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How to use _format_attributes method in localstack

Best Python code snippet using localstack_python

gtf.py

Source:gtf.py

1import tests.util2def _format_attributes(attrs):3    formatted_pairs = list()4    for k, v in attrs:5        formatted_pairs.append(' '.join([k, tests.util.double_quote(v)]))6    return '; '.join(formatted_pairs)7def _group_transcripts_by_gene_id(transcripts):8    transcripts_by_gene_id = dict()9    for transcript in transcripts:10        gene_id = transcript.gene_id11        transcripts_for_gene_id = transcripts_by_gene_id.get(gene_id)12        if not transcripts_for_gene_id:13            transcripts_for_gene_id = list()14            transcripts_by_gene_id[gene_id] = transcripts_for_gene_id15        transcripts_for_gene_id.append(transcript)16    return transcripts_by_gene_id17def _get_lines_for_transcript(transcript, gene_id, gene_name, chromosome,18                              strand, score_placeholder, frame_placeholder):19    lines_for_transcript = list()20    trans_min_start, trans_max_end = transcript.exons[0]21    for exon_start, exon_end in transcript.exons:22        if exon_start < trans_min_start:23            trans_min_start = exon_start24        if exon_end > trans_max_end:25            trans_max_end = exon_end26        attributes = [('gene_id', gene_id),27                      ('transcript_id', transcript.transcript_id),28                      ('gene_name', gene_name)]29        formatted_attributes = _format_attributes(attributes)30        lines_for_transcript.append('\t'.join([31            chromosome,32            'processed_transcript',33            'exon',34            str(exon_start),35            str(exon_end),36            score_placeholder,37            strand,38            frame_placeholder,39            formatted_attributes,40        ]))41    attributes = [('gene_id', gene_id),42                  ('transcript_id', transcript.transcript_id),43                  ('gene_name', gene_name)]44    formatted_attributes = _format_attributes(attributes)45    lines_for_transcript.insert(46        0, '\t'.join([47            chromosome,48            'processed_transcript',49            'transcript',50            str(trans_min_start),51            str(trans_max_end),52            score_placeholder,53            strand,54            frame_placeholder,55            formatted_attributes,56        ]))57    return {58        'lines_for_transcript': lines_for_transcript,59        'trans_min_start': trans_min_start,60        'trans_max_end': trans_max_end61    }62def _write_lines_for_gene_id(f_handle, gene_id, transcripts):63    score_placeholder = '.'64    frame_placeholder = '.'65    lines_for_gene = list()66    gene_min_start = None67    gene_max_end = None68    gene_name = None69    chromosome = None70    strand = None71    for transcript in transcripts:72        gene_name = transcript.gene_name73        chromosome = transcript.chromosome74        strand = transcript.strand75        if not transcript.exons:76            return 'no exons in transcript'77        lines_for_transcript_result = _get_lines_for_transcript(78            transcript, gene_id, gene_name, chromosome, strand,79            score_placeholder, frame_placeholder)80        lines_for_transcript = lines_for_transcript_result[81            'lines_for_transcript']82        trans_min_start = lines_for_transcript_result['trans_min_start']83        trans_max_end = lines_for_transcript_result['trans_max_end']84        lines_for_gene.extend(lines_for_transcript)85        if gene_min_start is None or trans_min_start < gene_min_start:86            gene_min_start = trans_min_start87        if gene_max_end is None or trans_max_end > gene_max_end:88            gene_max_end = trans_max_end89    attributes = [('gene_id', gene_id), ('gene_name', gene_name)]90    formatted_attributes = _format_attributes(attributes)91    lines_for_gene.insert(92        0, '\t'.join([93            chromosome,94            'pseudogene',95            'gene',96            str(gene_min_start),97            str(gene_max_end),98            score_placeholder,99            strand,100            frame_placeholder,101            formatted_attributes,102        ]))103    for line in lines_for_gene:104        f_handle.write('{}\n'.format(line))...

htmlbuilder.py

Source:htmlbuilder.py

...20                self.contents.append(obj)21    def __str__(self):22        html = "<{}{}>{}</{}>".format(23            self.name,24            self._format_attributes(),25            self._format_contents(),26            self.name,27        )28        if self.pretty:29            return BeautifulSoup(html, features="html.parser").prettify()30        return html31    def _format_attributes(self):32        string = "".join(33            ' {}="{}"'.format(attr, val) for attr, val in zip(34                self.attributes.keys(), self.attributes.values()35            )36        )37        return string38    def _format_contents(self):39        string = "".join(str(item) for item in self.contents)40        return string41    def add(self, item_list):42        """add an element to this tag."""...

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