/usr/lib/python2.7/dist-packages/cogent/parse/dotur.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | #!/usr/bin/env python
#file cogent.parse.dotur.py
"""Parses various Dotur output formats."""
from record_finder import is_empty
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
def get_otu_lists(data):
"""Returns list of lists of OTUs given data.
- data: list of OTUs in following format:
['seq_1,seq_2,seq_3','seq_4,seq_5','seq_6','seq_7,seq_8']
"""
return [i.split(',') for i in data]
def OtuListParser(lines,ignore=is_empty):
"""Parser for *.list file format dotur result.
- Result will be list of lists with following order:
[[OTU distance, number of OTUs, [list of OTUs]],
[OTU distance, number of OTUs, [list of OTUs]],
[etc...]]
"""
result = []
if not lines:
return result
for line in lines:
if ignore(line):
continue
curr_data = line.strip().split()
#Get distance. Replace 'unique' string with 0
distance = float(curr_data[0].upper().replace('UNIQUE','0'))
#number of OTUs is second column
num_otus = int(curr_data[1])
#remaining columns contain lists of OTUs
otu_list = get_otu_lists(curr_data[2:])
result.append([distance,num_otus,otu_list])
return result
|