How to convert nested list into list containing strings in python?

Question

I was trying to read a csv file:

SigGenelist = []
Sig = csv.reader(open('Genelist.csv'))
for row in Sig:
    SigGenelist.append(row)
print (SigGenelist)

the print out was like:

[['x'], ['0610010K14Rik'], ['0610011F06Rik'], ['1110032F04Rik'], ['1110034G24Rik'], ...

so I got a nested list, but I would like to have a list with each element as string, something like:

['x', '0610010K14Rik', '0610011F06Rik', '1110032F04Rik', '1110034G24Rik', ...

I tried to convert element into string like:

SigGenelist = []
Sig = csv.reader(open('Genelist.csv'))
for row in Sig:
    row = str(row) # try to change row into string instead of list
    SigGenelist.append(row)
print (SigGenelist)

but did not get what I would like to...

["['x']", "['0610010K14Rik']", "['0610011F06Rik']", "['1110032F04Rik']","['1110034G24Rik']"...

Any suggestion?

Be sure to mark an answer as "accepted"!

Christopher Apple
– Christopher Apple

2017-04-19 04:08:36 +00:00
Commented Apr 19, 2017 at 4:08 — Christopher Apple
– Christopher Apple, Commented Apr 19, 2017 at 4:08

umutto · Accepted Answer · 2017-04-19 03:27:04Z

3

Instead of append try using + operator, change your line

...
SigGenelist.append(row)
...

to use +=:

...
SigGenelist += row
...

Append is used to add a single element to your list, while += and extend is used to copy the list on the right hand side to the left hand side. And since extend is more expensive due to an additional function call (not that it matters, difference is very small), += is a good way in your situation.

edited Apr 19, 2017 at 3:27

answered Apr 19, 2017 at 3:19

umutto

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Comments

Christopher Apple · Accepted Answer · 2017-04-19 03:16:12Z

1

Try this:

my_list = [[1], [2], [3], [4], [5], [6]]
print [item for sublist in my_list for item in sublist]

This is a list comprehension that will flatten a list of lists into a single list.

Or, maybe the simpler option is not appending, but adding the rows to the list.

SigGenelist = []
Sig = csv.reader(open('Genelist.csv'))
for row in Sig:
    SigGenelist += row
print (SigGenelist)

.append will add the entire list to the end of the list, resulting in the nested lists. += will just concatenate the lists, making it a list of depth 1!

answered Apr 19, 2017 at 3:16

Christopher Apple

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2 Comments

Jun Over a year ago

Sorry that I did not realize that I could "accept answer" it seemed I could only accept one. But I gave a up vote for your answer. Thanks for the answer and explanation.

Christopher Apple Over a year ago

No problem! You should always accept the one that answers it the best, and umotto did it very succinctly!

gold_cy · Accepted Answer · 2017-04-19 03:22:49Z

1

Change this:

SigGenelist.append(row)

To this:

SigGenelist.extend(row)

answered Apr 19, 2017 at 3:22

gold_cy

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Comments

Jared Goguen · Accepted Answer · 2017-04-19 03:28:42Z

1

This might be idiomatic:

from itertools import chain
csv_reader = csv.reader(open('Genelist.csv'))
SigGeneList = list(chain.from_iterable(csv_reader))

answered Apr 19, 2017 at 3:28

Jared Goguen

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1 Comment

Jun Over a year ago

Not sure I messed up something or not, but it did not work out for me...

eguaio · Accepted Answer · 2017-04-19 14:22:31Z

0

Use the sum builtin function, since csv.reader returns a generator, the following code will do the job:

Sig = csv.reader(open('Genelist.csv'))
SigGenelist = sum(Sig, [])

edited Apr 19, 2017 at 14:22

answered Apr 19, 2017 at 3:27

eguaio

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7 Comments

Jun Over a year ago

Basically, it worked like other methods, but somehow the first element would not be in the new list...['x', '0610010K14Rik', '0610011F06Rik', '1110032F04Rik', '1110034G24Rik', ...] I only got ['0610010K14Rik', '0610011F06Rik', '1110032F04Rik', '1110034G24Rik', ...], not sure I did not mess up with something... though

eguaio Over a year ago

the sum(generator, []) is a code snipet I use often. I'm sure there is some code in the middle making some noise.

eguaio Over a year ago

All solutions seem equal, but you should use the one that is faster and uses less memory. Furthermore, you should also look for readability. Compare the for loops, and initializating a list outside the loop with the "one liners", which one is easier to read? which one has less chances to let you introduce a bug? In this case, I prefer to have the work done in just one line. And from all the other oneliners, I think the option I suggest is the most clear and easy to read, and does not require any other library import. I wouldn't be posting another answer If I thought the others are equal.

eguaio Over a year ago

You should only execute the two lines in my answer. If you add some extra code in the middle that extract an element of Sig generator, you lose the first item, namely, the 'x'. In fact, I think that directly doing: SigGenelist = sum(Sig, []) should work too.

Jun Over a year ago

Yes, they worked.SigGenelist = sum((row for row in Sig), []), SigGenelist = sum(Sig, []), apologize that I messed it up. Thank you for answer and explanation. (no idea why I could not cast a up vote for your answer...)

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