Ejemplo n.º 1
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    def add_phenotype(self, ind_obj, phenotype_id):
        """Add a phenotype term to the case."""
        if phenotype_id.startswith('HP:') or len(phenotype_id) == 7:
            logger.debug('querying on HPO term')
            hpo_results = phizz.query_hpo([phenotype_id])
        else:
            logger.debug('querying on OMIM term')
            hpo_results = phizz.query_disease([phenotype_id])

        added_terms = [] if hpo_results else None
        existing_ids = set(term.phenotype_id for term in ind_obj.phenotypes)
        for result in hpo_results:
            if result['hpo_term'] not in existing_ids:
                term = PhenotypeTerm(phenotype_id=result['hpo_term'],
                                     description=result['description'])
                logger.info('adding new HPO term: %s', term.phenotype_id)
                ind_obj.phenotypes.append(term)
                added_terms.append(term)

        logger.debug('storing new HPO terms')
        self.save()

        if added_terms is not None and len(added_terms) > 0:
            for case_obj in ind_obj.cases:
                self.update_hpolist(case_obj)

        return added_terms
Ejemplo n.º 2
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    def add_phenotype(self, ind_obj, phenotype_id):
        """Add a phenotype term to the case."""
        if phenotype_id.startswith('HP:') or len(phenotype_id) == 7:
            logger.debug('querying on HPO term')
            hpo_results = phizz.query_hpo([phenotype_id])
        else:
            logger.debug('querying on OMIM term')
            hpo_results = phizz.query_disease([phenotype_id])

        added_terms = [] if hpo_results else None
        existing_ids = set(term.phenotype_id for term in ind_obj.phenotypes)
        for result in hpo_results:
            if result['hpo_term'] not in existing_ids:
                term = PhenotypeTerm(phenotype_id=result['hpo_term'],
                                     description=result['description'])
                logger.info('adding new HPO term: %s', term.phenotype_id)
                ind_obj.phenotypes.append(term)
                added_terms.append(term)

        logger.debug('storing new HPO terms')
        self.save()

        if added_terms is not None and len(added_terms) > 0:
            for case_obj in ind_obj.cases:
                self.update_hpolist(case_obj)

        return added_terms
Ejemplo n.º 3
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def get_hpo(variant_str):
    samples=get_samples(variant_str)
    #chrom,pos,ref,alt,=str(variant_str.strip()).split('-')
    d=csv.DictReader(file('/data/uclex_data/UCLexInfo/uclex-samples.csv','r'),delimiter=',')
    hpo=[]
    for r in d:
        if r['sample'] not in samples: continue
        pheno=r['phenotype']
        print((r['sample'],pheno,))
        if pheno.startswith('HP'):
            hpo+=[phizz.query_hpo([pheno])]
        elif pheno.startswith('MIM'):
            hpo+=[phizz.query_disease([pheno])]
    return(hpo)
Ejemplo n.º 4
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def get_hpo(variant_str):
    samples=get_samples(variant_str)
    #chrom,pos,ref,alt,=str(variant_str.strip()).split('-')
    d=csv.DictReader(file('/data/uclex_data/UCLexInfo/uclex-samples.csv','r'),delimiter=',')
    hpo=[]
    for r in d:
        if r['sample'] not in samples: continue
        pheno=r['phenotype']
        print((r['sample'],pheno,))
        if pheno.startswith('HP'):
            hpo+=[phizz.query_hpo([pheno])]
        elif pheno.startswith('MIM'):
            hpo+=[phizz.query_disease([pheno])]
    return(hpo)
def phenotypes(variant):
    for s in variant['HOM']+variant['HET']:
        for hpo in phenotips.patient_hpo(eid=s,auth=args.login):
            if hpo.startswith('HP'):
                variant['HPO']=variant.get('HPO',[])+phizz.query_hpo([hpo])
            elif hpo.startswith('MIM'):
                variant['HPO']=variant.get('HPO',[])+phizz.query_disease([hpo])
    #for hpo in variant['HPO']: variant['HPO'+=get_ancestors(hpo['hpo_term'])
    if 'HPO' in variant:
        #variant['HPO']=list(set([h['hpo_term'] for h in variant['HPO']]))
        variant['HPO']=[h['hpo_term'] for h in variant['HPO']]
    else:
        variant['HPO']=[]
    return(variant)
Ejemplo n.º 6
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def phenotypes(variant):
    for s in variant['HOM'] + variant['HET']:
        for hpo in phenotips.patient_hpo(eid=s, auth=args.login):
            if hpo.startswith('HP'):
                variant['HPO'] = variant.get('HPO', []) + phizz.query_hpo(
                    [hpo])
            elif hpo.startswith('MIM'):
                variant['HPO'] = variant.get('HPO', []) + phizz.query_disease(
                    [hpo])
    #for hpo in variant['HPO']: variant['HPO'+=get_ancestors(hpo['hpo_term'])
    if 'HPO' in variant:
        #variant['HPO']=list(set([h['hpo_term'] for h in variant['HPO']]))
        variant['HPO'] = [h['hpo_term'] for h in variant['HPO']]
    else:
        variant['HPO'] = []
    return (variant)
Ejemplo n.º 7
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    def add_phenotype(self, ind_obj, phenotype_id):
        """Add a phenotype term to the case."""
        if phenotype_id.startswith("HP:") or len(phenotype_id) == 7:
            logger.debug("querying on HPO term")
            hpo_results = phizz.query_hpo([phenotype_id])
        else:
            logger.debug("querying on OMIM term")
            hpo_results = phizz.query_disease([phenotype_id])

