def test_NameToInfo_invalid_label(self):
"""NameToInfo: raises error on invalid label """
s = 'AA'
invalid_labels = ['U17136.1898-984','U17136.1/898984']
for l in invalid_labels:
self.assertRaises(RecordError,NameToInfo,\
Sequence(s, Name=l))
a = 'U17136.1/' #missing start/end positions
b = '/898-984' #missing genbank id
obs_info = NameToInfo(Sequence(s,Name=a))
exp = Info({'GenBank':'U17136.1','Start':None,'End':None})
self.assertEqual(obs_info,exp)
obs_info = NameToInfo(Sequence(s,Name=b))
exp = Info({'GenBank':None,'Start':897,'End':984})
self.assertEqual(obs_info,exp)
#strict = False
# in strict mode you want to get back as much info as possible
lab1 = 'U17136.1898-984'
lab2 = 'U17136.1/898984'
obs_info = NameToInfo(Sequence(s,Name=lab1), strict=False)
exp = Info({'GenBank':None,'Start':None,'End':None})
self.assertEqual(obs_info,exp)
obs_info = NameToInfo(Sequence(s,Name=lab2), strict=False)
exp = Info({'GenBank':'U17136.1','Start':None,'End':None})
self.assertEqual(obs_info,exp)
def test_single_constructor(self):
"""RdbParser should use constructors if supplied"""
to_dna = lambda x, Info: DnaSequence(str(x).replace('U','T'), \
Info=Info)
f = list(RdbParser(self.oneseq, to_dna))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, 'AGTCATCTAGATHCATHC')
self.assertEqual(a.Info, Info({'Species':'H.Sapiens',\
'OriginalSeq':'AGUCAUCUAGAUHCAUHC'}))
def alternativeConstr(header_lines):
info = Info()
for line in header_lines:
all = line.strip().split(':', 1)
#strip out empty lines, lines without name, lines without colon
if not all[0] or len(all) != 2:
continue
name = all[0].upper()
value = all[1].strip().upper()
info[name] = value
return info
f = list(RdbParser(self.oneseq, to_dna, alternativeConstr))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, 'AGTCATCTAGATHCATHC')
exp_info = Info({'OriginalSeq':'AGUCAUCUAGAUHCAUHC',\
'Refs':{}, 'SEQ':'H.SAPIENS'})
self.assertEqual(a.Info, Info({'OriginalSeq':'AGUCAUCUAGAUHCAUHC',\
'Refs':{}, 'SEQ':'H.SAPIENS'}))
def test_rich_label(self):
"""rich label correctly constructs label strings"""
# labels should be equal based on the result of applying their
# attributes to their string template
k = RichLabel(Info(species="rat"), "%(species)s")
l = RichLabel(Info(species="rat", seq_id="xy5"), "%(species)s")
self.assertEqual(k, l)
# labels should construct from Info components correctly
k = RichLabel(Info(species="rat", seq_id="xy5"),
"%(seq_id)s:%(species)s")
self.assertEqual(k, "xy5:rat")
k = RichLabel(Info(species="rat", seq_id="xy5"),
"%(species)s:%(seq_id)s")
self.assertEqual(k, "rat:xy5")
# extra components should be ignored
k = RichLabel(Info(species="rat", seq_id="xy5"), "%(species)s")
self.assertEqual(k, "rat")
# the label should have Info object
self.assertEqual(k.Info.species, "rat")
self.assertEqual(k.Info.seq_id, "xy5")
# label should be constructable just like a normal string
self.assertEqual(RichLabel('a'), 'a')
def test_init_data(self):
"""Info init with data should put items in correct places"""
#need to check init, setting, and resetting of attributes that belong
#in the Info object and attributes that belong in Info.Refs. Also need
#to check __getitem__, __setitem__, and __contains__.
