feature.sub_features: #detect 'join subfeature and calls the appropriate feature
if sub_feature.location_operator == 'join':
grfeat = features.SegmentedSeqFeature(
feature,
name=feature_name,
)
tracks2draw[feature.type].add_feature(grfeat)
drawn = True
break
else:
if not drawn:
'''Add here feature specific visualizations '''
if feature.type == 'gene': #'gene' specific visualization
grfeat = features.GeneSeqFeature(
feature,
name=feature_name,
)
tracks2draw[feature.type].add_feature(grfeat)
elif feature.location.start.position == feature.location.end.position: #single point feature
grfeat = features.SinglePositionFeature(
feature,
name=feature_name,
)
tracks2draw[feature.type].add_feature(grfeat)
elif 'transmembrane' in feature.type.lower(
): #add TM handling, cannot handle multiple TM annotations
if feature.type in tracks2draw:
del tracks2draw[feature.type]
if not 'transmembrane' in feat_collector:
feat_collector['transmembrane'] = dict(
TM=[],
cyto=[],
non_cyto=[],
)
feat_collector['transmembrane']['TM'].append(feature)
if 'name' not in feat_collector['transmembrane']:
feat_collector['transmembrane'][
'name'] = feature_name
elif 'topological domain' in feature.type.lower(
): #handles topological domains from uniprot
if feature.type in tracks2draw:
del tracks2draw[feature.type]
if not 'transmembrane' in feat_collector:
feat_collector['transmembrane'] = dict(TM=[],
cyto=[],
non_cyto=[])
if 'description' in feature.qualifiers:
cyto = False
if isinstance(feature.qualifiers['description'],
list):
for d in feature.qualifiers['description']:
if d.lower() == 'cytoplasmic':
cyto = True
else:
if feature.qualifiers['description'].lower(
) == 'cytoplasmic':
cyto = True
if cyto:
feat_collector['transmembrane']['cyto'].append(
feature)
else:
feat_collector['transmembrane'][
'non_cyto'].append(feature)
elif 'cytoplasm' in feature.type.lower(): #risky!!
if feature.type in tracks2draw:
del tracks2draw[feature.type]
if not 'transmembrane' in feat_collector:
feat_collector['transmembrane'] = dict(TM=[],
cyto=[],
non_cyto=[])
if ('not' in feature.type.lower()) or (
'non' in feature.type.lower()):
feat_collector['transmembrane']['non_cyto'].append(
feature)
else:
feat_collector['transmembrane']['cyto'].append(
feature)
elif feature.type == 'beta_strand': #add secondary structure handling
if feature.type in tracks2draw:
del tracks2draw[feature.type]
if not 'SecStructFeature' in feat_collector:
feat_collector['secondary structure'] = dict(
betas=[], alphah=[], coil=[])
feat_collector['secondary structure']['betas'].append(
feature)
elif feature.type == 'alpha_helix': #add secondary structure handling
if feature.type in tracks2draw:
del tracks2draw[feature.type]
if not 'secondary structure' in feat_collector:
feat_collector['secondary structure'] = dict(
betas=[], alphah=[], coil=[])
feat_collector['secondary structure']['alphah'].append(
feature)
elif feature.type == 'peptide_coil': #add secondary structure handling
if feature.type in tracks2draw:
del tracks2draw[feature.type]
if not 'secondary structure' in feat_collector:
feat_collector['secondary structure'] = dict(
betas=[], alphah=[], coil=[])
feat_collector['secondary structure']['coil'].append(
feature)
else: #generic feature
if 'score' in feature.qualifiers: #color by score
try:
color_by_score = False
if isinstance(feature.qualifiers['score'],
list):
score = float(
feature.qualifiers['score'][0])
if 0 <= score <= 1:
feat_score = score
color_by_score = True
else:
score = float(feature.qualifiers['score'])
if 0 <= score <= 1:
feat_score = score
color_by_score = True
if color_by_score:
grfeat = features.GenericSeqFeature(
