def make_gene(self):
"""
makes the gene which is a SeqRecord from Biopython. In this case the "gene" should
include all the sequence upstream of the annotated start all the way to the first
in frame stop codon.
"""
phage = new_phage(phage_id=self.phage_id)
self.phage_name = phage.get_name()
gene_no = self.db_id.split("_")[-1]
gene_no = gene_no.split(" ")[0]
self.gene_id = self.phage_name + "_" + gene_no
self.gene_id = self.gene_id.replace('-', "_")
checkDraft = re.compile('_draft', re.IGNORECASE)
if checkDraft.search(self.gene_id) is not None:
self.draftStatus = True
else:
self.draftStatus = False
phage_sequence = phage.get_sequence()
if self.orientation == 'R':
temp_start = self.stop
self.stop = self.start
self.start = temp_start
sequence, self.ahead_of_start = find_upstream_stop_site(
self.start, self.stop, self.orientation, phage_sequence)
gene = SeqRecord(sequence, id=self.gene_id , name=self.gene_id,
description="|%i-%i| %s" %(self.start, self.stop, self.orientation))
return gene
def __init__(self, name, is_phamerated, fasta_file=None, profile_file=None, gui=None, event=None):
self.name = name
self.phage = new_phage(name=name)
self.genes = {}
self.is_phamerated = is_phamerated
self.intermediate_dir = utils.INTERMEDIATE_DIR
self.final_dir = utils.FINAL_DIR
self.fasta = fasta_file
self.profile = profile_file
self.unphamerated_genes = {}
self.config = config
self.gui = gui
self.current_pham = [0, 0]
self.total_phams = None
self.event = event
def make_gene(self):
"""
makes the gene
"""
phage = new_phage(phage_id=self.phage_id)
self.phage_name = phage.get_name()
gene_no = self.db_id.split("_")[-1]
gene_no = gene_no.split(" ")[0]
self.gene_id = self.phage_name + "_" + gene_no
self.gene_id = self.gene_id.replace('-', "_")
phage_sequence = phage.get_sequence()
if self.orientation == 'R':
temp_start = self.stop
self.stop = self.start
self.start = temp_start
sequence, self.ahead_of_start = find_upstream_stop_site(
self.start, self.stop, self.orientation, phage_sequence)
gene = SeqRecord(sequence, id=self.gene_id , name=self.gene_id,
description="|%i-%i| %s" %(self.start, self.stop, self.orientation))
return gene
def __init__(self,
name,
is_phamerated,
fasta_file=None,
profile_file=None,
gui=None,
event=None):
self.name = name
self.phage = new_phage(name=name)
self.genes = {}
self.is_phamerated = is_phamerated
self.intermediate_dir = utils.INTERMEDIATE_DIR
self.final_dir = utils.FINAL_DIR
self.fasta = fasta_file
self.profile = profile_file
self.unphamerated_genes = {}
self.config = config
self.gui = gui
self.current_pham = [0, 0]
self.total_phams = None
self.event = event
def make_gene(self):
"""
makes the gene which is a SeqRecord from Biopython. In this case the "gene" should
include all the sequence upstream of the annotated start all the way to the first
in frame stop codon.
"""
phage = new_phage(phage_id=self.phage_id)
self.phage_name = phage.get_name()
gene_no = self.db_id.split("_")[-1]
gene_no = gene_no.split(" ")[0]
self.gene_id = self.phage_name + "_" + gene_no
self.gene_id = self.gene_id.replace('-', "_")
self.cluster = phage.cluster
if self.cluster == None:
self.cluster = "singleton"
self.cluster_hash = sum(
[pow(ord(elem), i + 1) for i, elem in enumerate(self.cluster)])
status = phage.get_status()
if status == 'final': # values of 'draft' or 'gbk' considered draft quality by starterator
self.draftStatus = False
else:
self.draftStatus = True
phage_sequence = phage.get_sequence()
if self.orientation == 'R':
temp_start = self.stop
self.stop = self.start
self.start = temp_start
sequence, self.ahead_of_start = find_upstream_stop_site(
self.start, self.stop, self.orientation, phage_sequence)
self.ahead_of_start_coord = self.start - self.ahead_of_start
gene = SeqRecord(sequence,
id=self.gene_id,
name=self.gene_id,
description="|%i-%i| %s" %
(self.start, self.stop, self.orientation))
return gene
def get_phams(self):
self.phage_ = phage.new_phage(name=self.name)
self._phams = self.phage_.get_phams()
self.seq_length = self.phage_.length()
def prepare_report(self):
self.phage_ = phage.new_phage(name=self.name)
self.genes = self.phage_.get_genes()
def get_phams(self):
self.phage_ = phage.new_phage(name=self.name)
self._phams = self.phage_.get_phams()
self.seq_length = self.phage_.length()
def prepare_report(self):
self.phage_ = phage.new_phage(name=self.name)
self.genes = self.phage_.get_genes()
