Develop Reference

Unable to store values in an array from for loop in python

First I tried directly storing values from a list having the name 'data' in an array variable 'c' using loop but 'none' got printed
for i in data:
print(i['name'])
c=i['name']
Here print(i['name']) perfectly worked and output appeared
This is the working ouput
Then I printed c in order to print the values generated using loop. The ouput came as none.
print(c)
Then I tried another way by storing the values and making the array iterable at the same time using for loop. An error occurred which I was unable to resolve.
for i in data:
b[c]=i['name']
c=c+1
The error apeared is as follow-
I have tried two ways, if there is any other way please help me out as I am new to python.

It looks like the variable 'data' is a dictionary.
If you want to add each name from that dictionary to a list:
# create a new list variable
names = []
for i in data:
name = i['name']
print(name)
# add the name to the list
names.append(name)
# output the new list
print(names)

Assuming your data object here is a list like [{"name": "Mr. Green", ...}, {"name": "Mr. Blue", ...}].
If your goal is to end up with c == ["Mr. Green", "Mr. Blue"], then you're looking for something like:
c = []
for i in data:
c.append(i['name'])
print(c)
or you can accomplish tasks like these using list comprehensions like:
c = [i['name'] for i in data]
print(c)
The first code example you posted is iterating through the items in data and reassigning the value of c to each item's name key - not adding them to a list("array"). Without knowing more about the code you ran to produce the screenshot and/or the contents of data, it's hard to say why you're seeing print(c) produce None. I'd guess the last item in data is something like {"name": None, ...} which if it's coming from JSON is possible if the value is null. Small note: I'd generally use .get("name") here instead so that your program doesn't blow up if an item is missing a "name" key entirely.
For your second code example, the error is different but I think falls along a similar logical fallacy which is that lists in python function differently from primitives(things like numbers and strings). For the interpreter to know that b or c are supposed to be lists("arrays"), they need to be instantiated differently and they have their own set of syntax/methods for mutation. For example, like arrays in other languages, lists are indexed by position so doing b[c] = <something> will only work if c is an integer. So something similar to your second example that would also produce a list of names like my above would be:
b = [None] * len(data)
c = 0
for i in data:
b[c]=i['name']
c=c+1
Note that if you only initialize b = [], you get an IndexError: list assignment index out of range on the initial assignment of b[0] = "some name" because the list is of size 0.

Add
b = []
above your first line of code. As the error is saying that you have not (and correctly so) defined the list to append.
I personally would use list comprehension here
b = [obj['name'] for obj in data]
where obj is i as you have defined it.

Dictionary access is stopping the code flow

I have a 3 seperate dictionaries that I manually enter values into. There is a loop that shows the value associated with the keys depending on a if condition
inv_dict_celltype and buf_dict_celltype are dictioanries. From the code below i observe that when i try to access both the dictionaries in different scenarios the code doesn't work. The output I get shows the dictionary values present in the first statement I give here, I get all the values in inv_dect_celltype but it doesn't proceed with next if statement, instead comes out
And the temp_list contains the following data :
temp_list = {'INV_X20B_NXP7P5PP96PTL_C16', 'INV_X6B_NXP7P5PP96PTL_C16',
'INV_X8B_NXP7P5PP96PTL_C16', 'INV_X16B_NXP7P5PP96PTL_C16',
'INV_X10B_NXP7P5PP96PTL_C16', 'BUF_X6N_A7P5PP96PTL_C16',
'BUF_X20N_A7P5PP96PTL_C16', 'BUF_X8N_A7P5PP96PTL_C16',
'BUF_X10N_A7P5PP96PTL_C16', 'BUF_X7N_A7P5PP96PTL_C16',
'BUF_X1P3N_A7P5PP96PTS_C18'}
for each_cell in temp_list:
if each_cell.startswith('INV_'):
print(inv_dict_celltype[each_cell])
if each_cell.startswith('BUF_'):
print(buf_dict_celltype[each_cell])

I am not sure what exactly you want to retrieve from your dictionaries, and how the other two dictionaries look like, but try with the following.
for each_cell in temp_list:
if each_cell.startswith('INV_'):
for i in inv_dict_celltype:
if i == each_cell:
print(i)
if each_cell.startswith('BUF_'):
for x in buf_dict_celltype:
if x == each_cell:
print(x)

How to create a nested python dictionary with keys as strings?

Summary of issue: I'm trying to create a nested Python dictionary, with keys defined by pre-defined variables and strings. And I'm populating the dictionary from regular expressions outputs. This mostly works. But I'm getting an error because the nested dictionary - not the main one - doesn't like having the key set to a string, it wants an integer. This is confusing me. So I'd like to ask you guys how I can get a nested python dictionary with string keys.
Below I'll walk you through the steps of what I've done. What is working, and what isn't. Starting from the top:
# Regular expressions module
import re
# Read text data from a file
file = open("dt.cc", "r")
dtcc = file.read()
# Create a list of stations from regular expression matches
stations = sorted(set(re.findall(r"\n(\w+)\s", dtcc)))
The result is good, and is as something like this:
stations = ['AAAA','BBBB','CCCC','DDDD']
# Initialize a new dictionary
rows = {}
# Loop over each station in the station list, and start populating
for station in stations:
rows[station] = re.findall("%s\s(.+)" %station, dtcc)
The result is good, and is something like this:
rows['AAAA'] = ['AAAA 0.1132 0.32 P',...]
However, when I try to create a sub-dictionary with a string key:
for station in stations:
rows[station] = re.findall("%s\s(.+)" %station, dtcc)
rows[station]["dt"] = re.findall("%s\s(\S+)" %station, dtcc)
I get the following error.
"TypeError: list indices must be integers, not str"
It doesn't seem to like that I'm specifying the second dictionary key as "dt". If I give it a number instead, it works just fine. But then my dictionary key name is a number, which isn't very descriptive.
Any thoughts on how to get this working?

