How to use find_skips method in tempest

Best Python code snippet using tempest_python

parse_gtf_exons.py

Source: parse_gtf_exons.py Github

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...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()...

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utils.py

Source: utils.py Github

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...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])...

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app.py

Source: app.py Github

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...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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