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How to use retrieve_references method in avocado

Best Python code snippet using avocado_python

build_db.py

Source:build_db.py

...29            else:30                seq.append(line.strip())31        if seq:32            yield header, ''.join(seq)33def retrieve_references(pubmed_ids):34    resp = requests.post(35        ESUMMARY_URL,36        data={37            'db': 'pubmed',38            'id': ','.join(pubmed_ids),39            'retmode': 'json'40        }41    )42    data = resp.json()43    references = OrderedDict()44    for uid in sorted(data['result']['uids']):45        ref = data['result'][uid]46        references[uid] = OrderedDict({47            'MedlineID': uid,48            'PubYear': ref.get('pubdate', '').split(' ')[0],49            'firstAuthor': ref['authors'][0]['name'],50            'Title': ref['title'],51            'Journal': ref['source']52        })53    return references54def list_subtypes(seqs):55    subtypes = set()56    for seq in seqs:57        subtypes.add(seq['Subtype'])58    return sorted(subtypes)59def list_sources(seqs):60    sources = set()61    for seq in seqs:62        sources.add(seq['Source'])63    return sorted(sources)64def main():65    facttable, fasta, sierra_report, outputdir = sys.argv[1:]66    with open(facttable) as fp1, open(sierra_report) as fp2:67        if fp1.read(1) != '\ufeff':68            fp1.seek(0)69        sequences = list(csv.DictReader(fp1))70        sequence_reports = json.load(fp2)71    sequence_reports = {72        sr['inputSequence']['header'].split('.', 1)[0]: sr73        for sr in sequence_reports74    }75    result_sequences = []76    pubmed_ids = set()77    min_days_offsets = {}78    for seq in sequences:79        pt = seq['PtIdentifier']80        offset = \81            datetime.strptime(seq['CollectionDate'], '%Y-%m-%d') - DATE_190082        offset = offset.days83        min_days_offsets[pt] = \84            min(min_days_offsets.get(pt, 0xffffffff), offset)85    for seq in sequences:86        pt = seq['PtIdentifier']87        offset = \88            datetime.strptime(seq['CollectionDate'], '%Y-%m-%d') - DATE_190089        offset = offset.days90        weeks = int('{:.0f}'.format((offset - min_days_offsets[pt]) / 7))91        seq = OrderedDict(seq)92        pubmed_ids.add(seq['MedlineID'])93        accs = seq['Accession']94        seqreport = sequence_reports[accs]95        subtype = seqreport['subtypeText'].split(' (', 1)[0]96        seq.update({97            'Weeks': weeks,98            'PR': 0,99            'RT': 0,100            'IN': 0,101            'NumPRMixtures': None,102            'NumPRMutations': None,103            'NumRTMixtures': None,104            'NumRTMutations': None,105            'NumINMixtures': None,106            'NumINMutations': None,107            'NumPRNAAmbiguities': None,108            'NumRTNAAmbiguities': None,109            'NumINNAAmbiguities': None,110            'Subtype': subtype,111        })112        for gene_seq in seqreport['alignedGeneSequences']:113            gene = gene_seq['gene']['name']114            seq['Num{}Mixtures'.format(gene)] = len([115                m for m in gene_seq['mutations']116                if PATTERN_MIXTURES.match(m['AAs'])])117            seq['Num{}Mutations'.format(gene)] = len(gene_seq['mutations'])118            seq[gene] = 1119            seq['Num{}NAAmbiguities'.format(gene)] = len([120                n for n in gene_seq['alignedNAs'].upper()121                if n in 'WSMKRYBDHVN'])122        result_sequences.append(seq)123    result_data = OrderedDict({124        'sequences': result_sequences,125        'references': retrieve_references(pubmed_ids),126        'subtypes': list_subtypes(result_sequences),127        'sources': list_sources(result_sequences),128    })129    factjson = os.path.join(outputdir, 'meta.json')130    with open(factjson, 'w') as outfp:131        json.dump(result_data, outfp)132    # We don't need this anymore133    # for header, seq in fasta_reader(fasta):134    #     accs = header.split('.', 1)[0]135    #     single = os.path.join(outputdir, 'sequences', '{}.json'.format(accs))136    #     with open(single, 'w') as outfas:137    #         json.dump({'header': header, 'sequence': seq}, outfas)138if __name__ == '__main__':139    main()

retrieve_biblio.py

Source:retrieve_biblio.py

...8def create_arxiv_url(result: str) -> str:9    if ARXIV_VERSION.match(result, len(result) - 2):10        result = result[:-2]11    return BASE_URL + result12def retrieve_references(search_result: u.SearchResult) -> List[str]:13    response = r.get(create_arxiv_url(search_result.id))14    if response.ok:15        references = j.loads(response.content)['references']16        return [reference['arxivId'] for reference in references if reference['arxivId']]17    else:18        response.raise_for_status()19if __name__ == '__main__':...

__init__.py

Source:__init__.py

12from .main import citation_to_paper_info34#from .main import paper_info_from_citation5#from .main import paper_info_from_link6#from .main import doi_and_title_from_citation7#from .main import doi_to_webscraped_info8#from .main import retrieve_all_info9#from .main import retrieve_only_references1011#from .ref_retrieval import retrieve_references
...

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