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 __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)
class SeqRecordDrawer(object):
'''
Takes in input a seqrecord and draws all the included features along a
reference object
======================= ================================================
Key Description
======================= ================================================
draw_type ``'simple'`` | ``'gene structure'``, default is
``'simple'``. if `simple` draw is selected all
the features will be drawn.
if `gene structure` is selected only features
reporting to a given gene in
``feature.qualifeirs['gene']`` will be drawn.
Gene can be set using the `gene_to_draw`
function.
gene_to_draw default is ``None`` if a string is specified
only features carrying that string in the
``feature.qualifeirs['gene']`` qualifier will
be drawn. if ``None``, the first feature of
type ``'gene'``is selected as the gene to draw.
feature_class_qualifier assign the qualifier key to use to set a
feature_class
feature_name_qualifier assign the qualifier key to use to set a
feature_name
======================= ================================================
all supplied kwargs are passed to the Panel object that is available at
self.panel
'''
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 save(self,output,**kwargs):
self.panel.save(output,**kwargs)
self.panel.close()
def imagemap(self, **kwargs):
return self.panel.imagemap(**kwargs)
def boxes(self):
return self.panel.boxes()
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)
def draw_features_ordered_by_gene_struct(self,gene_code=None):
'''
Draws 'gene structure' type.
The input SeqRecord should include a gene, mRNAs, CDSs and other allowed
features. they will be drawn in a defined order after fusing
corresponding mRNA and CDS. if exons are passed in the seqrecord they
are mapped to the gene patch then corresponding mRNA and CDS are coupled
and drawn then misc_RNA are drawed in the end the other feature present
in the seqrecord are drawn.
the mRNA and CDS are coupled by using a ``qualifier['note']`` containing
``'transcript_id=XXXXXXXXXXXX'`` this work for ensembl-derived
seqrecord, but can be impoved.
'''
# get gene info
for feat in self.seqrecord.features:
if (feat.type=='gene'):
if gene_code:
if gene_code==feat.qualifiers['gene'][0]:
Lgene_name=[gene_code]
if feat.qualifiers.has_key('locus'):
Lgene_name.extend(feat.qualifiers['locus'])
if feat.qualifiers.has_key('note'):
Lgene_name.extend(feat.qualifiers['note'])
gene_name=' - '.join(Lgene_name)
break
else:
gene_code=feat.qualifiers['gene'][0]
Lgene_name=[gene_code]
if feat.qualifiers.has_key('locus_tag'):
Lgene_name.extend(feat.qualifiers['locus_tag'])
if feat.qualifiers.has_key('note'):
Lgene_name.extend(feat.qualifiers['note'])
gene_name=' - '.join(Lgene_name)
break
if not gene_code:
raise ValueError("Cannot draw gene structure, without a gene code")
DFeature2Draw={'Gene':{'gene':[],'exons':[]},
'mRNA and CDS':[],
'Non coding RNA':[],
'Other':[],
'Feature not linked to gene':[],
}
'''couple mRNA and CDS, and collect exons, misc_RNA and other features '''
mRNA_codes=[]
for feature in self.seqrecord.features:
if feature.qualifiers.has_key('gene'):
if gene_code in feature.qualifiers['gene']:
if feature.type =='mRNA':
for note in feature.qualifiers['note']:#IMPROVE HERE
if 'transcript_id' in note:
transcript_id=note
mRNA_codes.append(note)
if feature.type =='mRNA':
for CDS in self.seqrecord.features:
if (CDS.type =='CDS') and (transcript_id in CDS.qualifiers['note']):
break
DFeature2Draw['mRNA and CDS'].append([feature,CDS])
elif feature.type !='CDS':
if feature.type =='gene':
DFeature2Draw['Gene']['gene'].append(feature)
elif feature.type =='exon':
DFeature2Draw['Gene']['exons'].append(feature)
elif feature.type =='misc_RNA':
DFeature2Draw['Non coding RNA'].append(feature)
else:
DFeature2Draw['Other'].append(feature)
else:
DFeature2Draw['Feature not linked to gene'].append(feature)
'''DRAW GENE'''
grfeat=feature.GeneSeqFeature(DFeature2Draw['Gene']['gene'][0],DFeature2Draw['Gene']['exons'],type='Gene',name=gene_name,height=1,cm_value=0.8,alpha=0.5,cm='Purples',linewidth=1)
self.panel.add_feature(grfeat,feature_class=1)
'''DRAW CODING RNA'''
c=0.