The issue is that by doing
rows[station] = re.findall(...)
You are creating a dictionary with the station names as keys and the return value of re.findall method as values, which happen to be lists. So by calling them again by
rows[station]["dt"] = re.findall(...)
on the LHS row[station] is a list that is indexed by integers, which is what the TypeError is complaining about. You could do rows[station][0] for example, you would get the first match from the regex. You said you want a nested dictionary. You could do
rows[station] = dict()
rows[station]["dt"] = re.findall(...)
To make it a bit nicer, a data structure that you could use instead is a defaultdict from the collections module.
The defaultdict is a dictionary that accepts a default type as a type for its values. You enter the type constructor as its argument. For example dictlist = defaultdict(list) defines a dictionary that has as values lists! Then immediately doing dictlist[key].append(item1) is legal as the list is automatically created when setting the key.
In your case you could do
from collections import defaultdict
rows = defaultdict(dict)
for station in stations:
rows[station]["bulk"] = re.findall("%s\s(.+)" %station, dtcc)
rows[station]["dt"] = re.findall("%s\s(\S+)" %station, dtcc)
Where you have to assign the first regex result to a new key, "bulk" here but you can call it whatever you like. Hope this helps.

Making several wordclouds out of list of dictionaries

I have a list of dictionaries in union_dicts. To give you an idea it's structured as follows
union_dicts = [{'bla' : 6, 'blub': 9}, {'lub': 20, 'pul':12}]
(The actual lists of dicts is many times longer, but this is to give the idea)
For this particular list of dictionaries I want to make a wordcloud. The function that makes a wordcloud is as follows (nothing wrong with this one):
def make_words(words):
return ' '.join([('<font size="%d">%s</font>'%(min(1+words[x]*5/max(words.values()), 5), x)) for x in words])
Now I have written the following code that should give every dictionary back. Return gives only the first dictionary back in the following function below:
def bupol():
for element in union_dicts:
return HTML(make_words(element))
bupol()
I have already tried to simply print it out, but then I simply get ''Ipython display object'' and not the actual display. I do want the display. Yield also doesn't work on this function and for some reason using list = [] along with list.apped() return list instead of returning in the current way also doesn't work. I'm quite clueless as how to properly iterate over this so I get a display of every single dictionary inside union_dicts which is a list of dictionaries.

How about something like this?
def bupol():
result = []
for element in union_dicts:
result.append(HTML(make_words(element)))
return result

use slice in for loop to build a list

I would like to build up a list using a for loop and am trying to use a slice notation. My desired output would be a list with the structure:
known_result[i] = (record.query_id, (align.title, align.title,align.title....))
However I am having trouble getting the slice operator to work:
knowns = "output.xml"
i=0
for record in NCBIXML.parse(open(knowns)):
known_results[i] = record.query_id
known_results[i][1] = (align.title for align in record.alignment)
i+=1
which results in:
list assignment index out of range.
I am iterating through a series of sequences using BioPython's NCBIXML module but the problem is adding to the list. Does anyone have an idea on how to build up the desired list either by changing the use of the slice or through another method?
thanks zach cp
(crossposted at [Biostar])1

You cannot assign a value to a list at an index that doesn't exist. The way to add an element (at the end of the list, which is the common use case) is to use the .append method of the list.
In your case, the lines
known_results[i] = record.query_id
known_results[i][1] = (align.title for align in record.alignment)
Should probably be changed to
element=(record.query_id, tuple(align.title for align in record.alignment))
known_results.append(element)
Warning: The code above is untested, so might contain bugs. But the idea behind it should work.

Use:
for record in NCBIXML.parse(open(knowns)):
known_results[i] = (record.query_id, None)
known_results[i][1] = (align.title for align in record.alignment)
i+=1

If i get you right you want to assign every record.query_id one or more matching align.title. So i guess your query_ids are unique and those unique ids are related to some titles. If so, i would suggest a dictionary instead of a list.
A dictionary consists of a key (e.g. record.quer_id) and value(s) (e.g. a list of align.title)
catalog = {}
for record in NCBIXML.parse(open(knowns)):
catalog[record.query_id] = [align.title for align in record.alignment]
To access this catalog you could either iterate through:
for query_id in catalog:
print catalog[query_id] # returns the title-list for the actual key
or you could access them directly if you know what your looking for.
query_id = XYZ_Whatever
print catalog[query_id]