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python script not joining strings as expected

I have a list of lists of sequences, and a corresponding list of lists of names.
testSequences = [
['aaaa', 'cccc'],
['tt', 'gg'],
['AAAAAAA', 'CCCCCC', 'TTTTTT', 'GGGGGG']]
testNames = [
['>xx_oneFish |xzx', '>xx_twoFish |zzx'],
['>xx_redFish |zxx', '>xx_blueFish |zxx'],
['>xx_oneFish |xzx', '>xx_twoFish |xzx', '>xz_redFish |xxx', '>zx_blueFish |xzz']]
I also have a list of all the identifying parts of the names:
taxonNames = ['oneFish', 'twoFish', 'redFish', 'blueFish']
I am trying to produce a new list, where each item in the list will correspond to one of the "identifying parts of the names", and the string will be made up of all the sequences for that name.
If a name and sequence does not appear in one of the lists in the lists (i.e. no redFish or blueFish in the first list of testNames) I want to add in a string of hyphens the same length as the sequences in that list. This would give me this output:
['aaaa--AAAAAA', 'cccc--CCCCCC', '----ttTTTTTT', '----ggGGGG']
I have this piece of code to do this.
complete = [''] * len(taxonNames)
for i in range(len(testSequences)):
for j in range(len(taxonNames)):
sequenceLength = len(testSequences[i][0])
for k in range(len(testSequences[i])):
if taxonNames[j] in testNames[i][k]:
complete[j].join(testSequences[i][k])
if taxonNames[j] not in testNames[i][k]:
hyphenString = "-" * sequenceLength
complete[j].join(hyphenString)
print complete
"complete" should give my final output as explained above, but it comes out looking like this:
['', '', '', '']
How can I fix my code to give me the correct answer?

The main issue with your code, which makes it very hard to understand, is you're not really leveraging the language elements that make Python so strong.
Here's a solution to your problem that works:
test_sequences = [
['aaaa', 'cccc'],
['tt', 'gg'],
['AAAAAAA', 'CCCCCC', 'TTTTTT', 'GGGGGG']]
test_names = [
['>xx_oneFish |xzx', '>xx_twoFish |zzx'],
['>xx_redFish |zxx', '>xx_blueFish |zxx'],
['>xx_oneFish |xzx', '>xx_twoFish |xzx', '>xz_redFish |xxx', '>zx_blueFish |xzz']]
taxon_names = ['oneFish', 'twoFish', 'redFish', 'blueFish']
def get_seqs(taxon_name, sequences_list, names_list):
for seqs, names in zip(sequences_list, names_list):
found_seq = None
for seq, name in zip(seqs, names):
if taxon_name in name:
found_seq = seq
break
yield found_seq if found_seq else '-' * len(seqs[0])
result = [''.join(get_seqs(taxon_name, test_sequences, test_names))
for taxon_name in taxon_names]
print(result)
The generator get_seqs pairs up lists from test_sequences and test_names and for each pair, tries to find the sequence (seq) for the name (name) that matches and yields it, or yields a string of the right number of hyphens for that list of sequences.
The generator (a function that yields multiple values) has code that quite literally follows the explanation above.
The result is then simply a matter of, for each taxon_name, getting all the resulting sequences that match in order and joining them together into a string, which is the result = ... line.
You could make it work with list indexing loops and string concatenation, but this is not a PHP question, now is it? :)
Note: for brevity, you could just access the global test_sequences and test_names instead of passing them in as parameters, but I think that would come back to haunt you if you were to actually use this code. Also, I think it makes semantic sense to change the order of names and sequences in the entire example, but I didn't to avoid further deviating from your example.

