Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 80:8336a4f2b647 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
| author | mheinzl |
|---|---|
| date | Tue, 26 Jul 2022 10:19:28 +0000 |
| parents | d7aea14291e8 |
| children | 612c110305db |
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| 79:d7aea14291e8 | 80:8336a4f2b647 |
|---|---|
| 1365 sum_highTiers = sum([tier_dict[key1][ij] for ij in list(sorted(tier_dict[key1].keys()))[:6]]) | 1365 sum_highTiers = sum([tier_dict[key1][ij] for ij in list(sorted(tier_dict[key1].keys()))[:6]]) |
| 1366 sum_highTiers_ref = sum([tier_dict_ref[key1][ij] for ij in list(sorted(tier_dict_ref[key1].keys()))[:6]]) | 1366 sum_highTiers_ref = sum([tier_dict_ref[key1][ij] for ij in list(sorted(tier_dict_ref[key1].keys()))[:6]]) |
| 1367 correct_tier = False | 1367 correct_tier = False |
| 1368 correct_tier_ref = False | 1368 correct_tier_ref = False |
| 1369 if tier_dict[key1]["tier 4"] > 0 and sum_highTiers > 0: | 1369 if tier_dict[key1]["tier 4"] > 0 and sum_highTiers > 0: |
| 1370 tier_dict[key1]["tier 2.5"] = tier_dict[key1]["tier 4"] | 1370 # tier_dict[key1]["tier 2.5"] = tier_dict[key1]["tier 4"] |
| 1371 tier_dict[key1]["tier 4"] = 0 | 1371 # tier_dict[key1]["tier 4"] = 0 |
| 1372 correct_tier = True | 1372 correct_tier = True |
| 1373 | 1373 elif tier_dict_ref[key1]["tier 4"] > 0 and sum_highTiers_ref > 0: |
| 1374 if tier_dict_ref[key1]["tier 4"] > 0 and sum_highTiers_ref > 0: | 1374 # tier_dict_ref[key1]["tier 2.5"] = tier_dict_ref[key1]["tier 4"] |
| 1375 tier_dict_ref[key1]["tier 2.5"] = tier_dict_ref[key1]["tier 4"] | 1375 # tier_dict_ref[key1]["tier 4"] = 0 |
| 1376 tier_dict_ref[key1]["tier 4"] = 0 | |
| 1377 correct_tier_ref = True | 1376 correct_tier_ref = True |
| 1378 # print(key1, "change tiers from tier 4 to tier 2.5 for {} DCS ...".format(len(change_tier_after_print))) | 1377 # print(key1, "change tiers from tier 4 to tier 2.5 for {} DCS ...".format(len(change_tier_after_print))) |
| 1379 if len(change_tier_after_print) > 0: | 1378 if len(change_tier_after_print) > 0: |
| 1380 for sample in change_tier_after_print: | 1379 for sample in change_tier_after_print: |
| 1381 # row_number = sample[0] | 1380 # row_number = sample[0] |
| 1387 line1 = list(line1) | 1386 line1 = list(line1) |
| 1388 line1[1] = "2.5" | 1387 line1[1] = "2.5" |
| 1389 line1 = tuple(line1) | 1388 line1 = tuple(line1) |
| 1390 counter_tier25 += 1 | 1389 counter_tier25 += 1 |
| 1391 counter_tier4 -= 1 | 1390 counter_tier4 -= 1 |
| 1392 if line1[2] == "ref" and correct_tier_ref and (current_tier == "4") and actual_high_tier: | 1391 tier_dict[key1]["tier 2.5"] += 1 |
| 1392 tier_dict[key1]["tier 4"] -= 1 | |
| 1393 elif line1[2] == "ref" and correct_tier_ref and (current_tier == "4") and actual_high_tier: | |
| 1393 line1 = list(line1) | 1394 line1 = list(line1) |
| 1394 line1[1] = "2.5" | 1395 line1[1] = "2.5" |
| 1395 line1 = tuple(line1) | 1396 line1 = tuple(line1) |
| 1396 counter_tier25 += 1 | 1397 counter_tier25 += 1 |
| 1397 counter_tier4 -= 1 | 1398 counter_tier4 -= 1 |
| 1399 tier_dict_ref[key1]["tier 2.5"] += 1 | |
| 1400 tier_dict_ref[key1]["tier 4"] -= 1 | |
| 1398 ws1.write_row(row, 0, line1) | 1401 ws1.write_row(row, 0, line1) |
| 1399 csv_writer.writerow(line1) | 1402 csv_writer.writerow(line1) |
| 1400 ws1.write_row(row + 1, 0, line2) | 1403 ws1.write_row(row + 1, 0, line2) |
| 1401 csv_writer.writerow(line2) | 1404 csv_writer.writerow(line2) |
| 1402 if line1[2] == "alt": | 1405 if line1[2] == "alt": |