コード例 #1
0
ファイル: phenomizer.py プロジェクト: stjmonde/puzzle-2
def hpo_genes(phenotype_ids, username, password):
    """Return list of HGNC symbols matching HPO phenotype ids.

    Args:
        phenotype_ids (list): list of phenotype ids
        username (str): username to connect to phenomizer
        password (str): password to connect to phenomizer

    Returns:
        query_result: a list of dictionaries on the form
        {
            'p_value': float,
            'gene_id': str,
            'omim_id': int,
            'orphanet_id': int,
            'decipher_id': int,
            'any_id': int,
            'mode_of_inheritance': str,
            'description': str,
            'raw_line': str
        }
    """
    if phenotype_ids:
        try:
            results = query_phenomizer.query(username, password, phenotype_ids)
            return [
                result for result in results if result['p_value'] is not None
            ]
        except SystemExit, RuntimeError:
            pass
コード例 #2
0
ファイル: controllers.py プロジェクト: rarmisen/scout
def hpo_diseases(username, password, hpo_ids, p_value_treshold=1):
    """Return the list of HGNC symbols that match annotated HPO terms.

    Args:
        username (str): username to use for phenomizer connection
        password (str): password to use for phenomizer connection

    Returns:
        query_result: a generator of dictionaries on the form
        {
            'p_value': float,
            'disease_source': str,
            'disease_nr': int,
            'gene_symbols': list(str),
            'description': str,
            'raw_line': str
        }
    """
    # skip querying Phenomizer unless at least one HPO terms exists
    try:
        results = query_phenomizer.query(username, password, *hpo_ids)
        diseases = [result for result in results if result["p_value"] <= p_value_treshold]
        return diseases
    except SystemExit:
        return None
コード例 #3
0
def hpo_diseases(username, password, hpo_ids, p_value_treshold=1):
    """Return the list of HGNC symbols that match annotated HPO terms.

    Args:
        username (str): username to use for phenomizer connection
        password (str): password to use for phenomizer connection

    Returns:
        query_result: a generator of dictionaries on the form
        {
            'p_value': float,
            'disease_source': str,
            'disease_nr': int,
            'gene_symbols': list(str),
            'description': str,
            'raw_line': str
        }
    """
    # skip querying Phenomizer unless at least one HPO terms exists
    try:
        results = query_phenomizer.query(username, password, *hpo_ids)
        diseases = [result for result in results
                    if result['p_value'] <= p_value_treshold]
        return diseases
    except SystemExit:
        return None
コード例 #4
0
ファイル: views.py プロジェクト: gpcr/scout
def hpo_genes(phenotype_terms):
  """Return the list of HGNC symbols that match annotated HPO terms.

  Returns:
    query_result: a list of dictionaries on the form
      {
        'p_value': float,
        'gene_id': str,
        'omim_id': int,
        'orphanet_id': int,
        'decipher_id': int,
        'any_id': int,
        'mode_of_inheritance': str,
        'description': str,
        'raw_line': str
      }
  """
  hpo_terms = [phenotype_term.phenotype_id for phenotype_term in phenotype_terms]

  # skip querying Phenomizer unless at least one HPO terms exists
  if hpo_terms:
    try:
      results = query_phenomizer.query(hpo_terms)
      return [result for result in results if result['p_value'] is not None]
    except SystemExit:
      return None
  else:
    return None
コード例 #5
0
ファイル: phenomizer.py プロジェクト: J35P312/puzzle
def hpo_genes(phenotype_ids, username, password):
    """Return list of HGNC symbols matching HPO phenotype ids.

    Args:
        phenotype_ids (list): list of phenotype ids
        username (str): username to connect to phenomizer
        password (str): password to connect to phenomizer

    Returns:
        query_result: a list of dictionaries on the form
        {
            'p_value': float,
            'gene_id': str,
            'omim_id': int,
            'orphanet_id': int,
            'decipher_id': int,
            'any_id': int,
            'mode_of_inheritance': str,
            'description': str,
            'raw_line': str
        }
    """
    if phenotype_ids:
        try:
            results = query_phenomizer.query(username, password, phenotype_ids)
            return [result for result in results
                    if result['p_value'] is not None]
        except SystemExit, RuntimeError:
            pass
コード例 #6
0
ファイル: views.py プロジェクト: BadSeby/scout
def hpo_genes(phenotype_terms):
    """Return the list of HGNC symbols that match annotated HPO terms.

