Help with BioPython manual example

Question

[tyleraelliott]

I wish to index a multi-fasta file I have but I'm having problems getting the BioPython manual example to work.

From section 5.4.2 (pg 59). I have the required fasta file in my Python folder

The first few lines work just as they do in the manual:

>>> from Bio import SeqIO
>>> orchid_dict = SeqIO.index("ls_orchid.fasta", "fasta")
>>> len(orchid_dict)
94

But the next line does not. Here's what it returns

>>> orchid_dict.keys()
<dict_keyiterator object at 0x0000000002245F98>

Would someone be able to explain what might be going on and why the output isn't the same as in the manual?

[Peter]

Thanks for reporting this, I have just updated the Biopython documentation which will be included with our next release: https://github.com/biopython/biopython/commit/f9b81d6d06a2259779404f1674ac0dde3747d52e

Answer 1

[russhh]

You're using python3 and in the update from 2.7 to 3, dict.keys() now returns an key iterator rather than a list of keynames. The code examples you are copying were written in python2.7, so you may see a few differences.

Nonetheless, list(orchid_dict.keys()) should give you the same result as in the example

[russhh]

Nonetheless, there are caveats to using list(dict.keys()): http://blog.labix.org/2008/06/27/watch-out-for-listdictkeys-in-python-3

[tyleraelliott]

Thanks! That did indeed give me output from the manual. Thanks to everyone else as well for helping.

[Peter]

Yep, the Tutorial will say that in the next release: https://github.com/biopython/biopython/commit/f9b81d6d06a2259779404f1674ac0dde3747d52e

Answer 2

[matted]

keys() is giving you an iterator, not a list. I imagine this is a code change that's newer than the documentation you referenced, performed to make the library more efficient and aligned with Python 3 behavior (see here).

If you want to see the reference names in an interactive session, just type list(orchid_dict.keys()) and it will work as you expect. Otherwise, you can use the keys() iterator in your code in exactly the same way as you would before.

Answer 3

[lelle]

Are you using Python 3? I think the behaviour of the keys function has changed from Python 2 to Python 3.

Try:

list(orchid_dict.keys())

to get the old behaviour.