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'
raise "seq_length cannot be obtained"
else:
raise "length has to be given by either --length, --seq_length or --seq"
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:
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')
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')
seq_length = seq_length
elif seq_file:
seq_objs = get_length_from_seq_file(seq_file,'fasta')
if seq_title in seq_objs:
seq_length = seq_objs[seq_title].length
else:
raise "seq_length cannot be obtained"
else:
raise "length has to be given by either --length, --seq_length or --seq"
for domain_obj in domain_objs:
print domain_obj.start
# draw domain structure using BioGraPy
panel = Panel(fig_dpi=100)
test_track = tracks.BaseTrack(name = seq_title, sort_by = None)
for index,domain_obj in enumerate(domain_objs):
feat = SeqFeature.SeqFeature()
start, stop = domain_obj.start, domain_obj.stop
feat.location = SeqFeature.FeatureLocation(start, stop)
feats.append(feat)
domain_names.append(domain_obj.short_name)
if is_domain_on_same_line:
continue
if index == 0:
dfeat = features.DomainFeature([feat], name=domain_obj.short_name, seq_line=(1,seq_length))
else:
dfeat = features.DomainFeature([feat], name=domain_obj.short_name)
#!usr/bin/python