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I'm using somebody else's code that stores a sequence in an array in python:

blah=array(<Sequence: 2TPS (2TPS refined (label=2TPS) refined (label=2TPS, rowocc>=0.8, colocc>=0.8)[0]; length 196; 196 residues and 0 gaps)>, dtype=object)

I can print the sequence using the following:

print blah
    SVYFIMGSNNTKADPVTVVQKALKGGATLYQFREKGLTGEARIKFAEKAQAACREAGVPFIVNDDVELALNLKADGIHIGQEDANAKEVRAAIGDMILGVSAHTMSEVKQAEEDGADYVGLGPIYPTETKKDTRVQGVSLIEAVRRQISIPIVGIGGITIDNAAPVIQAGADGVSMISAISQAEDPESAARKFREE

However, I want to be able to call this sequence and save it to a text file without using the "print" function. I've tried blah[0] etc, but nothing works.

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  • This just says "invalid syntax". Are you using numpy, scipy or something else ? Commented May 29, 2014 at 8:33

3 Answers 3

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It seems your array is a numpy array (dtype...)

Have you already tried just parsing it to a string?

result = str(blah)

or

result = blah.tostring()

another option is to parse it to a list

result = list(blah)

Now you should be able to use the variable result and write it to a file or do whatever you want.

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Don't you mean array.tofile() or looking at Bob's answer numpy.ndarray.tofile()?

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I assume that you want to save a python list to a text file and you want to read it later.

You can write list to text file as:

with open('filename', 'wb') as a:
        pickle.dump(blah, a)

You can read the file and store each lines in a list:

with open('filename', 'rb') as a:
    blah = pickle.load(a)

you can access your data like: blah[0]

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