Beispiel #1
0
    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
Beispiel #2
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 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
Beispiel #3
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 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
Beispiel #4
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 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
Beispiel #5
0
    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
Beispiel #6
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 def get_phams(self):
     self.phage_ = phage.new_phage(name=self.name)
     self._phams = self.phage_.get_phams()
     self.seq_length = self.phage_.length()
Beispiel #7
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 def prepare_report(self):
     self.phage_ = phage.new_phage(name=self.name)
     self.genes = self.phage_.get_genes()
Beispiel #8
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 def get_phams(self):
     self.phage_ = phage.new_phage(name=self.name)
     self._phams = self.phage_.get_phams()
     self.seq_length = self.phage_.length()
Beispiel #9
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 def prepare_report(self):
     self.phage_ = phage.new_phage(name=self.name)
     self.genes = self.phage_.get_genes()