def __init__(self, aln_fname, outgroup, include_ref_strains = True, outdir = './', formats = ['pdf','png'], verbose = 0, **kwargs):
process.__init__(self, **kwargs)
flu_filter.__init__(self, alignment_file = aln_fname, **kwargs)
tree_refine.__init__(self, **kwargs)
virus_clean.__init__(self, **kwargs)
self.midpoint_rooting = False
self.include_ref_strains = include_ref_strains
self.verbose = verbose
self.formats = formats
self.outdir = outdir.rstrip('/')+'/'
self.auspice_tree_fname = self.outdir + 'tree.json'
self.auspice_align_fname = self.outdir + 'aln.fasta'
self.auspice_aa_align_fname = self.outdir + 'aa_aln.fasta'
self.auspice_sequences_fname = self.outdir + 'sequences.json'
self.auspice_frequencies_fname = None
self.auspice_meta_fname = self.outdir + 'meta.json'
self.path_to_augur = path_to_augur
if os.path.isfile(outgroup):
tmp = [{'strain':seq.name, 'seq':str(record.seq).upper(), 'desc':seq.description}
for seq in SeqIO.parse(outgroup, 'fasta') ]
if len(tmp):
self.outgroup = tmp[0]
if len(tmp)>1:
print "More than one sequence in ", outgroup, "taking first"
if self.verbose:
print "using outgroup found in file ", outgroup
elif outgroup=='auto':
print "automatically determine outgroup"
self.auto_outgroup_blast()
elif isinstance(outgroup, basestring):
seq_names = [x['strain'] for x in self.viruses]
if outgroup in seq_names:
self.outgroup = self.viruses.pop(seq_names.index(outgroup))
if self.verbose:
print "using outgroup found in alignment", outgroup
else:
standard_outgroups = self.load_standard_outgroups()
if outgroup in standard_outgroups:
self.outgroup = standard_outgroups[outgroup]
if self.verbose:
print "using standard outgroup", outgroup
else:
raise ValueError("outgroup %s not found" % outgroup)
return
if "anno:" in self.outgroup['desc']:
anno = [x for x in self.outgroup['desc'].split() if "anno:" in x][0]
anno = (anno.split(':')[1]).split('_')
tmp = [(anno[2*i], int(anno[2*i+1])) for i in range(len(anno)/2)]
self.anno = sorted(tmp, key=lambda x:x[1])
print("Using annotation",self.anno)
else:
self.anno = None
print("No annotation found")
#self.anno = sorted((('SP',0), ('HA1',16), ('HA2',329+16)), key=lambda x:x[1])
self.viruses.append(self.outgroup)
self.filter_geo(prune=False)
self.make_strain_names_unique()
def __init__(self,
aln_fname,
outgroup,
outdir='./',
formats=['pdf', 'svg', 'png'],
verbose=0,
**kwargs):
process.__init__(self, **kwargs)
flu_filter.__init__(self, alignment_file=aln_fname, **kwargs)
tree_refine.__init__(self, **kwargs)
virus_clean.__init__(self, **kwargs)
self.verbose = verbose
self.formats = formats
self.outdir = outdir.rstrip('/') + '/'
self.auspice_tree_fname = self.outdir + 'tree.json'
self.auspice_sequences_fname = self.outdir + 'sequences.json'
self.auspice_frequencies_fname = None
self.auspice_meta_fname = self.outdir + 'meta.json'
if os.path.isfile(outgroup):
tmp = [{
'strain': seq.name,
'seq': str(record.seq).upper(),
'desc': seq.description
} for seq in SeqIO.parse(outgroup, 'fasta')]
if len(tmp):
self.outgroup = tmp[0]
if len(tmp) > 1:
print "More than one sequence in ", outgroup, "taking first"
if self.verbose:
print "using outgroup found in file ", outgroup
elif isinstance(outgroup, basestring):
seq_names = [x['strain'] for x in self.viruses]
if outgroup in seq_names:
self.outgroup = self.viruses.pop(seq_names.index(outgroup))
if self.verbose:
print "using outgroup found in alignment", outgroup
else:
standard_outgroups = [{
'strain': seq.name,
'seq': str(seq.seq).upper(),
'desc': seq.description
} for seq in SeqIO.parse(std_outgroup_file, 'fasta')]
outgroup_names = [x['strain'] for x in standard_outgroups]
if outgroup in outgroup_names:
self.outgroup = standard_outgroups[outgroup_names.index(
outgroup)]
if self.verbose:
print "using standard outgroup", outgroup
else:
raise ValueError("outgroup %s not found" % outgroup)
return
self.viruses.append(self.outgroup)
self.filter_geo(prune=False)
#self.filter_host(prune=False)
self.make_strain_names_unique()
def __init__(self, aln_fname, outgroup, outdir = './', formats = ['pdf','svg','png'], verbose = 0, **kwargs):
