コード例 #1
0
ファイル: main.py プロジェクト: ryanraaum/mitomotifsapp
def process_seq2sites(handler):
    """Process data submitted in seq2sites form"""
    # get posted parameters
    content = handler.request.get('content')
    wNN = handler.request.get('wNN') == 'yes'

    # submission validation and error reporting
    problems = []
    valid = True

    # get the submitted data
    content = content.encode('utf8')

    # make sure something was submitted
    if len(content) == 0:
        valid = False
        handler.redirect("/seq2sites/")

    # determine format
    format = None
    if content.startswith('>'):
        format = 'fasta'
    else:
        format = 'single_seq'
        
    # pull names and sequence out of submitted content
    names = []
    seqs = []
    if format == 'fasta':
        try:
            fnames = []
            fseqs = []
            for entry in fasta(content, 's'):
                fnames.append(entry['name'])
                fseqs.append(RE_NON_IUPAC.sub('', entry['sequence'].upper()))
            names = fnames
            seqs = fseqs
        except:
            valid = False
            problems.append('There was an error in the FASTA format')
    else:
        names = ['']
        seqs = [RE_NON_IUPAC.sub('', content.upper())]

    # enforce limits for multisequence submissions
    if format == 'fasta':
        max_length = 0
        for seq in seqs:
            if len(seq) > max_length:
                max_length = len(seq)
        if max_length <= LONG_SEQ_CUTOFF:
            if len(seqs) > MAX_SEQS_SHORT:
                valid = False
                problems.append('too many sequences submitted')
        elif len(seqs) > MAX_SEQS_LONG:
            valid = False
            problems.append('too many sequences submitted')

    if not valid:
        return (False, {'problems': problems})

    result_lines = []
    sites_by_line = []
    for seq in seqs:
        try:
            sites = seq2sites(seq)
            sites_by_line.append(sites)
            result_lines.append(sites2str(sites))
        except Exception, e:
            result_lines.append('There was an error: %s' % e)
コード例 #2
0
ファイル: main.py プロジェクト: ryanraaum/mitomotifsapp
    for seq in seqs:
        try:
            sites = seq2sites(seq)
            sites_by_line.append(sites)
            result_lines.append(sites2str(sites))
        except Exception, e:
            result_lines.append('There was an error: %s' % e)

    if wNN:
        names = ['']*len(sites_by_line)
        result_lines = []
        for sites in sites_by_line:
            curr_hvs1 = list(x for x in sites 
                             if int(x.position) in range(16023, 16570)
                             and not x.is_deletion())
            result_lines.append(sites2str(curr_hvs1))
        # un-comment the following when it is possible to POST 
        # a multipart/form-data form from google app engine
        #form_fields = {'samples': '\n'.join(hvs1_lines)}
        #form_data = urllib.urlencode(form_fields)
        #url = "http://nnhgtool.nationalgeographic.com/cgi-bin/classify/classify.ksh"
        #result = urlfetch.fetch(url=url,
        #           payload=form_data,
        #           method=urlfetch.POST,
        #           headers={'Content-Type': 'multipart/form-data'})
        #logging.info('urlfetch content: %s' % result.content)

    results = list(Result(x,y) for x,y in zip(names,result_lines))
    template_values = {'results': results}
    if wNN:
        template_values['show_note'] = 'wNN'