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fix problem of double root lines messing up tree #103

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fix problem of double root lines messing up tree #103

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7128e0d
fix problem of double root lines messing up tree
JCSzamosi May 2, 2025
405855b
forgot to delete a print statement
JCSzamosi May 2, 2025
9fd616d
fix the fact that it's missing things
JCSzamosi May 13, 2025
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34 changes: 30 additions & 4 deletions extract_kraken_reads.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@ def process_kraken_output(kraken_line):
# - taxonomy ID
# - level number (number of spaces before name)
# - level_type (type of taxonomy level - U, R, D, P, C, O, F, G, S, etc)
def process_kraken_report(report_line):
def process_kraken_report_old(report_line):
l_vals = report_line.strip().split('\t')
if len(l_vals) < 5:
return []
Expand All @@ -122,7 +122,7 @@ def process_kraken_report(report_line):
return []
#Extract relevant information
try:
taxid = int(l_vals[-3])
taxid = int(l_vals[-3])
level_type = l_vals[-2]
map_kuniq = {'species':'S', 'genus':'G','family':'F',
'order':'O','class':'C','phylum':'P','superkingdom':'D',
Expand All @@ -143,6 +143,32 @@ def process_kraken_report(report_line):
break
level_num = int(spaces/2)
return[taxid, level_num, level_type]

def process_kraken_report(report_line):
l_vals = report_line.strip().split('\t')
if len(l_vals) < 5:
return []
try:
int(l_vals[1])
except ValueError:
return[]
taxid = int(l_vals[-2])
level_type = l_vals[-3]
map_kuniq = {'species': 'S', 'genus': 'G', 'family': 'F',
'order': 'O', 'class': 'C', 'phylum': 'P', 'superkingdom': 'D',
'kingdom': 'K'}
if (len(level_type) == 0) or (level_type[0] not in map_kuniq):
level_type = '-'
else:
level_type = map_kuniq[level_type]
spaces = 0
for char in l_vals[-1]:
if char == ' ':
spaces += 1
else:
break
level_num = int(spaces/2)
return[taxid, level_num, level_type]
################################################################################
#Main method
def main():
Expand Down Expand Up @@ -224,7 +250,7 @@ def main():
if taxid == 0:
continue
#tree root
if taxid == 1:
if taxid == 1 and prev_node == -1:
level_id = 'R'
root_node = Tree(taxid, level_num, level_id)
prev_node = root_node
Expand All @@ -236,7 +262,7 @@ def main():
while level_num != (prev_node.level_num + 1):
prev_node = prev_node.parent
#determine correct level ID
if level_id == '-' or len(level_id) > 1:
if (level_id in ['-','']) or len(level_id) > 1:
if prev_node.level_id in main_lvls:
level_id = prev_node.level_id + '1'
else:
Expand Down