  Returns:
    query_result: a list of dictionaries on the form
      {
        'p_value': float,
        'gene_id': str,
        'omim_id': int,
        'orphanet_id': int,
        'decipher_id': int,
        'any_id': int,
        'mode_of_inheritance': str,
        'description': str,
        'raw_line': str
      }
  """
    hpo_terms = [
        phenotype_term.phenotype_id for phenotype_term in phenotype_terms
    ]

    # skip querying Phenomizer unless at least one HPO terms exists
    if hpo_terms:
        try:
            results = query_phenomizer.query(hpo_terms)
            return [
                result for result in results if result['p_value'] is not None
            ]
        except SystemExit:
            return None
    else:
        return None
コード例 #7
0
def cli(ctx, hpo_term, check_terms, output, p_value_limit, verbose, username,
        password, to_json):
    "Give hpo terms either on the form 'HP:0001623', or '0001623'"
    loglevel = LEVELS.get(min(verbose, 3))
    configure_stream(level=loglevel)

    if not hpo_term:
        logger.info(
            "Please specify at least one hpo term with '-t/--hpo_term'.")
        ctx.abort()

    if not (username and password):
        logger.info("Please specify username with -u and password with -p.")
        logger.info("Contact [email protected].")
        ctx.abort()

    hpo_list = []
    for term in hpo_term:
        if len(term.split(':')) < 2:
            term = ':'.join(['HP', term])
        hpo_list.append(term)

    logger.info("HPO terms used: {0}".format(','.join(hpo_list)))

    if check_terms:
        for term in hpo_list:
            try:
                if not validate_term(username, password, term):
                    logger.info("HPO term : {0} does not exist".format(term))
                else:
                    logger.info("HPO term : {0} does exist!".format(term))
            except RuntimeError as err:
                click.echo(err)
                ctx.abort()
        ctx.abort()
    else:
        try:
            for result in query(username, password, *hpo_list):
                if to_json:
                    click.echo(json.dumps(result))
                else:
                    print_string = "{0}\t{1}:{2}\t{3}\t{4}".format(
                        result['p_value'], result['disease_source'],
                        result['disease_nr'], result['description'],
                        ','.join(result['gene_symbols']))
                    p_value = result['p_value']
                    if p_value <= p_value_limit:
                        click.echo(print_string)

        except RuntimeError as e:
            click.echo(e)
            ctx.abort()
コード例 #8
0
ファイル: phenomizer.py プロジェクト: brainstorm/puzzle
def hpo_genes(phenotype_ids):
    """Return list of HGNC symbols matching HPO phenotype ids.

    Returns:
        query_result: a list of dictionaries on the form
        {
            'p_value': float,
            'gene_id': str,
            'omim_id': int,
            'orphanet_id': int,
            'decipher_id': int,
            'any_id': int,
            'mode_of_inheritance': str,
            'description': str,
            'raw_line': str
        }
    """
    try:
        results = query_phenomizer.query(phenotype_ids)
        return [result for result in results if result["p_value"] is not None]
    except SystemExit:
        return None
コード例 #9
0
ファイル: cli.py プロジェクト: svandenhoek/query_phenomizer
def cli(ctx, hpo_term, check_terms, output, p_value_limit, verbose, username,
        password, to_json):
    """Give hpo terms either on the form 'HP:0001623', or '0001623'.

    If -p is not used, a password prompt will appear instead."""
    loglevel = LEVELS.get(min(verbose, 3))
    configure_stream(level=loglevel)

    if not hpo_term:
        logger.info(
            "Please specify at least one hpo term with '-t/--hpo_term'.")
        ctx.abort()

    if not username:
        logger.info("Please specify username with -u (and password with -p).")
        logger.info("Contact [email protected].")
        ctx.abort()

    if not password:
        password = getpass("password:"******"HPO terms used: {0}".format(','.join(hpo_list)))

    if check_terms:
        for term in hpo_list:
            try:
                if not validate_term(username, password, term):
                    logger.info("HPO term : {0} does not exist".format(term))
                else:
                    logger.info("HPO term : {0} does exist!".format(term))
            except RuntimeError as err:
                click.echo(err)
                ctx.abort()
        ctx.abort()
    else:
        try:
            if output:
                header = "p-value\tdisease-id\tdisease-name\tgene-symbols" + linesep  # The file header.
                output.write(
                    header.encode())  # "a bytes-like object is required"
            for result in query(username, password, *hpo_list):
                if to_json:
                    click.echo(json.dumps(result))
                else:
                    print_string = "{0}\t{1}:{2}\t{3}\t{4}".format(
                        result['p_value'], result['disease_source'],
                        result['disease_nr'], result['description'],
                        ','.join(result['gene_symbols']))
                    p_value = result['p_value']
                    if p_value <= p_value_limit:
                        if output:
                            print_string += linesep  # Adds line separator to output.
                            output.write(print_string.encode()
                                         )  # "a bytes-like object is required"
                        else:
                            click.echo(print_string)

        except RuntimeError as e:
            click.echo(e)
            ctx.abort()
        finally:
            if output:
                output.flush()
                output.close()
コード例 #10
0
def test_query_unicode(username, password):
    res = query(username, password, "HP:0000252")
    assert res
コード例 #11
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def test_query_ataxia(ataxia, username, password):
    res = query(username, password, ataxia)
    assert res