CODEWITHSUNDEEP
pythonpython-3.xstringlist
JHa
JHa

Reputation: 13

Converting a string to a list: troubleshooting

I'm trying out the GC Content problem over at Rosalind. I figured I could read the contents of the provided FASTA format file into a list. Use the list to make a dictionary with the Rosalind ID as the key and the ATGC string as value. In order to do that I read the file into a string variable, remove the newlines, and split at the '>'. My problem is the list that is returned has an empty entry at index 0.

    with open('rosalind_gc.txt','r') as fileA:
        contents = fileA.read()
        contents = contents.replace('\n','')

        listA = contents.split('>')

        print(listA)

Upvotes: 0

Views: 77

Answers (3)

Adi219
Adi219

Reputation: 4814

Does the constants string start with >?

If it does, constants.split(">", "") will return ["", ...] as there's a symbol at the start, which could explain why listA[0] returns ''.

Based on your comment, it seems that this is the case, and if you wish to remove all the '' items, then simply add listA = [element for elements in contents if element].

Upvotes: 1

kederrac
kederrac

Reputation: 17322

if you want to eliminate the empty strings you could use:

listA = [e for e in contents.split('>') if e]

Upvotes: 0

user11375907
user11375907

Reputation:

if your text file begins with ">" it's normal. For example :

'>test'.split(">")

will return :

['', 'test']

Upvotes: 0

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