Here is a solution that may do what you want. It begins, not with your data structures from this post, but with the three example files from your previous post (which you used to build this post's data structures).
The only thing I couldn't figure out was how many hyphens to use for a missing sequence from a file.
differentNames = ['oneFish', 'twoFish', 'redFish', 'blueFish']
files = ['f1.txt', 'f2.txt', 'f3.txt']
data = [[] for _ in range(len(differentNames))]
final = []
for file in files:
d = dict()
with open(file, 'r') as fin:
for line in fin:
line = line.rstrip()
if line.startswith('>'): # for ex., >xx_oneFish |xxx
underscore = line.index('_')
space = line.index(' ')
key = line[underscore+1:space]
else:
d[key] = line
for i, key in enumerate(differentNames):
data[i].append(d.get(key, '-' * 4))
for array in data:
final.append(''.join(array))
print(final)
Prints:
['AAAAAAAaaaa----', 'CCCCCCcccc----', 'TTTTTT----tt', 'GGGGGG----gg']

Converting plural to singular in a text file with Python

I have txt files that look like this:
word, 23
Words, 2
test, 1
tests, 4
And I want them to look like this:
word, 23
word, 2
test, 1
test, 4
I want to be able to take a txt file in Python and convert plural words to singular. Here's my code:
import nltk
f = raw_input("Please enter a filename: ")
def openfile(f):
with open(f,'r') as a:
a = a.read()
a = a.lower()
return a
def stem(a):
p = nltk.PorterStemmer()
[p.stem(word) for word in a]
return a
def returnfile(f, a):
with open(f,'w') as d:
d = d.write(a)
#d.close()
print openfile(f)
print stem(openfile(f))
print returnfile(f, stem(openfile(f)))
I have also tried these 2 definitions instead of the stem definition:
def singular(a):
for line in a:
line = line[0]
line = str(line)
stemmer = nltk.PorterStemmer()
line = stemmer.stem(line)
return line
def stem(a):
for word in a:
for suffix in ['s']:
if word.endswith(suffix):
return word[:-len(suffix)]
return word
Afterwards I'd like to take duplicate words (e.g. test and test) and merge them by adding up the numbers next to them. For example:
word, 25
test, 5
I'm not sure how to do that. A solution would be nice but not necessary.

If you have complex words to singularize, I don't advise you to use stemming but a proper python package link pattern :
from pattern.text.en import singularize
plurals = ['caresses', 'flies', 'dies', 'mules', 'geese', 'mice', 'bars', 'foos',
'families', 'dogs', 'child', 'wolves']
singles = [singularize(plural) for plural in plurals]
print(singles)
returns:
>>> ['caress', 'fly', 'dy', 'mule', 'goose', 'mouse', 'bar', 'foo', 'foo', 'family', 'family', 'dog', 'dog', 'child', 'wolf']
It's not perfect but it's the best I found. 96% based on the docs : http://www.clips.ua.ac.be/pages/pattern-en#pluralization

