Example #1
0
def _post(request):
    """
    Post a sequence and run the sequence through blast and orf detection.
    Expects: db and sequence
    Response: JSON list of features
    """

    db_name = request.REQUEST['db'].strip()
    sequence = features.clean_dna_sequence(request.REQUEST['sequence'])

    # feature detection
    feature_list = features.blast(sequence, db_name)

    # restriction site search
    cutter_list = features.find_restriction_sites(sequence)

    # ORFs and tags
    orf_list, tag_list = orfs.detect_orfs_and_tags(sequence)

    res = [x.to_dict() for x in feature_list+cutter_list+orf_list+tag_list]

    # now sort everything by start
    res.sort(cmp=lambda x,y:cmp(int(x['start']),int(y['start'])))

    res = [len(sequence),res,sequence]
    j = json.JSONEncoder().encode(res)

    if 'jsonp' in request.REQUEST:
        j = request.REQUEST['jsonp']+'('+j+')'
        http_res = HttpResponse(j,mimetype="text/javascript",status=httplib.OK)

    else:
	# technically we should be returning "application/json", but in that
	# case browsers force user to download into a file, and for debugging
	# we want to be able to see the JSON list in browser. looks like most
	# browsers will handle JSON sent back as text/html anyways.
        if request.is_ajax():
            http_res = HttpResponse(j,mimetype="application/json",status=httplib.OK)
        else:
            http_res = HttpResponse(j,status=httplib.OK)

    # allow cross origin API calls
    http_res['Access-Control-Allow-Origin'] = '*'
    http_res['Access-Control-Allow-Methods'] = 'POST, GET, OPTIONS'
    http_res['Access-Control-Max-Age'] = 1000

    return http_res
Example #2
0
def _post(params, is_ajax):
    """
    Post a sequence and run the sequence through blast and orf detection.
    Expects: db and sequence
    Response: JSON list of features
    """

    from hippo.models import Feature_Database

    is_gb = False
    db_name = params['db'].strip()
    db = Feature_Database.objects.get(name=db_name)

    sequence = params['sequence']
    gb_features = []

    # parse genbank
    if sequence.strip().startswith('LOCUS'):
        is_gb = True
        try:
            sequence, gb_features = gb.parse_genbank(sequence.lstrip())
        except Exception as e:
            sequence = ""
            gb_features = []

    # clean sequence
    input_type = params['input'] if 'input' in params else 'dna'
    if input_type in ['protein']:
        sequence = clean_sequence(sequence, alphabet=IUPAC.protein)
    else:
        sequence = clean_sequence(sequence)

    feature_list = gb_features
    gbonly = 'gbonly' in params and params['gbonly'] in ['1', 'true', 'True']
    blastonly = 'blastonly' in params and params['blastonly'] in [
        '1', 'true', 'True'
    ]

    if not is_gb or gbonly is False:
        args = {}
        if 'identity_threshold' in params:
            args['identity_threshold'] = float(params['identity_threshold'])
        if 'feature_threshold' in params:
            args['feature_threshold'] = float(params['feature_threshold'])
        circular = True
        if 'circular' in params and str(
                params['circular']).strip().lower() in ['false', 0, '0']:
            circular = False

        # feature detection
        feature_list += features.blast(sequence,
                                       db,
                                       input_type=input_type,
                                       protein=False,
                                       circular=circular,
                                       **args)
        feature_list += features.blast(sequence,
                                       db,
                                       input_type=input_type,
                                       protein=True,
                                       circular=circular,
                                       **args)

        if input_type == 'dna' and blastonly is False:
            # restriction site search
            feature_list += features.find_restriction_sites(sequence,
                                                            circular=circular)
            # ORFs and tags
            orf_list, tag_list = orfs.detect_orfs_and_tags(sequence,
                                                           circular=circular)
            feature_list += orf_list
            feature_list += tag_list

    res = [x.to_dict() for x in feature_list]
    # print 'returning %s' % (res,)

