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utils.py
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utils.py
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from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from core.utils import get_voucher_codes
from core.utils import get_gene_codes
from core.utils import flatten_taxon_names_dict
from public_interface.models import Genes
from public_interface.models import Sequences
from public_interface.models import Vouchers
from .dataset import Dataset
class CreateFasta(Dataset):
pass
class CreateTNT(Dataset):
def __init__(self, *args, **kwargs):
super(CreateTNT, self).__init__(*args, **kwargs)
self.number_taxa = len(self.voucher_codes)
self.number_chars = self.get_number_chars_from_gene_codes()
def convert_lists_to_dataset(self, partitions):
"""
Overriden method from base clase in order to add headers and footers depending
on needed dataset.
"""
out = 'nstates dna;\nxread\n'
out += str(self.number_chars) + ' ' + str(self.number_taxa)
for i in partitions:
out += '\n'
out += '\n'.join(i)
out += '\n;\nproc/;'
return out.strip()
def get_number_chars_from_gene_codes(self):
chars = 0
res = Genes.objects.all().values('gene_code', 'length')
gene_lengths = {i['gene_code']: i['length'] for i in res}
for gene in self.gene_codes:
chars += gene_lengths[gene]
return chars
class CreateNEXUS(Dataset):
def __init__(self, *args, **kwargs):
super(CreateNEXUS, self).__init__(*args, **kwargs)
self.gene_codes_and_lengths = None
self.number_taxa = len(self.voucher_codes)
self.number_chars = self.get_number_chars_from_gene_codes()
def get_charset_block(self):
charset_block = []
bp_count_start = 0
bp_count_end = 0
self.gene_codes.sort()
for gene in self.gene_codes:
bp_count_end += self.gene_codes_and_lengths[gene]
line = ' charset ' + gene + ' = ' + str(
bp_count_start + 1) + '-' + str(bp_count_end) + ';'
bp_count_start += self.gene_codes_and_lengths[gene]
charset_block.append(line)
return charset_block
def get_partitions_block(self):
line = 'partition GENES = ' + str(len(self.gene_codes))
line += ': ' + ', '.join(self.gene_codes) + ';\n'
line += '\nset partition = GENES;\n'
return [line]
def get_final_block(self):
block = "set autoclose=yes;"
if self.outgroup != '':
block += '\noutgroup ' + self.voucher_codes_metadata[self.outgroup] + ";"
block += """
prset applyto=(all) ratepr=variable brlensp=unconstrained:Exp(100.0) shapepr=exp(1.0) tratiopr=beta(2.0,1.0);
lset applyto=(all) nst=mixed rates=gamma [invgamma];
unlink statefreq=(all);
unlink shape=(all) revmat=(all) tratio=(all) [pinvar=(all)];
mcmc ngen=10000000 printfreq=1000 samplefreq=1000 nchains=4 nruns=2 savebrlens=yes [temp=0.11];
sump relburnin=yes [no] burninfrac=0.25 [2500];
sumt relburnin=yes [no] burninfrac=0.25 [2500] contype=halfcompat [allcompat];
END;
"""
return [block.strip()]
def convert_lists_to_dataset(self, partitions):
"""
Overriden method from base clase in order to add headers and footers depending
on needed dataset.
"""
out = [
'#NEXUS\n',
'BEGIN DATA;',
'DIMENSIONS NTAX=' + str(self.number_taxa) + ' NCHAR=' + str(self.number_chars) + ';',
'FORMAT INTERLEAVE DATATYPE=DNA MISSING=? GAP=-;',
'MATRIX',
]
for i in partitions:
out += i
out += [';\nEND;']
out += ['\nbegin mrbayes;']
out += self.get_charset_block()
out += self.get_partitions_block()
out += self.get_final_block()
return '\n'.join(out)
def get_number_chars_from_gene_codes(self):
chars = 0
res = Genes.objects.all().values('gene_code', 'length')
self.gene_codes_and_lengths = {i['gene_code']: i['length'] for i in res}
for gene in self.gene_codes:
chars += self.gene_codes_and_lengths[gene]
return chars
class CreateDataset(object):
"""
Accept form input to create a dataset in several formats, codon positions,
for list of codes and genes. Also takes into account the vouchers passed as
taxonset.
Attributes:
``dataset_str``: output dataset to pass to users.
