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Fixed error where incertae sedis classifications can result in misran…
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…ked taxon assignments.
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@liberjul
liberjul committed Jul 15, 2023
1 parent 0a559e7 commit df0a66c
Showing 1 changed file with 17 additions and 40 deletions.
57 changes: 17 additions & 40 deletions CombineTaxonomy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -398,12 +398,13 @@ def real_hier(filename):
def vote(cla1, cla2, cla3, conservative):
winner = ""
taxa = [cla1[0].replace("NA", ""), cla2[0].replace("NA", ""), cla3[0].replace("NA", "")]
taxa = ["" if "ncertae_sedis" in x else x for x in taxa]
scores = [cla1[1], cla2[1], cla3[1]]
tally = ["0","0","0"]
duplicates_notempty = [i for i, x in enumerate(taxa) if x!= "" and taxa.count(x) > 1]
unique_2empty = [i for i, x in enumerate(taxa) if x!="" and taxa.count("") > 1]
unique = [i for i, x in enumerate(taxa) if x!="" and taxa.count("") == 1]
for j in range(0,3):
duplicates_notempty = [i for i, x in enumerate(taxa) if x!= "" and taxa.count(x) > 1] # 2 of the same assignment
unique_2empty = [i for i, x in enumerate(taxa) if x!="" and taxa.count("") > 1] # 2 no assignments
unique = [i for i, x in enumerate(taxa) if x!="" and taxa.count("") == 1] # Each unique
for j in range(3):
if taxa[j]!="":
if j in duplicates_notempty:
winner = taxa[j]
Expand Down Expand Up @@ -636,7 +637,7 @@ def str2bool(v):
combined.write("\tOrder_Consensus\tFamily_RDP\tFamily_BLAST\tFamily_SINTAX\tFamily_Consensus\tGenus_RDP\tGenus_BLAST\tGenus_SINTAX")
combined.write("\tGenus_Consensus\tSpecies_RDP\tSpecies_BLAST\tSpecies_SINTAX\tSpecies_Consensus\n")

for otu in rdp_dict.keys():
for otu in rdp_dict:
consensus.write(otu+"\t")
combined.write(otu)
levels = []
Expand All @@ -646,19 +647,13 @@ def str2bool(v):
if level != "":
levels.append(level)
combined.write(level)
levels_clean = []
for x in levels:
if "ncertae_sedis" in x:
levels_clean.append("")
else:
levels_clean.append(x)
consensus.write('\t'.join(levels_clean+[""]*(len(ranks)-len(levels_clean))))
consensus.write('\t'.join(levels+[""]*(len(ranks)-len(levels))))
if args.isolates == "True":
consensus.write(F"\t{iso_dict[otu][0]}\t{iso_dict[otu][1]}\t{iso_dict[otu][2]}")
if args.hl != "null":
consensus.write(F"\t{hl_dict[otu][0]}\t{hl_dict[otu][1]}\t{hl_dict[otu][2]}")
if args.consistent:
tax_string = '\t'.join(levels_clean)
tax_string = '\t'.join(levels)
consensus.write(F"\t{int(tax_string.replace(' ', '_').strip('_') in taxa_set)}\n")
else:
consensus.write("\n")
Expand All @@ -678,7 +673,7 @@ def str2bool(v):
combined.write("\tOrder_Consensus\tFamily_RDP\tFamily_SINTAX\tFamily_UTAX\tFamily_Consensus\tGenus_RDP\tGenus_SINTAX\tGenus_UTAX")
combined.write("\tGenus_Consensus\tSpecies_RDP\tSpecies_SINTAX\tSpecies_UTAX\tSpecies_Consensus\n")

for otu in rdp_dict.keys():
for otu in rdp_dict:
consensus.write(otu+"\t")
combined.write(otu)
levels = []
Expand All @@ -688,19 +683,13 @@ def str2bool(v):
if level != "":
levels.append(level)
combined.write(level)
levels_clean = []
for x in levels:
if "ncertae_sedis" in x:
levels_clean.append("")
else:
levels_clean.append(x)
consensus.write('\t'.join(levels_clean+[""]*(len(ranks)-len(levels_clean))))
consensus.write('\t'.join(levels+[""]*(len(ranks)-len(levels))))
if args.isolates == "True":
consensus.write(F"\t{iso_dict[otu][0]}\t{iso_dict[otu][1]}\t{iso_dict[otu][2]}")
if args.hl != "null":
consensus.write(F"\t{hl_dict[otu][0]}\t{hl_dict[otu][1]}\t{hl_dict[otu][2]}")
if args.consistent:
tax_string = '\t'.join(levels_clean)
tax_string = '\t'.join(levels)
consensus.write(F"\t{int(tax_string.replace(' ', '_').strip('_') in taxa_set)}\n")
else:
consensus.write("\n")
Expand Down Expand Up @@ -798,7 +787,7 @@ def str2bool(v):
consensus.write("\n")
combined.write("\n")

for otu in rdp_dict.keys():
for otu in rdp_dict:
consensus.write(otu+"\t")
combined.write(otu)
levels = []
Expand All @@ -808,19 +797,13 @@ def str2bool(v):
if level != "":
levels.append(level)
combined.write(level)
levels_clean = []
for x in levels:
if "ncertae_sedis" in x:
levels_clean.append("")
else:
levels_clean.append(x)
consensus.write('\t'.join(levels_clean+[""]*(len(ranks)-len(levels_clean))))
consensus.write('\t'.join(levels+[""]*(len(ranks)-len(levels))))
if args.isolates == "True":
consensus.write(F"\t{iso_dict[otu][0]}\t{iso_dict[otu][1]}\t{iso_dict[otu][2]}")
if args.hl != "null":
consensus.write(F"\t{hl_dict[otu][0]}\t{hl_dict[otu][1]}\t{hl_dict[otu][2]}")
if args.consistent:
tax_string = '\t'.join(levels_clean)
tax_string = '\t'.join(levels)
consensus.write(F"\t{int(tax_string in taxa_set)}\n")
else:
consensus.write("\n")
Expand Down Expand Up @@ -855,7 +838,7 @@ def str2bool(v):
combined.write("\n")
consensus.write("\n")

for otu in rdp_dict.keys():
for otu in rdp_dict:
consensus.write(otu+"\t")
combined.write(otu)
levels = []
Expand All @@ -865,19 +848,13 @@ def str2bool(v):
if level != "":
levels.append(level)
combined.write(level)
levels_clean = []
for x in levels:
if "ncertae_sedis" in x:
levels_clean.append("")
else:
levels_clean.append(x)
consensus.write('\t'.join(levels_clean+[""]*(len(ranks)-len(levels_clean))))
consensus.write('\t'.join(levels+[""]*(len(ranks)-len(levels))))
if args.isolates == "True":
consensus.write(F"\t{iso_dict[otu][0]}\t{iso_dict[otu][1]}\t{iso_dict[otu][2]}")
if args.hl != "null":
consensus.write(F"\t{hl_dict[otu][0]}\t{hl_dict[otu][1]}\t{hl_dict[otu][2]}")
if args.consistent:
tax_string = '\t'.join(levels_clean)
tax_string = '\t'.join(levels)
consensus.write(F"\t{int(tax_string in taxa_set)}\n")
else:
consensus.write("\n")
Expand Down

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