d = Info({'x':3, 'GO':12345})
self.assertEqual(d.x, 3)
self.assertEqual(d.GO, [12345])
self.assertEqual(d.Refs.GO, [12345])
try:
del d.Refs
except AttributeError:
pass
else:
raise Exception, "Failed to prevent deletion of required key Refs"""
d.GenBank = ('qaz', 'wsx')
self.assertEqual(d.GenBank, ['qaz', 'wsx'])
self.assertContains(d.Refs, 'GenBank')
self.assertContains(d, 'GenBank')
d.GenBank = 'xyz'
self.assertEqual(d.GenBank, ['xyz'])
self.assertSameObj(d.GenBank, d.Refs.GenBank)
d.GO = 'x'
self.assertEqual(d.GO, ['x'])
d.GO.append('y')
self.assertEqual(d.GO, ['x', 'y'])
d.ZZZ = 'zzz'
self.assertEqual(d.ZZZ, 'zzz')
self.assertNotContains(d.Refs, 'ZZZ')
self.assertNotContains(d, 'XXX')
self.assertEqual(d.XXX, None)
def CutgSpeciesParser(infile, strict=True, constructor=CodonUsage):
"""Yields successive sequences from infile as CodonUsage objects.
If strict is True (default), raises RecordError when label or seq missing.
"""
if not strict: #easier to see logic without detailed error handling
for rec in CutgSpeciesFinder(infile):
try:
label, counts = rec
if not is_cutg_species_label(label):
continue
species, genes = species_label_splitter(label)
info = Info({'Species': species, 'NumGenes': int(genes)})
freqs = constructor(zip(codon_order, map(int, counts.split())),
Info=info)
yield freqs
except:
continue
else:
for rec in CutgSpeciesFinder(infile):
try:
label, counts = rec
except ValueError: #can't have got any counts
raise RecordError, "Found label without sequences: %s" % rec
if not is_cutg_species_label(label):
raise RecordError, "Found CUTG record without label: %s" % rec
species, genes = species_label_splitter(label)
info = Info({'Species': species, 'NumGenes': int(genes)})
try:
d = zip(codon_order, map(int, counts.split()))
freqs = constructor(d, Info=info)
except:
raise RecordError, "Unable to convert counts: %s" % counts
yield freqs
def test_full(self):
"""InfoMaker should return Info object with name, value pairs"""
test_header = ['acc: X3402','abc:1','mty: ssu','seq: Mit. X3402',\
'','nonsense',':no_name']
obs = InfoMaker(test_header)
exp = Info()
exp.rRNA = 'X3402'
exp.abc = '1'
exp.Species = 'Mit. X3402'
exp.Gene = 'ssu'
self.assertEqual(obs,exp)
def GroupFastaParser(data,
label_to_name,
group_key="Group",
aligned=False,
moltype=ASCII,
done_groups=None,
DEBUG=False):
"""yields related sequences as a separate seq collection
Arguments:
- data: line iterable data source
- label_to_name: LabelParser callback
- group_key: name of group key in RichLabel.Info object
- aligned: whether sequences are to be considered aligned
- moltype: default is ASCII
- done_groups: series of group keys to be excluded
"""
done_groups = [[], done_groups][done_groups is not None]
parser = MinimalFastaParser(data,
label_to_name=label_to_name,
finder=XmfaFinder)
group_ids = []
current_collection = {}
for label, seq in parser:
seq = moltype.makeSequence(seq, Name=label, Info=label.Info)
if DEBUG:
print "str(label) ", str(label), "repr(label)", repr(label)
if not group_ids or label.Info[group_key] in group_ids:
current_collection[label] = seq
if not group_ids:
group_ids.append(label.Info[group_key])
else:
# we finish off check of current before creating a collection
if group_ids[-1] not in done_groups:
info = Info(Group=group_ids[-1])
if DEBUG:
print "GroupParser collection keys", current_collection.keys(
)
seqs = cogent.LoadSeqs(data=current_collection,
moltype=moltype,
aligned=aligned)
seqs.Info = info
yield seqs
current_collection = {label: seq}
group_ids.append(label.Info[group_key])
info = Info(Group=group_ids[-1])
seqs = cogent.LoadSeqs(data=current_collection,
moltype=moltype,
aligned=aligned)
seqs.Info = info
yield seqs
def NcbiFastaLabelParser(line):
"""Creates an Info object and populates it with the line contents.