"""
def __init__(self, cleaned_data):
self.errors = []
self.seq_objs = dict()
self.codon_positions = cleaned_data['positions']
self.file_format = cleaned_data['file_format']
self.partition_by_positions = cleaned_data['partition_by_positions']
self.cleaned_data = cleaned_data
self.voucher_codes = get_voucher_codes(cleaned_data)
self.gene_codes = get_gene_codes(cleaned_data)
self.taxon_names = cleaned_data['taxon_names']
self.voucher_codes_metadata = dict()
self.gene_codes_metadata = self.get_gene_codes_metadata()
self.warnings = []
self.outgroup = cleaned_data['outgroup']
self.dataset_str = self.create_dataset()
def create_dataset(self):
self.voucher_codes = get_voucher_codes(self.cleaned_data)
self.gene_codes = get_gene_codes(self.cleaned_data)
self.create_seq_objs()
if self.file_format == 'FASTA':
fasta = CreateFasta(self.codon_positions, self.partition_by_positions,
self.seq_objs, self.gene_codes, self.voucher_codes,
self.file_format)
fasta_dataset = fasta.from_seq_objs_to_dataset()
self.warnings += fasta.warnings
return fasta_dataset
if self.file_format == 'TNT':
tnt = CreateTNT(self.codon_positions, self.partition_by_positions,
self.seq_objs, self.gene_codes, self.voucher_codes, self.file_format, self.outgroup)
tnt_dataset = tnt.from_seq_objs_to_dataset()
self.warnings += tnt.warnings
return tnt_dataset
if self.file_format == 'NEXUS':
nexus = CreateNEXUS(self.codon_positions, self.partition_by_positions,
self.seq_objs, self.gene_codes, self.voucher_codes,
self.file_format, self.outgroup, self.voucher_codes_metadata)
nexus_dataset = nexus.from_seq_objs_to_dataset()
self.warnings += nexus.warnings
return nexus_dataset
def create_seq_record(self, s):
"""
Adds ? if the sequence is not long enough
:param s:
:return:
"""
gene_code = s['gene_code']
length = self.gene_codes_metadata[gene_code]
sequence = s['sequences']
length_difference = length - len(sequence)
sequence += '?' * length_difference
seq = Seq(sequence)
seq_obj = SeqRecord(seq)
return seq_obj
def create_seq_objs(self):
"""Generate a list of sequence objects. Also takes into account the
genes passed as geneset.
Returns:
list of sequence objects as produced by BioPython.
"""
# We might need to update our list of vouches and genes
vouchers = set()
gene_codes = set()
our_taxon_names = self.get_taxon_names_for_taxa()
all_seqs = Sequences.objects.all().values('code_id', 'gene_code', 'sequences').order_by('code_id')
for s in all_seqs:
code = s['code_id']
gene_code = s['gene_code']
if code in self.voucher_codes and gene_code in self.gene_codes:
vouchers.add(code)
gene_codes.add(gene_code)
seq_obj = self.create_seq_record(s)
seq_obj.id = flatten_taxon_names_dict(our_taxon_names[code])
if 'GENECODE' in self.taxon_names:
seq_obj.id += '_' + gene_code
seq_obj.name = gene_code
seq_obj.description = code
self.voucher_codes_metadata[code] = seq_obj.id
if gene_code not in self.seq_objs:
self.seq_objs[gene_code] = []
self.seq_objs[gene_code].append(seq_obj)
self.voucher_codes = list(vouchers)
self.gene_codes = list(gene_codes)
self.add_missing_seqs()
def get_gene_codes_metadata(self):
"""
:return: dictionary with genecode and base pair number.
"""
queryset = Genes.objects.all().values('gene_code', 'length')
gene_codes_metadata = dict()
for i in queryset:
gene_code = i['gene_code']
gene_codes_metadata[gene_code] = i['length']
return gene_codes_metadata
def add_missing_seqs(self):
"""
Loops over the created seq_objects and adds sequences full of ? if
those where not found in our database.
Uses the updated lists of voucher_codes and gene_codes
"""
for gene_code in self.seq_objs:
for code in self.voucher_codes:
found = False
for seq_obj in self.seq_objs[gene_code]:
if code == seq_obj.description:
found = True
if found is False:
seq = Seq('?' * self.gene_codes_metadata[gene_code])
empty_seq_obj = SeqRecord(seq)
empty_seq_obj.id = self.voucher_codes_metadata[code]
empty_seq_obj.name = gene_code
empty_seq_obj.description = code
self.seq_objs[gene_code].append(empty_seq_obj)
def get_taxon_names_for_taxa(self):
"""Returns dict: {'CP100-10': {'taxon': 'name'}}
Takes list of voucher_codes and list of taxon_names from cleaned form.
Returns:
Dictionary with data, also as dicts.
"""
vouchers_with_taxon_names = {}
all_vouchers = Vouchers.objects.all().order_by('code').values('code', 'orden', 'superfamily',
'family', 'subfamily', 'tribe',
'subtribe', 'genus', 'species',
'subspecies', 'author', 'hostorg',)
for voucher in all_vouchers:
code = voucher['code']
if code in self.voucher_codes:
obj = dict()
for taxon_name in self.taxon_names:
if taxon_name != 'GENECODE':
taxon_name = taxon_name.lower()
obj[taxon_name] = voucher[taxon_name]
vouchers_with_taxon_names[code] = obj
return vouchers_with_taxon_names