Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 64:fd342f5a97d9 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Thu, 18 Mar 2021 10:14:24 +0000 |
| parents | f0fc93b7945c |
| children | 712a37137b1f |
comparison
equal
deleted
inserted
replaced
| 63:f0fc93b7945c | 64:fd342f5a97d9 |
|---|---|
| 960 tier = "4" | 960 tier = "4" |
| 961 counter_tier4 += 1 | 961 counter_tier4 += 1 |
| 962 tier_dict[key1]["tier 4"] += 1 | 962 tier_dict[key1]["tier 4"] += 1 |
| 963 | 963 |
| 964 # assign tiers | 964 # assign tiers |
| 965 if ((all(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) & | 965 if ((all(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) & |
| 966 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) | | 966 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) | |
| 967 (all(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) & | 967 (all(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) & |
| 968 all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))): | 968 all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))): |
| 969 trimmed_actual_high_tier = True | 969 trimmed_actual_high_tier = True |
| 970 elif (all(int(ij) >= 1 for ij in [total1new_trim, total2new_trim, total3new_trim, total4new_trim]) & | 970 elif (all(int(ij) >= 1 for ij in [total1new_trim, total2new_trim, total3new_trim, total4new_trim]) & |
| 971 any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) & | 971 any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) & |
| 972 any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) & | 972 any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) & |
| 973 all(float(ij) >= 0.75 for ij in [alt1ff, alt2ff, alt3ff, alt4ff])): | 973 all(float(ij) >= 0.75 for ij in [alt1ff, alt2ff, alt3ff, alt4ff])): |
| 974 trimmed_actual_high_tier = True | 974 trimmed_actual_high_tier = True |
| 975 elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) & | 975 elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) & |
| 976 any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) & | 976 any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) & |
| 977 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) | | 977 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) | |
| 978 (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) & | 978 (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) & |
| 979 any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) & | 979 any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) & |
| 980 all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))): | 980 all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))): |
| 981 trimmed_actual_high_tier = True | 981 trimmed_actual_high_tier = True |
| 982 elif (all(int(ij) >= 1 for ij in [total1new_trim, total2new_trim, total3new_trim, total4new_trim]) & | 982 elif (all(int(ij) >= 1 for ij in [total1new_trim, total2new_trim, total3new_trim, total4new_trim]) & |
| 983 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt2ff_trim, alt3ff_trim, alt4ff_trim])): | 983 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt2ff_trim, alt3ff_trim, alt4ff_trim])): |
| 984 trimmed_actual_high_tier = True | 984 trimmed_actual_high_tier = True |
| 985 elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) & | 985 elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) & |
| 986 any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) & | 986 any(int(ij) >= 3 for ij in [total2new_trim, total3new_trim]) & |
| 987 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim]) & | 987 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim]) & |
| 988 any(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim])) | | 988 any(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim])) | |
| 989 (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) & | 989 (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) & |
| 990 any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) & | 990 any(int(ij) >= 3 for ij in [total1new_trim, total4new_trim]) & |
| 991 all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]) & | 991 all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]) & |
| 992 any(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim]))): | 992 any(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim]))): |
| 993 trimmed_actual_high_tier = True | 993 trimmed_actual_high_tier = True |
| 994 elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) & | 994 elif ((all(int(ij) >= 1 for ij in [total1new_trim, total4new_trim]) & |
| 995 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) | | 995 all(float(ij) >= 0.75 for ij in [alt1ff_trim, alt4ff_trim])) | |
| 996 (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) & | 996 (all(int(ij) >= 1 for ij in [total2new_trim, total3new_trim]) & |
| 997 all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))): | 997 all(float(ij) >= 0.75 for ij in [alt2ff_trim, alt3ff_trim]))): |
| 998 trimmed_actual_high_tier = True | 998 trimmed_actual_high_tier = True |
| 999 else: | 999 else: |
| 1000 trimmed_actual_high_tier = False | 1000 trimmed_actual_high_tier = False |
| 1001 | 1001 |
| 1002 elif softclipped_mutation_allMates: | 1002 elif softclipped_mutation_allMates: |
| 1003 tier = "5.1" | 1003 tier = "5.1" |
| 1004 counter_tier51 += 1 | 1004 counter_tier51 += 1 |
| 1005 tier_dict[key1]["tier 5.1"] += 1 | 1005 tier_dict[key1]["tier 5.1"] += 1 |