As of 11/12/03, all records in genpept.fsa and the human RefSeq fasta
files were consistent with this format.
"""
info = Info()
try:
ignore, gi, db, db_ref, description = map(strip, line.split('|', 4))
except ValueError: #probably got wrong value
raise RecordError, "Unable to parse label line %s" % line
info.GI = gi
info[NcbiLabels[db]] = db_ref
info.Description = description
return gi, info
def test_single(self):
"""RdbParser should read single record as (header,seq) tuple"""
res = list(RdbParser(self.oneseq))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, Sequence('AGUCAUCUAGAUHCAUHC'))
self.assertEqual(first.Info, Info({'Species':'H.Sapiens',\
'OriginalSeq':'AGUCAUCUAGAUHCAUHC'}))
res = list(RdbParser(self.multiline))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, Sequence('AGUCAUUAGAUHCAUHC'))
self.assertEqual(first.Info, Info({'Species':'H.Sapiens',\
'OriginalSeq':'AGUCAUUAGAUHCAUHC'}))
def NcbiFastaLabelParser(line):
"""Creates an Info object and populates it with the line contents.
As of 11/12/03, all records in genpept.fsa and the human RefSeq fasta
files were consistent with this format.
"""
info = Info()
try:
ignore, gi, db, db_ref, description = map(strip, line.split('|', 4))
except ValueError: #probably got wrong value
raise RecordError, "Unable to parse label line %s" % line
info.GI = gi
info[NcbiLabels[db]] = db_ref
info.Description = description
return gi, info
def parse_header(header_lines):
"""Return Info object from header information.
header_lines -- list of lines or anything that behaves like it.
Parses only the first three header lines with Filename, Organism, and
Accession number. In general lines that contain a colon will be parsed.
There's no error checking in here. If it fails to split on ':', the
information is simply not added to the dictionary. The expected format
for header lines is "key: value". The citation lane is parsed differently.
"""
info = {}
for line in header_lines:
if line.startswith('Citation'):
info['Citation'] = line.split()[-1].strip()
elif ':' in line:
try:
field, value = map(strip, line.split(':', 1))
info[field] = value
except ValueError:
#no interesting header line
continue
else:
continue
return Info(info)
def test_init_empty(self):
"""Info empty init should work as expected"""
d = Info()
self.assertEqual(len(d), 1)
self.assertContains(d, 'Refs')
self.assertEqual(d.Refs, DbRefs())
self.assertTrue(isinstance(d.Refs, DbRefs))
def setUp(self):
"""Setup for Fasta tests."""
self.strings = ['AAAA', 'CCCC', 'gggg', 'uuuu']
self.labels = ['1st', '2nd', '3rd', '4th']
self.infos = ["Dog", "Cat", "Mouse", "Rat"]
self.sequences_with_labels = map(Sequence, self.strings)
self.sequences_with_names = map(Sequence, self.strings)
for l,sl,sn in zip(self.labels,self.sequences_with_labels,\
self.sequences_with_names):
sl.Label = l
sn.Name = l
self.fasta_no_label = '>0\nAAAA\n>1\nCCCC\n>2\ngggg\n>3\nuuuu'
self.fasta_with_label=\
'>1st\nAAAA\n>2nd\nCCCC\n>3rd\nGGGG\n>4th\nUUUU'
self.fasta_with_label_lw2=\
'>1st\nAA\nAA\n>2nd\nCC\nCC\n>3rd\nGG\nGG\n>4th\nUU\nUU'
self.alignment_dict = {
'1st': 'AAAA',
'2nd': 'CCCC',
'3rd': 'GGGG',
'4th': 'UUUU'
}
self.alignment_object = Alignment(self.alignment_dict)
