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# Usage: python count_word.py /home/hui/network/v03/Data/information/rnaseq_info_database.txt
#
# Purpose: get all words in a file, order them by their frequencies.
#
# 20 Apr 2017, slcu, hui
FILE_NAME = '/home/hui/network/v03/Data/information/rnaseq_info_database.txt'
from collections import Counter
import operator
import string
import sys
FILE_NAME = sys.argv[1]
def remove_punctuation(s):
result = ''
for x in s.split():
result += ' ' + x.translate(None, string.punctuation)
return result.strip()
f = open(FILE_NAME)
lines = f.readlines()
f.close()
yourtext = ''
for line in lines[1:]: # don't include header line
line = line.strip()
lst = line.split('\t')
for x in lst[4:]: # only consider fields from 5th column.
yourtext += ' ' + remove_punctuation(x.lower())
d = Counter(yourtext.split())
sd = sorted(d.items(), key=operator.itemgetter(1), reverse=True)
for t in sd:
k = t[0]
print('%s\t\t%s' % (k, d[k]))
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