for mRNA,CDS in DFeature2Draw['mRNA and CDS']:
c+=1
try:
mRNA_name=', '.join(mRNA.qualifiers['note']).replace('_', ' ')+' - '+CDS.qualifiers['protein_id'][0]
except:
try:
mRNA_name=', '.join(mRNA.qualifiers['note']).replace('_', ' ')
except:
mRNA_name='Transcript '+str(int(c))
grfeat=features.CoupledmRNAandCDS(mRNA,CDS,alpha=0.75,type='mRNA',cm_value=c/len(DFeature2Draw['mRNA and CDS']),cm='autumn',name=mRNA_name)
self.panel.add_feature(grfeat,feature_class=2)
'''DRAW NON CODING RNA'''
c=0.
for RNA in DFeature2Draw['Non coding RNA']:
c+=1
try:
RNA_name=', '.join(RNA.qualifiers['note']).replace('_', ' ')
except:
RNA_name='Non coding transcript '+str(int(c))
grfeat=features.SegmentedSeqFeature(RNA,alpha=0.75,type='Non coding RNA',cm_value=c/len(DFeature2Draw['Non coding RNA']),cm='winter',name=RNA_name)
self.panel.add_feature(grfeat,feature_class=3)
'''DRAW OTHER FEATURES'''
c=0.
for feat in DFeature2Draw['Other']:
c+=1
try:
feat_name=', '.join(mRNA.qualifiers['hit_name']).replace('_', ' ')
except:
feat_name=''
grfeat=features.GenericSeqFeature(RNA,alpha=0.75,type='Other',cm_value=c/len(DFeature2Draw['Other']),name=feat_name)
self.panel.add_feature(grfeat,feature_class=4)
class SeqRecordDrawer(object):
'''
Takes in input a seqrecord and draws all the included features along a
reference object
======================= ================================================
Key Description
======================= ================================================
draw_type ``'simple'`` | ``'gene structure'``, default is
``'simple'``. if `simple` draw is selected all
the features will be drawn.
if `gene structure` is selected only features
reporting to a given gene in
``feature.qualifeirs['gene']`` will be drawn.
Gene can be set using the `gene_to_draw`
function.
gene_to_draw default is ``None`` if a string is specified
only features carrying that string in the
``feature.qualifeirs['gene']`` qualifier will
be drawn. if ``None``, the first feature of
type ``'gene'``is selected as the gene to draw.
feature_class_qualifier assign the qualifier key to use to set a
feature_class
feature_name_qualifier assign the qualifier key to use to set a
feature_name
======================= ================================================
all supplied kwargs are passed to the Panel object that is available at
self.panel
'''
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 save(self, output, **kwargs):
self.panel.save(output, **kwargs)
self.panel.close()
def imagemap(self, **kwargs):
return self.panel.imagemap(**kwargs)
def boxes(self):
return self.panel.boxes()
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)
def draw_features_ordered_by_gene_struct(self, gene_code=None):
'''
Draws 'gene structure' type.
The input SeqRecord should include a gene, mRNAs, CDSs and other allowed
features. they will be drawn in a defined order after fusing
corresponding mRNA and CDS. if exons are passed in the seqrecord they
are mapped to the gene patch then corresponding mRNA and CDS are coupled
and drawn then misc_RNA are drawed in the end the other feature present
in the seqrecord are drawn.
the mRNA and CDS are coupled by using a ``qualifier['note']`` containing
``'transcript_id=XXXXXXXXXXXX'`` this work for ensembl-derived
seqrecord, but can be impoved.