It seems like you're pretty familiar with Python, but I'll still try to explain some of the steps. Let's start with the first question of depluralizing words. When you read in a multiline file (the word, number csv in your case) with a.read(), you're going to be reading the entire body of the file into one big string.
def openfile(f):
with open(f,'r') as a:
a = a.read() # a will equal 'soc, 32\nsoc, 1\n...' in your example
a = a.lower()
return a
This is fine and all, but when you want to pass the result into stem(), it will be as one big string, and not as a list of words. This means that when you iterate through the input with for word in a, you will be iterating through each individual character of the input string and applying the stemmer to those individual characters.
def stem(a):
p = nltk.PorterStemmer()
a = [p.stem(word) for word in a] # ['s', 'o', 'c', ',', ' ', '3', '2', '\n', ...]
return a
This definitely doesn't work for your purposes, and there are a few different things we can do.
We can change it so that we read the input file as one list of lines
We can use the big string and break it down into a list ourselves.
We can go through and stem each line in the list of lines one at a time.
Just for expedience's sake, let's roll with #1. This will require changing openfile(f) to the following:
def openfile(f):
with open(f,'r') as a:
a = a.readlines() # a will equal 'soc, 32\nsoc, 1\n...' in your example
b = [x.lower() for x in a]
return b
This should give us b as a list of lines, i.e. ['soc, 32', 'soc, 1', ...]. So the next problem becomes what do we do with the list of strings when we pass it to stem(). One way is the following:
def stem(a):
p = nltk.PorterStemmer()
b = []
for line in a:
split_line = line.split(',') #break it up so we can get access to the word
new_line = str(p.stem(split_line[0])) + ',' + split_line[1] #put it back together
b.append(new_line) #add it to the new list of lines
return b
This is definitely a pretty rough solution, but should adequately iterate through all of the lines in your input, and depluralize them. It's rough because splitting strings and reassembling them isn't particularly fast when you scale it up. However, if you're satisfied with that, then all that's left is to iterate through the list of new lines, and write them to your file. In my experience it's usually safer to write to a new file, but this should work fine.
def returnfile(f, a):
with open(f,'w') as d:
for line in a:
d.write(line)
print openfile(f)
print stem(openfile(f))
print returnfile(f, stem(openfile(f)))
When I have the following input.txt
soc, 32
socs, 1
dogs, 8
I get the following stdout:
Please enter a filename: input.txt
['soc, 32\n', 'socs, 1\n', 'dogs, 8\n']
['soc, 32\n', 'soc, 1\n', 'dog, 8\n']
None
And input.txt looks like this:
soc, 32
soc, 1
dog, 8
The second question regarding merging numbers with the same words changes our solution from above. As per the suggestion in the comments, you should take a look at using dictionaries to solve this. Instead of doing this all as one big list, the better (and probably more pythonic) way to do this is to iterate through each line of your input, and stemming them as you process them. I'll write up code about this in a bit, if you're still working to figure it out.

The Nodebox English Linguistics library contains scripts for converting plural form to single form and vice versa. Checkout tutorial: https://www.nodebox.net/code/index.php/Linguistics#pluralization
To convert plural to single just import singular module and use singular() function. It handles proper conversions for words with different endings, irregular forms, etc.
from en import singular
print(singular('analyses'))
print(singular('planetoids'))
print(singular('children'))
>>> analysis
>>> planetoid
>>> child

How to use for loop in the write method?

The program is supposed to read a given file, count the occurrence of each word with a dictionary, then create a file called report.txt and output the list of words and their frequencies
infile = open('text file.txt','r')
dictionary = {}
# count words' frequency
for i in range(1,14):
temp = infile.readline().strip().split()
for item in temp:
if dictionary.has_key(item) == False:
dictionary[item] = 1
elif dictionary.has_key:
temp2 = dictionary.get(item)
dictionary[item] = temp2 + 1
infile.close()
outfile = open('report.txt','w')
outfile.write( for words in dictionary:
print '%15s :' %words, dictionary[words])
everything works at the counting part, but
just right at the last part of writing the output, I realize I can't put a for loop in the write method

You need to put the write inside the for loop:
for words in dictionary:
outfile.write('%15s : %s\n' % (words, dictionary[words]))
Alternatively you can use a comprehension, but they're a bit ninja and can be harder to read:
outfile.write('\n'.join(['%15s : %s' % key_value for key_value in dictionary.items()]))

As has been said already in the accepted answer, you need the write inside the for loop. However, when using files it is also good practice to perform your actions within a with context as this will automatically handle the closing of the file. e.g.
with open('report.txt','w') as outfile:
for words in dictionary:
outfile.write('%15s : %s\n' % (words, dictionary[words]))

Your code contains several deficiencies:
You don't use has_key and you don't compare to True / False directly - it is redundant and bad style (in any language)
if dictionary.has_key(item) == False:
should be
`if not item in dictionary`
It is worth mentioning that using positive test first will be more efficient - because you'll probably have more than 1 occurrence of most words in the file
dictionary.has_key returns a reference to has_key method - which in boolean equivalent is True (your code accidentally works, because regardless of the 1st conditions second is always True). Simple else would be enough
The last 2 statements in the condition may be just rewritten as
dictionary[item] += 1
That said, you may use collections.Counter to count words
dictionary = Counter()
for lines in source_file:
dictionary.update(line.split())
(BTW, strip before split is redundant)