for label, info in zip(self.labels, self.infos):
self.alignment_object.NamedSeqs[label].Info = Info(species=info)
self.fasta_with_label_species=\
'>1st:Dog\nAAAA\n>2nd:Cat\nCCCC\n>3rd:Mouse\nGGGG\n>4th:Rat\nUUUU'
self.alignment_object.RowOrder = ['1st', '2nd', '3rd', '4th']
def alternativeConstr(header_lines):
info = Info()
for line in header_lines:
all = line.strip().split(':', 1)
#strip out empty lines, lines without name, lines without colon
if not all[0] or len(all) != 2:
continue
name = all[0].upper()
value = all[1].strip().upper()
info[name] = value
return info
def test_RfamParser_single_family(self):
"""RfamParser: should work on a single family in stockholm format"""
exp_header = Info()
exp_aln = {'K02120.1/628-682':\
'AUGGGAAAUUCCCCCUCCUAUAACCCCCCCGCUGGUAUCUCCCCCUCAGACUGGC',\
'D00647.1/629-683':\
'AUGGGAAACUCCCCCUCCUAUAACCCCCCCGCUGGCAUCUCCCCCUCAGACUGGC'}
exp_struct = '<<<<<<.........>>>>>>.........<<<<<<.............>>>>>>'
h, a, s = list(RfamParser(self.single_family))[0]
self.assertEqual(h,exp_header)
self.assertEqual(a,exp_aln)
self.assertEqual(s,exp_struct)
def test_init_data(self):
"""Info init with data should put items in correct places"""
#need to check init, setting, and resetting of attributes that belong
#in the Info object and attributes that belong in Info.Refs. Also need
#to check __getitem__, __setitem__, and __contains__.
d = Info({'x': 3, 'GO': 12345})
self.assertEqual(d.x, 3)
self.assertEqual(d.GO, [12345])
self.assertEqual(d.Refs.GO, [12345])
try:
del d.Refs
except AttributeError:
pass
else:
raise Exception, "Failed to prevent deletion of required key Refs" ""
d.GenBank = ('qaz', 'wsx')
self.assertEqual(d.GenBank, ['qaz', 'wsx'])
self.assertContains(d.Refs, 'GenBank')
self.assertContains(d, 'GenBank')
d.GenBank = 'xyz'
self.assertEqual(d.GenBank, ['xyz'])
self.assertSameObj(d.GenBank, d.Refs.GenBank)
d.GO = 'x'
self.assertEqual(d.GO, ['x'])
d.GO.append('y')
self.assertEqual(d.GO, ['x', 'y'])
d.ZZZ = 'zzz'
self.assertEqual(d.ZZZ, 'zzz')
self.assertNotContains(d.Refs, 'ZZZ')
self.assertNotContains(d, 'XXX')
self.assertEqual(d.XXX, None)
def test_full(self):
"""RdbParser: full data, valid and invalid"""
# when only good record, should work independent of strict
r1 = RnaSequence("-??GG-UGAA--CGCU---ACGU-N???---",\
Info=Info({'Species': "unidentified Thermus OPB AF027020",\
'Refs':{'rRNA':['AF027020']},\
'OriginalSeq':'-o[oGG-U{G}AA--C^GC]U---ACGU-Nooo---'}))
r2 = RnaSequence("---CGAUCG--UAUACG-N???-",\
Info=Info({'Species':'Thermus silvanus X84211',\
'Refs':{'rRNA':['X84211']},\
'OriginalSeq':'---CGAU[C(G){--UA}U]ACG-Nooo-'}))
obs = list(RdbParser(RDB_LINES_ONLY_GOOD.split('\n'), strict=True))
self.assertEqual(len(obs), 2)
self.assertEqual(obs[0], r1)
self.assertEqual(str(obs[0]), str(r1))
self.assertEqual(obs[0].Info, r1.Info)
self.assertEqual(obs[1], r2)
self.assertEqual(str(obs[1]), str(r2))
self.assertEqual(obs[1].Info, r2.Info)
obs = list(RdbParser(RDB_LINES_ONLY_GOOD.split('\n'), strict=False))
self.assertEqual(len(obs), 2)
self.assertEqual(obs[0], r1)
self.assertEqual(str(obs[0]), str(r1))
self.assertEqual(obs[0].Info, r1.Info)
# when strict, should raise error on invalid record
f = RdbParser(RDB_LINES_GOOD_BAD.split('\n'), strict=True)