        added_terms = []
        existing_ids = set(term.phenotype_id for term in ind_obj.phenotypes)
        for result in hpo_results:
            if result["hpo_term"] not in existing_ids:
                term = PhenotypeTerm(phenotype_id=result["hpo_term"], description=result["description"])
                logger.info("adding new HPO term: %s", term.phenotype_id)
                ind_obj.phenotypes.append(term)
                added_terms.append(term)

        logger.debug("storing new HPO terms")
        self.save()

        return added_terms
Ejemplo n.º 8
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    def add_phenotype(self, institute, case, user, link, hpo_term=None,
                      omim_term=None):
        """Add a new phenotype term to a case

            Create a phenotype term and event with the given information

            Args:
                institute (Institute): A Institute object
                case (Case): Case object
                user (User): A User object
                link (str): The url to be used in the event
                hpo_term (str): A hpo id
                omim_term (str): A omim id

        """
        try:
            if hpo_term:
                logger.debug("Fetching info for hpo term {0}".format(hpo_term))
                hpo_results = phizz.query_hpo([hpo_term])
            elif omim_term:
                logger.debug("Fetching info for mim term {0}".format(omim_term))
                hpo_results = phizz.query_disease([omim_term])
            else:
                raise ValueError('Must supply either hpo or omim term')
            logger.debug("Got result {0}".format(
                ', '.join(res['hpo_term'] for res in hpo_results)))
        except ValueError as e:
            #TODO Should ve raise a more proper exception here?
            raise e

        phenotype_terms = []
        for hpo_result in hpo_results:
            phenotype_name = hpo_result['hpo_term']
            description = hpo_result['description']
            phenotype_term = PhenotypeTerm(
                                    phenotype_id=phenotype_name,
                                    feature=description
            )
            phenotype_terms.append(phenotype_term)

            logger.info("Append the phenotype term {0} to case {1}".format(
                phenotype_name, case.display_name
            ))
            case.phenotype_terms.append(phenotype_term)

            logger.info("Creating event for adding phenotype term for case"\
                        " {0}".format(case.display_name))

            self.create_event(
                institute=institute,
                case=case,
                user=user,
                link=link,
                category='case',
                verb='add_phenotype',
                subject=case.display_name,
                content = phenotype_name
            )

        case.save()
        logger.debug("Case updated")
Ejemplo n.º 9
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def get_awesomebar_result(db, query):
    """
    Similar to the above, but this is after a user types enter
    We need to figure out what they meant - could be gene, variant, region
    Return tuple of (datatype, identifier)
    Where datatype is one of 'gene', 'variant', or 'region'
    And identifier is one of:
    - ensembl ID for gene
    - variant ID string for variant (eg. 1-1000-A-T)
    - region ID string for region (eg. 1-1000-2000)
    Follow these steps:
    - if query is an ensembl ID, return it
    - if a gene symbol, return that gene's ensembl ID
    - if an RSID, return that variant's string
    Finally, note that we don't return the whole object here - only it's identifier.
    This could be important for performance later
    """
    query = query.strip()
    print 'Query: %s' % query
    if query.startswith('HP:'):
        description=phizz.query_hpo([query])
        #description=hpo_db.hpo.find_one({'hpo_id':query})
        return 'hpo', query
    if query.startswith('MIM'):
        disease=phizz.query_disease([query])
        return 'mim', query
    # Variant
    variant = orm.get_variants_by_rsid(db, query.lower())
    if variant:
        if len(variant) == 1:
            return 'variant', variant[0]['variant_id']
        else:
            return 'dbsnp_variant_set', variant[0]['rsid']
    variant = get_variants_from_dbsnp(db, query.lower())
    if variant:
        return 'variant', variant[0]['variant_id']
    # variant = get_variant(db, )
    # TODO - https://github.com/brettpthomas/exac_browser/issues/14
    gene = get_gene_by_name(db, query)
    if gene:
        return 'gene', gene['gene_id']
    # From here out, all should be uppercase (gene, tx, region, variant_id)
    query = query.upper()
    gene = get_gene_by_name(db, query)
    if gene:
        return 'gene', gene['gene_id']
    # Ensembl formatted queries
    if query.startswith('ENS'):
        # Gene
        gene = get_gene(db, query)
        if gene:
            return 'gene', gene['gene_id']
        # Transcript
        transcript = get_transcript(db, query)
        if transcript:
            return 'transcript', transcript['transcript_id']
    # From here on out, only region queries
    if query.startswith('CHR'):
        query = query.lstrip('CHR')
    # Region
    m = R1.match(query)
    if m:
        if int(m.group(3)) < int(m.group(2)):
            return 'region', 'invalid'
        return 'region', '{}-{}-{}'.format(m.group(1), m.group(2), m.group(3))
    m = R2.match(query)
    if m:
        return 'region', '{}-{}-{}'.format(m.group(1), m.group(2), m.group(2))
    m = R3.match(query)
    if m:
        return 'region', '{}'.format(m.group(1))
    m = R4.match(query)
    if m:
        return 'variant', '{}-{}-{}-{}'.format(m.group(1), m.group(2), m.group(3), m.group(4))
    return 'not_found', query