Python: create dict from list and auto-gen/increment the keys (list is the actual key values)?

i've searched pretty hard and cant find a question that exactly pertains to what i want to..
I have a file called "words" that has about 1000 lines of random A-Z sorted words...
10th
1st
2nd
3rd
4th
5th
6th
7th
8th
9th
a
AAA
AAAS
Aarhus
Aaron
AAU
ABA
Ababa
aback
abacus
abalone
abandon
abase
abash
abate
abater
abbas
abbe
abbey
abbot
Abbott
abbreviate
abc
abdicate
abdomen
abdominal
abduct
Abe
abed
Abel
Abelian
I am trying to load this file into a dictionary, where using the word are the key values and the keys are actually auto-gen/auto-incremented for each word
e.g {0:10th, 1:1st, 2:2nd} ...etc..etc...
below is the code i've hobbled together so far, it seems to sort of works but its only showing me the last entry in the file as the only dict pair element
f3data = open('words')
mydict = {}
for line in f3data:
print line.strip()
cmyline = line.split()
key = +1
mydict [key] = cmyline
print mydict

key = +1
+1 is the same thing as 1. I assume you meant key += 1. I also can't see a reason why you'd split each line when there's only one item per line.
However, there's really no reason to do the looping yourself.
with open('words') as f3data:
mydict = dict(enumerate(line.strip() for line in f3data))

dict(enumerate(x.rstrip() for x in f3data))
But your error is key += 1.

f3data = open('words')
print f3data.readlines()

The use of zero-based numeric keys in a dict is very suspicious. Consider whether a simple list would suffice.
Here is an example using a list comprehension:
>>> mylist = [word.strip() for word in open('/usr/share/dict/words')]
>>> mylist[1]
'A'
>>> mylist[10]
"Aaron's"
>>> mylist[100]
"Addie's"
>>> mylist[1000]
"Armand's"
>>> mylist[10000]
"Loyd's"
I use str.strip() to remove whitespace and newlines, which are present in /usr/share/dict/words. This may not be necessary with your data.
However, if you really need a dictionary, Python's enumerate() built-in function is your friend here, and you can pass the output directly into the dict() function to create it:
>>> mydict = dict(enumerate(word.strip() for word in open('/usr/share/dict/words')))
>>> mydict[1]
'A'
>>> mydict[10]
"Aaron's"
>>> mydict[100]
"Addie's"
>>> mydict[1000]
"Armand's"
>>> mydict[10000]
"Loyd's"

With keys that dense, you don't want a dict, you want a list.
with open('words') as fp:
data = map(str.strip, fp.readlines())
But if you really can't live without a dict:
with open('words') as fp:
data = dict(enumerate(X.strip() for X in fp))

{index: x.strip() for index, x in enumerate(open('filename.txt'))}
This code uses a dictionary comprehension and the enumerate built-in, which takes an input sequence (in this case, the file object, which yields each line when iterated through) and returns an index along with the item. Then, a dictionary is built up with the index and text.
One question: why not just use a list if all of your keys are integers?
Finally, your original code should be
f3data = open('words')
mydict = {}
for index, line in enumerate(f3data):
cmyline = line.strip()
mydict[index] = cmyline
print mydict

Putting the words in a dict makes no sense. If you're using numbers as keys you should be using a list.
from __future__ import with_statement
with open('words.txt', 'r') as f:
lines = f.readlines()
words = {}
for n, line in enumerate(lines):
words[n] = line.strip()
print words