self.assertRaises(RecordError, list, f)
# when not strict, malicious record is skipped
obs = list(RdbParser(RDB_LINES_GOOD_BAD.split('\n'), strict=False))
self.assertEqual(len(obs), 2)
self.assertEqual(obs[0], r1)
self.assertEqual(str(obs[0]), str(r1))
self.assertEqual(obs[0].Info, r1.Info)
self.assertEqual(obs[1], r2)
self.assertEqual(str(obs[1]), str(r2))
self.assertEqual(obs[1].Info, r2.Info)
def test_multiple_constructor_bad(self):
"""RdbParser should complain or skip bad records w/ constructor"""
def dnastrict(x, **kwargs):
try:
return DnaSequence(x, **kwargs)
except Exception:
raise RecordError, "Could not convert sequence"
self.assertRaises(RecordError, list, RdbParser(self.oneX, dnastrict))
f = list(RdbParser(self.oneX, dnastrict, strict=False))
self.assertEqual(len(f), 2)
a, b = f
self.assertEqual(a, 'ACT')
self.assertEqual(a.Info, Info({
'Species': 'mit',
'OriginalSeq': 'ACT'
}))
self.assertEqual(b, 'AAA')
self.assertEqual(b.Info, Info({
'Species': 'pla',
'OriginalSeq': 'AAA'
}))
def call(label):
label = [label, label[1:]][label[0] == ">"]
label = sep.split(label)
if DEBUG:
print(label)
info = Info()
for index, name, converter in field_formatters:
if isinstance(converter, collections.Callable):
try:
info[name] = converter(label[index])
except IndexError:
raise IndexError('parsing label %s failed for property %s at index %s' % (label, name, index))
else:
info[name] = label[index]
return RichLabel(info, display_template)
def InfoMaker(header_lines):
"""Returns an Info object constructed from the headerLines."""
info = Info()
for line in header_lines:
all = line.strip().split(':', 1)
#strip out empty lines, lines without name, lines without colon
if not all[0] or len(all) != 2:
continue
try:
name = _field_names[all[0]]
except KeyError:
name = all[0]
value = all[1].strip()
info[name] = value
return info
def call(label):
label = [label, label[1:]][label[0] == ">"]
label = sep.split(label)
if DEBUG:
print label
info = Info()
for index, name, converter in field_formatters:
if callable(converter):
try:
info[name] = converter(label[index])
except IndexError:
print label, index, name
raise
else:
info[name] = label[index]
return RichLabel(info, display_template)
def InfoFromLabel(line):
"""Takes a CUTG codon description line and returns an Info object.
Raises RecordError if wrong number of fields etc.
"""
try:
raw_fields = line.split('\\')
result = Info(
dict(list(zip(field_order, list(map(strip, raw_fields[1:]))))))
#extra processing for first field
first = raw_fields[0]
if '#' in first:
locus, cds_num = list(map(strip, raw_fields[0].split('#')))
else:
locus, cds_num = first, '1'
result['Locus'] = locus[1:] #remove leading '>'
result['CdsNumber'] = cds_num
#additional processing for last field: mostly key="value" pairs
description = result['Description']
descrs = description.split('/')
for d in descrs:
if '=' in d: #assume key-value pair
key, val = list(map(strip, d.split('=',
1))) #might be '=' in value
#cut off leading and trailing " if present, but _not_ internal!
if val.startswith('"'):
val = val[1:]
if val.endswith('"'):
val = val[:-1]
if key == 'db_xref': #handle cross-refs specially
try:
key, val = val.split(':')
except ValueError: #missing actual reference?