    # now sort everything by start
    res.sort(
        cmp=lambda x, y: cmp(int(x['query_start']), int(y['query_start'])))

    res = [len(sequence), res, sequence]
    j = json.JSONEncoder().encode(res)

    if 'jsonp' in params:
        j = params['jsonp'] + '(' + j + ')'
        http_res = HttpResponse(j,
                                mimetype="text/javascript",
                                status=httplib.OK)

    else:
        # technically we should be returning "application/json", but in that
        # case browsers force user to download into a file, and for debugging
        # we want to be able to see the JSON list in browser. looks like most
        # browsers will handle JSON sent back as text/html anyways.
        if is_ajax:
            http_res = HttpResponse(j,
                                    mimetype="application/json",
                                    status=httplib.OK)
        else:
            http_res = HttpResponse(j, status=httplib.OK)

    # allow cross origin API calls
    http_res['Access-Control-Allow-Origin'] = '*'
    http_res['Access-Control-Allow-Methods'] = 'POST, GET, OPTIONS'
    http_res['Access-Control-Max-Age'] = 1000

    return http_res
Example #3
0
def _post(params, is_ajax):
    """
    Post a sequence and run the sequence through blast and orf detection.
    Expects: db and sequence
    Response: JSON list of features
    """

    from hippo.models import Feature_Database

    is_gb = False
    db_name = params['db'].strip()
    db = Feature_Database.objects.get(name=db_name)

    sequence = params['sequence']
    gb_features = []

    # parse genbank
    if sequence.strip().startswith('LOCUS'):
      is_gb = True
      try:
        sequence, gb_features = gb.parse_genbank(sequence.lstrip())
      except Exception as e:
        sequence = ""
        gb_features = []

    # clean sequence
    input_type = params['input'] if 'input' in params else 'dna'
    if input_type in ['protein']:
      sequence = clean_sequence(sequence, alphabet=IUPAC.protein)
    else:
      sequence = clean_sequence(sequence)

    feature_list = gb_features
    gbonly = 'gbonly' in params and params['gbonly'] in ['1', 'true', 'True']
    blastonly = 'blastonly' in params and params['blastonly'] in ['1', 'true', 'True']

    if not is_gb or gbonly is False:
      args = {}
      if 'identity_threshold' in params:
        args['identity_threshold'] = float(params['identity_threshold'])
      if 'feature_threshold' in params:
        args['feature_threshold'] = float(params['feature_threshold'])
      circular = True
      if 'circular' in params and str(params['circular']).strip().lower() in ['false', 0, '0']:
        circular = False

      # feature detection
      feature_list += features.blast(sequence, db, input_type=input_type, protein=False, circular=circular, **args)
      feature_list += features.blast(sequence, db, input_type=input_type, protein=True, circular=circular, **args)

      if input_type == 'dna' and blastonly is False:
        # restriction site search
        feature_list += features.find_restriction_sites(sequence, circular=circular)
        # ORFs and tags
        orf_list, tag_list = orfs.detect_orfs_and_tags(sequence, circular=circular)
        feature_list += orf_list
        feature_list += tag_list

    res = [x.to_dict() for x in feature_list]
    # print 'returning %s' % (res,)

    # now sort everything by start
    res.sort(cmp=lambda x,y:cmp(int(x['query_start']),int(y['query_start'])))

    res = [len(sequence),res,sequence]
    j = json.JSONEncoder().encode(res)

    if 'jsonp' in params:
        j = params['jsonp']+'('+j+')'
        http_res = HttpResponse(j,mimetype="text/javascript",status=httplib.OK)

    else:
        # technically we should be returning "application/json", but in that
        # case browsers force user to download into a file, and for debugging
        # we want to be able to see the JSON list in browser. looks like most
        # browsers will handle JSON sent back as text/html anyways.
        if is_ajax:
            http_res = HttpResponse(j,mimetype="application/json",status=httplib.OK)
        else:
            http_res = HttpResponse(j,status=httplib.OK)

    # allow cross origin API calls
    http_res['Access-Control-Allow-Origin'] = '*'
    http_res['Access-Control-Allow-Methods'] = 'POST, GET, OPTIONS'
    http_res['Access-Control-Max-Age'] = 1000

    return http_res