parsers.py 文件源码

def parse_gb(self):
        """
        Take a genbank file and parse to items/SBOL
        """
        items = []
        elements = OrderedDict()
        sbol = None
        try:
            record = SeqIO.read(self.file_data, 'genbank')
            features = record.features  # sorted(record.features, key=attrgetter('location.start'))
            for feat in features:
                # The file sometimes has lowercase and sometimes uppercase
                # types so normalise to lowercase.
                if feat.type.lower() in self.GENBANK_FEATURE_TYPES:
                    name = ''
                    # Look for the label key. Other keys can be set but
                    # most software simply sets the label key and nothing
                    # else.
                    for key, value in feat.qualifiers.items():
                        if key == 'label':
                            name = value[0]
                    if name:
                        feature_type = feat.type.lower()
                        if feature_type == 'rbs':
                            feature_type = 'ribosome entry site'
                        elif feature_type == 'primer_bind':
                            feature_type = 'primer binding site'
                        seq = str(feat.extract(record.seq))
                        elements[name] = self.genbank_to_sbol_component(name, seq, feature_type)
                        item = self.get_inventory_item(name)
                        if item:
                            items.append(item)
        except Exception as e:
            print(e)
            pass
        else:
            if len(elements.values()) > 0:
                self.make_sbol_construct(list(elements.values()))
                sbol = self.make_sbol_xml()
        return items, sbol