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Replace tabs with spaces in add_tax.py #38

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Replace tabs with spaces in add_tax.py #38

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ad93bf3
Replace tabs with spaces in add_tax.py
cezar77 Jul 9, 2021
5c98cc4
Fix more whitespace
Jul 11, 2021
ccf00ee
Remove unnecessary parentheses
Jul 11, 2021
9f8c06e
Remove duplicate whitespace before assignment
Jul 11, 2021
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36 changes: 18 additions & 18 deletions scripts/add_tax.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,17 +45,17 @@
"genus"
]

print('\t'.join(map(str,titles)))
print('\t'.join(map(str, titles)))

# iterate over file
for row in checkm_file:
# split on whitespace
arr = row.split()

# only consider data lines
if (len(arr) > 1):
if len(arr) > 1:
# get taxonomy free of the k__ bit
if (arr[1] == "root"):
if arr[1] == "root":
tax = "root"
else:
tax = arr[1].split("__")[1]
Expand All @@ -65,12 +65,12 @@

# empty variables unless we change them
sk = ''
k = ''
p = ''
c = ''
o = ''
f = ''
g = ''
k = ''
p = ''
c = ''
o = ''
f = ''
g = ''

# check we got what we asked for
if tax in name2taxid.keys():
Expand All @@ -92,26 +92,26 @@
sk = names[l]

if rank[l] == 'kingdom':
k = names[l]
k = names[l]

if rank[l] == 'phylum':
if rank[l] == 'phylum':
p = names[l]

if rank[l] == 'class':
if rank[l] == 'class':
c = names[l]

if rank[l] == 'order':
if rank[l] == 'order':
o = names[l]

if rank[l] == 'family':
if rank[l] == 'family':
f = names[l]

if rank[l] == 'genus':
if rank[l] == 'genus':
g = names[l]

# print it all out
print('\t'.join(map(str,arr)),'\t',end='')
print("%s\t%s\t%s\t%s\t%s\t%s\t%s" % (sk,k,p,c,o,f,g))
print('\t'.join(map(str, arr)), '\t', end='')
print("%s\t%s\t%s\t%s\t%s\t%s\t%s" % (sk, k, p, c, o, f, g))

# close file
checkm_file.close()