How to refactor this python code block to be more efficient

This code block works - it loops through a file that has a repeating number of sets of data
and extracts out each of the 5 pieces of information for each set.
But I I know that the current factoring is not as efficient as it can be since it is looping
through each key for each line found.
Wondering if some python gurus can offer better way to do this more efficiently.
def parse_params(num_of_params,lines):
for line in lines:
for p in range(1,num_of_params + 1,1):
nam = "model.paramName "+str(p)+" "
par = "model.paramValue "+str(p)+" "
opt = "model.optimizeParam "+str(p)+" "
low = "model.paramLowerBound "+str(p)+" "
upp = "model.paramUpperBound "+str(p)+" "
keys = [nam,par,opt,low,upp]
for key in keys:
if key in line:
a,val = line.split(key)
if key == nam: names.append(val.rstrip())
if key == par: params.append(val.rstrip())
if key == opt: optimize.append(val.rstrip())
if key == upp: upper.append(val.rstrip())
if key == low: lower.append(val.rstrip())
print "Names = ",names
print "Params = ",params
print "Optimize = ",optimize
print "Upper = ",upper
print "Lower = ",lower

Though this doesn't answer your question (other answers are getting at that) something that has helped me a lot in doing things similar to what you're doing are List Comprehensions. They allow you to build lists in a concise and (I think) easy to read way.
For instance, the below code builds a 2-dimenstional array with the values you're trying to get at. some_funct here would be a little regex, if I were doing it, that uses the index of the last space in the key as the parameter, and looks ahead to collect the value you're trying to get in the line (the value which corresponds to the key currently being looked at) and appends it to the correct index in the seen_keys 2D array.
Wordy, yes, but if you get list-comprehension and you're able to construct the regex to do that, you've got a nice, concise solution.
keys = ["model.paramName ","model.paramValue ","model.optimizeParam ""model.paramLowerBound ","model.paramUpperBound "]
for line in lines:
seen_keys = [[],[],[],[],[]]
[seen_keys[keys.index(k)].some_funct(line.index(k) for k in keys if k in line]

It's not totally easy to see the expected format. From what I can see, the format is like:
lines = [
"model.paramName 1 foo",
"model.paramValue 2 bar",
"model.optimizeParam 3 bat",
"model.paramLowerBound 4 zip",
"model.paramUpperBound 5 ech",
"model.paramName 1 foo2",
"model.paramValue 2 bar2",
"model.optimizeParam 3 bat2",
"model.paramLowerBound 4 zip2",
"model.paramUpperBound 5 ech2",
]
I don't see the above code working if there is more than one value in each line. Which means the digit is not really significant unless I'm missing something. In that case this works very easily:
import re
def parse_params(num_of_params,lines):
key_to_collection = {
"model.paramName":names,
"model.paramValue":params,
"model.optimizeParam":optimize,
"model.paramLowerBound":upper,
"model.paramUpperBound":lower,
}
reg = re.compile(r'(.+?) (\d) (.+)')
for line in lines:
m = reg.match(line)
key, digit, value = m.group(1, 2, 3)
key_to_collection[key].append(value)

It's not entirely obvious from your code, but it looks like each line can have one "hit" at most; if that's indeed the case, then something like:
import re
def parse_params(num_of_params, lines):
sn = 'Names Params Optimize Upper Lower'.split()
ks = '''paramName paramValue optimizeParam
paramLowerBound paramUpperBound'''.split()
vals = dict((k, []) for k in ks)
are = re.compile(r'model\.(%s) (\d+) (.*)' % '|'.join(ks))
for line in lines:
mo = are.search(line)
if not mo: continue
p = int(mo.group(2))
if p < 1 or p > num_of_params: continue
vals[mo.group(1)].append(mo.group(3).rstrip())
for k, s in zip(ks, sn):
print '%-8s =' % s,
print vals[k]
might work -- I exercised it with a little code as follows:
if __name__ == '__main__':
lines = '''model.paramUpperBound 1 ZAP
model.paramLowerBound 1 zap
model.paramUpperBound 5 nope'''.splitlines()
parse_params(2, lines)
and it emits
Names = []
Params = []
Optimize = []
Upper = ['zap']
Lower = ['ZAP']
which I think is what you want (if some details must differ, please indicate exactly what they are and let's see if we can fix it).
The two key ideas are: use a dict instead of lots of ifs; use a re to match "any of the following possibilities" with parenthesized groups in the re's pattern to catch the bits of interest (the keyword after model., the integer number after that, and the "value" which is the rest of the line) instead of lots of if x in y checks and string manipulation.

