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How to use find_skips method in tempest

Best Python code snippet using tempest_python

parse_gtf_exons.py

Source:parse_gtf_exons.py

...44                    genes[d['gene_id']][d['transcript_id']] = [t]45            else:46                genes[d['gene_id']] = {d['transcript_id']: [t]}47    return genes48def find_skips(exons1, exons2):49    pat1 = ''.join(['T' if k in exons1 else 'F' for k in exons2])50    pat2 = ''.join(['T' if k in exons2 else 'F' for k in exons1])51    if re.match(r"""TF+T""", pat1) or re.match(r"""TF+T""", pat2):52        return True53    else:54        return False55def find_skipped_exons(mytranscripts):56    myexons = {k: [t[8]['exon_id'] for t in v] for k,v in mytranscripts.items()}57    for i, ex1 in enumerate(myexons.values()):58        for ex2 in myexons.values()[i+1:]:59            if find_skips(ex1, ex2):60                return True61    return False62if 'exons' not in locals():63    print 'Reading exons'64    exons = read_exons(fname)65if 'transcripts' not in locals():66    print 'Reading transcripts'67    transcripts = read_transcripts(fname)68print 'Finding skips'69hasskips = [find_skipped_exons(k) for k in transcripts.values()]70geneskips = pd.DataFrame(hasskips, index=transcripts.keys())71geneskips = geneskips.sort_index()...

utils.py

Source:utils.py

...15    final_index = 0  # position of selected file/folder in its list16    # Final position of element will always be of the form data[folder_index][contents_index][final_index]17    for i in range(len(selection) - 1):18        for j in range(selection[i]):19            folder_index += find_skips(data, folder_index)[0]20        folder_index += 121    folder_index -= 122    if selection[-1] >= len(data[folder_index][1]):23        # search inside files list24        contents_index = 225        final_index = selection[-1] - len(data[folder_index][1])26    else:27        contents_index = 128        final_index = selection[-1]29    selection_name = data[folder_index][contents_index][final_index]30    selection_path = os.path.join(data[folder_index][0], selection_name)31    return_dict = {"path": selection_path, "name": selection_name, "type": ""}32    if os.path.isfile(selection_path):33        return_dict["type"] = "file"34    else:35        return_dict["type"] = "folder"36    return return_dict37    # print(folder_index, contents_index, final_index)38    # print(data[folder_index][contents_index][final_index])39    # print(selection)40def find_skips(data, index):41    if len(data[index][1]) == 0:42        return [1, 0]43    output = [1, 0]44    sum = 045    for i in range(len(data[index][1])):46        if index == 7:47            print(index + sum + 1)48        rec = find_skips(data, index + sum + 1)49        sum += rec[1] + 150        output[0] += rec[0]51    output[1] = len(data[index][1])...

app.py

Source:app.py

...17    if auth_key_submitted != auth_key:18        return jsonify({"status": "unauthorized"}), 40119    tmp_storage.update(seq)20    # immediately count the number of steps in this chunk sent by the client21    skips_count = find_skips(seq)22    # also, keep "tmp_count" updated with the number of skips that we have23    # currently (i.e. since the latest storage) sent the client24    tmp_count += skips_count25    print(len(tmp_storage)) # debug message (TODO: use logging)26    if len(tmp_storage) > 500:27        min_ts = min(tmp_storage.keys())28        # now count the "correct" number of skips (i.e. on the entire "tmp_storage" buffer29        # The result is then compared with "tmp_count" (the count that has been sent thus far)30        # Only the delta is sent (to provide the correct count to the client)31        skips_count = find_skips(tmp_storage) # "true" count32        # now skips_count contains the "adjusting" value (i.e. the offset from what we33        # previously told the client to the "correct" number. We send this offset so34        # that the client has a valid estimate (can be positive or negative)35        skips_count = skips_count - tmp_count 36        with open(os.path.join(outdir, f"{min_ts}.json"), "w") as f:37            json.dump(tmp_storage, f)38            tmp_storage = {}39            tmp_count = 0 # reset count40    return jsonify({"status": "OK", "count": skips_count }), 20041    42if __name__ == "__main__":...

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