process.__init__(self, **kwargs)
flu_filter.__init__(self, alignment_file = aln_fname, **kwargs)
tree_refine.__init__(self, **kwargs)
virus_clean.__init__(self, **kwargs)
self.verbose = verbose
self.formats = formats
self.outdir = outdir.rstrip('/')+'/'
self.auspice_tree_fname = self.outdir + 'tree.json'
self.auspice_sequences_fname = self.outdir + 'sequences.json'
self.auspice_frequencies_fname = None
self.auspice_meta_fname = self.outdir + 'meta.json'
if os.path.isfile(outgroup):
tmp = [{'strain':seq.name, 'seq':str(record.seq).upper(), 'desc':seq.description}
for seq in SeqIO.parse(outgroup, 'fasta') ]
if len(tmp):
self.outgroup = tmp[0]
if len(tmp)>1:
print "More than one sequence in ", outgroup, "taking first"
if self.verbose:
print "using outgroup found in file ", outgroup
elif isinstance(outgroup, basestring):
seq_names = [x['strain'] for x in self.viruses]
if outgroup in seq_names:
self.outgroup = self.viruses.pop(seq_names.index(outgroup))
if self.verbose:
print "using outgroup found in alignment", outgroup
else:
standard_outgroups = [{'strain':seq.name, 'seq':str(seq.seq).upper(), 'desc':seq.description}
for seq in SeqIO.parse(std_outgroup_file, 'fasta') ]
outgroup_names = [x['strain'] for x in standard_outgroups]
if outgroup in outgroup_names:
self.outgroup = standard_outgroups[outgroup_names.index(outgroup)]
if self.verbose:
print "using standard outgroup", outgroup
else:
raise ValueError("outgroup %s not found" % outgroup)
return
self.viruses.append(self.outgroup)
self.filter_geo(prune=False)
#self.filter_host(prune=False)
self.make_strain_names_unique()
def __init__(self,**kwargs): virus_clean.__init__(self, **kwargs)
def __init__(self, **kwargs):
virus_clean.__init__(self, **kwargs)
def __init__(self,
aln_fname,
outgroup,
include_ref_strains=True,
outdir='./',
formats=['pdf', 'png'],
verbose=0,
**kwargs):
process.__init__(self, **kwargs)
flu_filter.__init__(self, alignment_file=aln_fname, **kwargs)
tree_refine.__init__(self, **kwargs)
virus_clean.__init__(self, **kwargs)
self.midpoint_rooting = False
self.include_ref_strains = include_ref_strains
self.verbose = verbose
self.formats = formats
self.outdir = outdir.rstrip('/') + '/'
self.auspice_tree_fname = self.outdir + 'tree.json'
self.auspice_align_fname = self.outdir + 'aln.fasta'
self.auspice_aa_align_fname = self.outdir + 'aa_aln.fasta'
self.auspice_sequences_fname = self.outdir + 'sequences.json'
self.auspice_frequencies_fname = None
self.auspice_meta_fname = self.outdir + 'meta.json'
self.path_to_augur = path_to_augur
if os.path.isfile(outgroup):
tmp = [{
'strain': seq.name,
'seq': str(record.seq).upper(),
'desc': seq.description
} for seq in SeqIO.parse(outgroup, 'fasta')]
if len(tmp):
self.outgroup = tmp[0]
if len(tmp) > 1:
print "More than one sequence in ", outgroup, "taking first"
if self.verbose:
print "using outgroup found in file ", outgroup
elif outgroup == 'auto':
print "automatically determine outgroup"
self.auto_outgroup_blast()
elif isinstance(outgroup, basestring):
seq_names = [x['strain'] for x in self.viruses]
if outgroup in seq_names:
self.outgroup = self.viruses.pop(seq_names.index(outgroup))
if self.verbose:
print "using outgroup found in alignment", outgroup
else:
standard_outgroups = self.load_standard_outgroups()
if outgroup in standard_outgroups:
self.outgroup = standard_outgroups[outgroup]
if self.verbose:
print "using standard outgroup", outgroup
else:
raise ValueError("outgroup %s not found" % outgroup)
return
if "anno:" in self.outgroup['desc']:
anno = [x for x in self.outgroup['desc'].split()
if "anno:" in x][0]
anno = (anno.split(':')[1]).split('_')
tmp = [(anno[2 * i], int(anno[2 * i + 1]))
for i in range(len(anno) / 2)]
self.anno = sorted(tmp, key=lambda x: x[1])
print("Using annotation", self.anno)
else:
self.anno = None
print("No annotation found")
#self.anno = sorted((('SP',0), ('HA1',16), ('HA2',329+16)), key=lambda x:x[1])
self.viruses.append(self.outgroup)
self.filter_geo(prune=False)
self.make_strain_names_unique()