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Support strain level #70

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Support strain level #70

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48ee55b
support strain level
alienzj Mar 15, 2023
fa88233
combine strain level too
alienzj Mar 15, 2023
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4 changes: 2 additions & 2 deletions combine_kreports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,8 +158,8 @@ def main():


#Initialize combined values
main_lvls = ['U','R','D','K','P','C','O','F','G','S']
map_lvls = {'kingdom':'K', 'superkingdom':'D','phylum':'P','class':'C','order':'O','family':'F','genus':'G','species':'S'}
main_lvls = ['U','R','D','K','P','C','O','F','G','S', 'S1', 'T']
map_lvls = {'kingdom':'K', 'superkingdom':'D','phylum':'P','class':'C','order':'O','family':'F','genus':'G','species':'S', 'strain': 'T'}
count_samples = 0
num_samples = len(args.r_files)
sample_names = args.s_names
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6 changes: 4 additions & 2 deletions kreport2mpa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ def process_kraken_report(curr_str):
try:
taxid = int(split_str[-3])
level_type = split_str[-2]
map_kuniq = {'species':'S', 'genus':'G','family':'F',
map_kuniq = {'strain': 'T', 'species':'S', 'genus':'G','family':'F',
'order':'O','class':'C','phylum':'P','superkingdom':'D',
'kingdom':'K'}
if level_type not in map_kuniq:
Expand Down Expand Up @@ -138,7 +138,7 @@ def main():
o_file.write("#Classification\t" + os.path.basename(args.r_file) + "\n")

#Read through report file
main_lvls = ['R','K','D','P','C','O','F','G','S']
main_lvls = ['R','K','D','P','C','O','F','G','S','S1','T']
for line in r_file:
report_vals = process_kraken_report(line)
#If header line, skip
Expand All @@ -155,6 +155,8 @@ def main():
level_type = "k"
elif level_type == "D":
level_type = "k"
elif level_type == "S1":
level_type = "t"
level_str = level_type.lower() + "__" + name
#Determine full string to add
if prev_lvl_num == -1:
Expand Down