continue #just skip the bad db records
try:
if result[key]:
result[key].append(val)
else:
result[key] = [val]
except (KeyError, TypeError): #didn't recognize database
result[key] = val
else:
#remember to convert the key to MixedCase naming convention
result[cfu(key)] = val
return result
except:
raise RecordError("Failed to read label line:\n%s" % line)
def test_full(self):
"""InfoMaker should return Info object with name, value pairs"""
test_header = ['acc: X3402','abc:1','mty: ssu','seq: Mit. X3402',\
'','nonsense',':no_name']
obs = InfoMaker(test_header)
exp = Info()
exp.rRNA = 'X3402'
exp.abc = '1'
exp.Species = 'Mit. X3402'
exp.Gene = 'ssu'
self.assertEqual(obs, exp)
def NameToInfo(sequence, strict=True):
"""Returns an Info object constructed from the sequence Name
sequence: Sequence object with a Name attribute
The label will be split on Genbank acc. no. and sequence coordinates.
The coordinates will be shifted one position, since in Python the first
position is 0.
"""
#adjust label
label = sequence.Name
try:
gb, pos = label.split('/', 1) #split genbank label and pos
if not gb:
gb = None
if not pos:
pos = None
except: #unable to split, so string doesn't contain '/'
if strict:
raise RecordError, "Failed to extract genbank id and positions" +\
" from label %s"%label
else:
gb = None
pos = None
if pos:
try:
start, end = pos.split('-', 1) #split start and end pos
except:
if strict:
raise RecordError,\
"Failed to extract genbank id and positions from label %s"\
%label
else:
start = None
end = None
else:
start = None
end = None
if start:
# adjust start position to do the correct thing in python
# see comment in docstring
start = int(start) - 1
if end:
end = int(end)
info = Info({'GenBank': gb, 'Start': start, 'End': end})
return info
def HeaderToInfo(header, strict=True):
"""Returns an Info object constructed from the header lines.
Header is a list of lines that contain header information.
Fields that can occur multiple times in a header are stored in a list.
Fields that (should) occur only once are stored as a single value
Comments are joined by ' ' to one field.
Fields concerning the references are ignored, except for MedLine ID.
"""
# construct temporary dictionary containing all original information
initial_info = {}
for line in header:
line = line.strip()
if not line:
continue
try:
init, label, content = line.split(' ', 2)
if not init == '#=GF' or len(label) != 2:
raise RecordError
except:
if strict:
raise RecordError, "Failed to extract label and content " +\
"information from line %s"%(line)
else:
continue
if label in ['BM', 'DR', 'RM', 'CC']:
if label in initial_info:
initial_info[label].append(content.strip())
else:
initial_info[label] = [content.strip()]
else:
initial_info[label] = content.strip()
# transform initial dict into final one
# throw away useless information; group information
final_info = {}
for key in initial_info.keys():
name = _field_names.get(key, key)
if name == 'Comment':
value = ' '.join(initial_info[key])
else:
value = initial_info[key]
final_info[name] = value
return Info(final_info)
def TreeAlign(model, seqs, tree=None, indel_rate=0.01, indel_length=0.01,
ui = None, ests_from_pairwise=True, param_vals=None):
"""Returns a multiple alignment and tree.
Uses the provided substitution model and a tree for determining the
progressive order. If a tree is not provided a Neighbour Joining tree is
constructed from pairwise distances estimated from pairwise aligning the
sequences. If running in parallel, only the distance estimation is
parallelised and only the master CPU returns the alignment and tree, other
CPU's return None, None.
Arguments:
- model: a substitution model
- seqs: a sequence collection
- indel_rate, indel_length: parameters for the progressive pair-HMM
- ests_from_pairwise: if no tree provided and True, the median value
of the substitution model parameters are used
- param_vals: named key, value pairs for model parameters. These
override ests_from_pairwise.