There is a lot of duplication there, and if you ever add another key or param, you're going to have to add it in many places, which leaves you ripe for errors. What you want to do is pare down all of the places you have repeated things and use some sort of data model, such as a dict.
Some others have provided some excellent examples, so I'll just leave my answer here to give you something to think about.

Are you sure that parse_params is the bottle-neck? Have you profiled your app?
import re
from collections import defaultdict
names = ("paramName paramValue optimizeParam "
"paramLowerBound paramUpperBound".split())
stmt_regex = re.compile(r'model\.(%s)\s+(\d+)\s+(.*)' % '|'.join(names))
def parse_params(num_of_params, lines):
stmts = defaultdict(list)
for m in (stmt_regex.match(s) for s in lines):
if m and 1 <= int(m.group(2)) <= num_of_params:
stmts[m.group(1)].append(m.group(3).rstrip())
for k, v in stmts.iteritems():
print "%s = %s" % (k, ' '.join(v))

The code given in the OP does multiple tests per line to try to match against the expected set of values, each of which is being constructed on the fly. Rather than construct paramValue1, paramValue2, etc. for each line, we can use a regular expression to try to do the matching in a cheaper (and more robust) manner.
Here's my code snippet, drawing from some ideas that have already been posted. This lets you add a new keyword to the key_to_collection dictionary and not have to change anything else.
import re
def parse_params(num_of_params, lines):
pattern = re.compile(r"""
model\.
(.+) # keyword
(\d+) # index to keyword
[ ]+ # whitespace
(.+) # value
""", re.VERBOSE)
key_to_collection = {
"paramName": names,
"paramValue": params,
"optimizeParam": optimize,
"paramLowerBound": upper,
"paramUpperBound": lower,
}
for line in lines:
match = pattern.match(line)
if not match:
print "Invalid line: " + line
elif match[1] not in key_to_collection:
print "Invalid key: " + line
# Not sure if you really care about enforcing this
elif match[2] > num_of_params:
print "Invalid param: " + line
else:
key_to_collection[match[1]].append(match[3])
Full disclosure: I have not compiled/tested this.

It can certainly be made more efficient. But, to be honest, unless this function is called hundreds of times a second, or works on thousands of lines, is it necessary?
I would be more concerned about making it clear what is happening... currently, I'm far from clear on that aspect.
Just eyeballing it, the input seems to look like this:
model.paramName 1 A model.paramValue 1 B model.optimizeParam 1 C model.paramLowerBound 1 D model.paramUpperBound 1 E model.paramName 2 F model.paramValue 2 G model.optimizeParam 2 H model.paramLowerBound 2 I model.paramUpperBound 2 J
And your desired output seems to be something like:
Names = AF
Params = BG
etc...
Now, since my input certainly doesn't match yours, the output is likely off too, but I think I have the gist.
There are a few points. First, does it matter how many parameters are passed to the function? For example, if the input has two sets of parameters, do I just want to read both, or is it necessary to allow the function to only read one? For example, your code allows me to call parse_params(1,1) and have it only read parameters ending in a 1 from the same input. If that's not actually a requirement, you can skip a large chunk of the code.
Second, is it important to ONLY read the given parameters? If I, for example, have a parameter called 'paramFoo', is it bad if I read it? You can also simplify the procedure by just grabbing all parameters regardless of their name, and extracting their value.
def parse_params(input):
parameter_list = {}
param = re.compile(r"model\.([^ ]+) [0-9]+ ([^ ]+)")
each_parameter = param.finditer(input)
for match in each_parameter:
key = match[0]
value = match[1]
if not key in paramter_list:
parameter_list[key] = []
parameter_list[key].append(value)
return parameter_list
The output, in this instance, will be something like this:
{'paramName':[A, F], 'paramValue':[B, G], 'optimizeParam':[C, H], etc...}
Notes: I don't know Python well, I'm a Ruby guy, so my syntax may be off. Apologies.