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 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')
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'
name=domain_obj.short_name,
fc=12)
else:
dfeat = features.DomainFeature([feat],
name=domain_obj.short_name,
fc=colors_4_this_domain)
dfeat = features.DomainFeature([feat], name=domain_obj.short_name)
test_track.append(dfeat)
if is_domain_on_same_line:
#dfeat = features.DomainFeature(feats, name=domain_names, seq_line=(1,seq_length), fc=colors[0:len(feats)])
colors_4_this_domain = map(lambda x: domain_colors[x], domain_names)
print domain_names
dfeat = features.DomainFeature(
feats,
name=domain_names,
seq_line=(1, seq_length),
#ec = 'None', fc=colors_4_this_domain, color_by_cm = False)
ec='None',
color_by_cm=False)
test_track.append(dfeat)
panel.add_track(test_track)
#panel.tracks = [test_track]
if not output:
output = os.path.join(outdir, seq_title + '.png')
#if counter==6: print output
print output
panel.save(output)
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)
test_track = tracks.BaseTrack(name = 'domains', sort_by = None, cm = 'Set3')
dfeat = features.DomainFeature([feat,feat2],name = ['test domain 1', 'test domain 2'], height = 1.5, boxstyle = ['sawtooth, tooth_size=1.4', 'rarrow, pad = 0.1'], seq_line = (1, 766), ec = 'None')
test_track.append(dfeat)
dfeat = features.DomainFeature([feat,feat2],name = ['', 'test domain 2'],height = 1.5, boxstyle = ['round4, rounding_size=1.4', 'larrow, pad = 0.1'], ec = 'None', fc = ['y', 'c'], color_by_cm = False)
test_track.append(dfeat)
panel.add_track(test_track)
panel.save('domain_test.png')