feature,
name=feature_name,
score=feat_score,
use_score_for_color=True,
cm='RdYlGn')
else:
raise ValueError(
'Score value cannot be handled, should be a float between 0 and 1. Actual value: %f'
% score)
except: #draw normal feature
grfeat = features.GenericSeqFeature(
feature, name=feature_name)
else:
grfeat = features.GenericSeqFeature(
feature, name=feature_name)
tracks2draw[feature.type].add_feature(grfeat)
'''draw complex features '''
for feat_group in feat_collector:
if feat_group not in tracks2draw:
tracks2draw[feat_group] = tracks.BaseTrack(name=feat_group)
if feat_group == 'transmembrane':
grfeat = features.TMFeature(
fill_color='k',
cyto_color='r',
#cyto_label = 'in',
non_cyto_color='g',
non_cyto_linestyle='-',
#non_cyto_label = 'out',
TM_ec='orange',
TM_fc='orange',
TM_label='',
**feat_collector[feat_group])
elif feat_group == 'secondary structure':
grfeat = features.SecStructFeature(
**feat_collector[feat_group])
tracks2draw[feat_group].add_feature(grfeat)
'''add tracks to panel'''
for key in sorted(tracks2draw.keys()):
self.panel.add_track(tracks2draw[key])
if self.seqrecord.letter_annotations:
per_letter_feats = []
ymax = ymin = 0
for quality in self.seqrecord.letter_annotations:
if isinstance(self.seqrecord.letter_annotations[quality][0],
(int, float)):
'''draw numeric per letter annotation as line plot feature '''
feat = features.PlotFeature(
self.seqrecord.letter_annotations[quality],
range(
1,
len(self.seqrecord.letter_annotations[quality]) +
1),
label=str(quality),
)
per_letter_feats.append(feat)
if min(self.seqrecord.letter_annotations[quality]) <= ymin:
ymin = min(self.seqrecord.letter_annotations[quality])
if max(self.seqrecord.letter_annotations[quality]) >= ymax:
ymax = max(self.seqrecord.letter_annotations[quality])
per_letter_track = tracks.PlotTrack(ymin=ymin, ymax=ymax)
for feat in per_letter_feats:
per_letter_track.append(feat)
self.panel.add_track(per_letter_track)
from biograpy import Panel, tracks, features from Bio import SeqFeature panel = Panel(fig_width=900) test_track = tracks.BaseTrack(name = 'domains', sort_by = None, cm = 'Set3') feat = SeqFeature.SeqFeature() feat.location = SeqFeature.FeatureLocation(100, 300) dfeat = features.DomainFeature([feat], name = 'test domain 1', seq_line = (1, 766)) test_track.append(dfeat) dfeat = features.DomainFeature([feat],name = 'test domain 1', height = 1.5, seq_line = (1, 766)) test_track.append(dfeat) dfeat = features.DomainFeature([feat],name = 'test domain 1', height = 1.5, boxstyle = 'round4, rounding_size=1.4', seq_line = (1, 766)) test_track.append(dfeat) dfeat = features.DomainFeature([feat],name = 'test domain 1',height = 1.5, boxstyle = 'larrow, pad = 0', seq_line = (1, 766)) test_track.append(dfeat) dfeat = features.DomainFeature([feat], name = 'test domain 1',height = 1.5, boxstyle = 'round ', seq_line = (1, 766)) test_track.append(dfeat) feat2 = SeqFeature.SeqFeature() feat2.location = SeqFeature.FeatureLocation(500, 700) dfeat = features.DomainFeature([feat,feat2], name = 'test domain 1',height = 1.5, boxstyle = 'roundtooth, pad = 0.1, tooth_size=1.2', seq_line = (1, 766), alpha = 0.7) test_track.append(dfeat)
from biograpy import Panel, tracks, features
panel = Panel(fig_width=1000, ) #initialize a drawer
test_track = tracks.BaseTrack(features.Simple(
name='feat1',
start=100,
end=756,
),
features.Simple(
name='feat2',
start=300,
end=1056,
),
features.Simple(
name='feat3',
start=600,
end=1356,
),
features.Simple(
name='feat4',
start=800,
end=1356,
),
features.Simple(
name='feat5',
start=1357,
end=1806,
),
name='test')
panel.append(test_track)
panel.save('test.png')