"""
_exclude_params = ['mprobs', 'rate', 'bin_switch']
if param_vals:
param_vals = dict(param_vals)
else:
param_vals = {}
if isinstance(seqs, dict):
seq_names = list(seqs.keys())
else:
seq_names = seqs.getSeqNames()
two_seqs = len(seq_names) == 2
if tree:
tip_names = tree.getTipNames()
tip_names.sort()
seq_names.sort()
assert tip_names == seq_names, \
"names don't match between seqs and tree: tree=%s; seqs=%s" % \
(tip_names, seq_names)
ests_from_pairwise = False
elif two_seqs:
tree = LoadTree(tip_names=seqs.getSeqNames())
ests_from_pairwise = False
else:
if ests_from_pairwise:
est_params = [param for param in model.getParamList() \
if param not in _exclude_params]
else:
est_params = None
dcalc = EstimateDistances(seqs, model, do_pair_align=True,
est_params=est_params)
dcalc.run()
dists = dcalc.getPairwiseDistances()
tree = NJ.nj(dists)
LF = model.makeLikelihoodFunction(tree.bifurcating(name_unnamed=True), aligned=False)
if ests_from_pairwise and not param_vals:
# we use the Median to avoid the influence of outlier pairs
param_vals = {}
for param in est_params:
numbers = dcalc.getParamValues(param)
print("Param Estimate Summary Stats: %s" % param)
print(numbers.summarize())
param_vals[param] = numbers.Median
ui.display("Doing %s alignment" % ["progressive", "pairwise"][two_seqs])
with LF.updatesPostponed():
for param, val in list(param_vals.items()):
LF.setParamRule(param, value=val, is_constant=True)
LF.setParamRule('indel_rate', value=indel_rate, is_constant=True)
LF.setParamRule('indel_length', value=indel_length, is_constant=True)
LF.setSequences(seqs)
edge = LF.getLogLikelihood().edge
align = edge.getViterbiPath().getAlignment()
info = Info()
info["AlignParams"] = param_vals
info["AlignParams"].update(dict(indel_length=indel_length, indel_rate=indel_rate))
align.Info = info
return align, tree
def test_empty(self):
"""InfoMaker: should return empty Info from empty header"""
empty_header = []
obs = InfoMaker(empty_header)
exp = Info()
self.assertEqual(obs, exp)
def test_identity(self):
"""Info should get its own new Refs when created"""
i = Info()
j = Info()
self.assertNotSameObj(i, j)
self.assertNotSameObj(i.Refs, j.Refs)
def RichGenbankParser(handle,
info_excludes=None,
moltype=None,
skip_contigs=False):
"""Returns annotated sequences from GenBank formatted file.
Arguments:
- info_excludes: a series of fields to be excluded from the Info object
- moltype: a MolType instance, such as PROTEIN, DNA. Default is ASCII.
- skip_contigs: ignores records with no actual sequence data, typically
a genomic contig."""
info_excludes = info_excludes or []
moltype = moltype or ASCII
for rec in MinimalGenbankParser(handle):
info = Info()
# populate the Info object, excluding the sequence
for label, value in rec.items():
if label in info_excludes:
continue
info[label] = value
if rec['mol_type'] == 'protein': # which it doesn't for genbank
moltype = PROTEIN
elif rec['mol_type'] == 'DNA':
moltype = DNA
try:
seq = moltype.makeSequence(rec['sequence'].upper(),
Info=info,
Name=rec['locus'])
except KeyError:
if not skip_contigs:
if 'contig' in rec:
yield rec['locus'], rec['contig']
elif 'WGS' in rec:
yield rec['locus'], rec['WGS']
else:
yield rec['locus'], None
continue
for feature in rec['features']:
spans = []
reversed = None
if feature['location'] == None or feature['type'] in ['source', \
'organism']:
continue
for location in feature['location']:
(lo, hi) = (location.first() - 1, location.last())
if location.Strand == -1:
(lo, hi) = (hi, lo)
assert reversed is not False
reversed = True
else:
assert reversed is not True
reversed = False
# ensure we don't put in a span that starts beyond the sequence
if lo > len(seq):
continue
# or that's longer than the sequence
hi = [hi, len(seq)][hi > len(seq)]
spans.append((lo, hi))
if reversed:
spans.reverse()
for id_field in ['gene', 'note', 'product', 'clone']:
if id_field in feature:
name = feature[id_field]
if not isinstance(name, basestring):
name = ' '.join(name)
break
else:
name = None
seq.addAnnotation(Feature, feature['type'], name, spans)
yield (rec['locus'], seq)