'''
# get gene info
for feat in self.seqrecord.features:
if (feat.type == 'gene'):
if gene_code:
if gene_code == feat.qualifiers['gene'][0]:
Lgene_name = [gene_code]
if feat.qualifiers.has_key('locus'):
Lgene_name.extend(feat.qualifiers['locus'])
if feat.qualifiers.has_key('note'):
Lgene_name.extend(feat.qualifiers['note'])
gene_name = ' - '.join(Lgene_name)
break
else:
gene_code = feat.qualifiers['gene'][0]
Lgene_name = [gene_code]
if feat.qualifiers.has_key('locus_tag'):
Lgene_name.extend(feat.qualifiers['locus_tag'])
if feat.qualifiers.has_key('note'):
Lgene_name.extend(feat.qualifiers['note'])
gene_name = ' - '.join(Lgene_name)
break
if not gene_code:
raise ValueError, "Cannot draw gene structure, without a gene code"
DFeature2Draw = {
'Gene': {
'gene': [],
'exons': []
},
'mRNA and CDS': [],
'Non coding RNA': [],
'Other': [],
'Feature not linked to gene': [],
}
'''couple mRNA and CDS, and collect exons, misc_RNA and other features '''
mRNA_codes = []
for feature in self.seqrecord.features:
if feature.qualifiers.has_key('gene'):
if gene_code in feature.qualifiers['gene']:
if feature.type == 'mRNA':
for note in feature.qualifiers['note']: #IMPROVE HERE
if 'transcript_id' in note:
transcript_id = note
mRNA_codes.append(note)
if feature.type == 'mRNA':
for CDS in self.seqrecord.features:
if (CDS.type == 'CDS') and (
transcript_id
in CDS.qualifiers['note']):
break
DFeature2Draw['mRNA and CDS'].append(
[feature, CDS])
elif feature.type != 'CDS':
if feature.type == 'gene':
DFeature2Draw['Gene']['gene'].append(feature)
elif feature.type == 'exon':
DFeature2Draw['Gene']['exons'].append(feature)
elif feature.type == 'misc_RNA':
DFeature2Draw['Non coding RNA'].append(feature)
else:
DFeature2Draw['Other'].append(feature)
else:
DFeature2Draw['Feature not linked to gene'].append(feature)
'''DRAW GENE'''
grfeat = feature.GeneSeqFeature(DFeature2Draw['Gene']['gene'][0],
DFeature2Draw['Gene']['exons'],
type='Gene',
name=gene_name,
height=1,
cm_value=0.8,
alpha=0.5,
cm='Purples',
linewidth=1)
self.panel.add_feature(grfeat, feature_class=1)
'''DRAW CODING RNA'''
c = 0.
for mRNA, CDS in DFeature2Draw['mRNA and CDS']:
c += 1
try:
mRNA_name = ', '.join(mRNA.qualifiers['note']).replace(
'_', ' ') + ' - ' + CDS.qualifiers['protein_id'][0]
except:
try:
mRNA_name = ', '.join(mRNA.qualifiers['note']).replace(
'_', ' ')
except:
mRNA_name = 'Transcript ' + str(int(c))
grfeat = features.CoupledmRNAandCDS(
mRNA,
CDS,
alpha=0.75,
type='mRNA',
cm_value=c / len(DFeature2Draw['mRNA and CDS']),
cm='autumn',
name=mRNA_name)
self.panel.add_feature(grfeat, feature_class=2)
'''DRAW NON CODING RNA'''
c = 0.
for RNA in DFeature2Draw['Non coding RNA']:
c += 1
try:
RNA_name = ', '.join(RNA.qualifiers['note']).replace('_', ' ')
except:
RNA_name = 'Non coding transcript ' + str(int(c))
grfeat = features.SegmentedSeqFeature(
RNA,
alpha=0.75,
type='Non coding RNA',
cm_value=c / len(DFeature2Draw['Non coding RNA']),
cm='winter',
name=RNA_name)
self.panel.add_feature(grfeat, feature_class=3)
'''DRAW OTHER FEATURES'''
c = 0.
for feat in DFeature2Draw['Other']:
c += 1
try:
feat_name = ', '.join(mRNA.qualifiers['hit_name']).replace(
'_', ' ')
except:
feat_name = ''
grfeat = features.GenericSeqFeature(RNA,
alpha=0.75,
type='Other',
cm_value=c /
len(DFeature2Draw['Other']),
name=feat_name)
self.panel.add_feature(grfeat, feature_class=4)
