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#1
March 24th, 2013, 03:42 AM
 miclow
Registered User

Join Date: Mar 2013
Posts: 1
Time spent in forums: 2 m 34 sec
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Phyton script for fasta file

Hi everyone,

Can someone please help me with the following phyton script? I received the error message DeprecationWarning: the sets module is deprecated
from sets import Set.

After googling, I have tried the methods others suggest: change sets to set or delete the from sets import Set but none of them works.

Can someone suggest me how to modify the following codes so that the input file is read from standard input?
I'd like to execute them with unix command

script.py < sequence.fna

Thanks a bunch.

#!/usr/local/bin/python

import math
from sets import Set

line = file("sequence.fna", "r")

for x in line:
if x [0] == ">" :

#determine the length of sequences
s=line.next()
s=s.rstrip()
length = len(s)

# determine the GC content
G = s.count('G')
C = s.count('C')
GC= 100 * (float(G + C) / length)

stList = list(s)
alphabet = list(Set(stList))

freqList = []
for symbol in alphabet:
ctr = 0
for sym in stList:
if sym == symbol:
ctr += 1
freqList.append(float(ctr)/len(stList))

# Shannon entropy
ent = 0.0
for freq in freqList:
ent = ent + freq * math.log(freq, 2)
ent = -ent

print x
print "Length:" , length
print "G+C:" ,round(GC),"%"
print 'Shannon entropy:'
print ent
print 'Minimum number of bits required to encode each symbol:'
print int(math.ceil(ent))

#2
March 24th, 2013, 01:30 PM
 partoj
Contributing User

Join Date: Feb 2013
Posts: 138
Time spent in forums: 1 Day 12 h 26 m 47 sec
Reputation Power: 1
Quote:
 Originally Posted by miclow Hi everyone, Can someone please help me with the following phyton script? I received the error message DeprecationWarning: the sets module is deprecated from sets import Set. After googling, I have tried the methods others suggest: change sets to set or delete the from sets import Set but none of them works.

Could you please elaborate on what "none of them works" means?

Quote:
 Can someone suggest me how to modify the following codes so that the input file is read from standard input? I'd like to execute them with unix command script.py < sequence.fna

Code:
```import fileinput

for line in fileinput.input():
for x in line:
# do work here```

#3
March 24th, 2013, 03:36 PM
 b49P23TIvg
Contributing User

Join Date: Aug 2011
Posts: 4,213
Time spent in forums: 1 Month 3 Weeks 2 Days 17 h 59 m 58 sec
Reputation Power: 455
#set is a builtin data type in pythons 2.7 and 3+.

alphabet = list(set(stList))

#alphabet is now the unique characters from stList
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