planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl Thu, 18 Mar 2021 10:14:24 +0000 f0fc93b7945c 712a37137b1f
comparison
equal 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