added calculate Neff script

[qiyunzhu]

Hello @tkosciol @sjanssen2 I have created this code in response to issue #26 .

I am not 100% certain the calculation is correct. Please review the code with your scientific mind. Specifically, what I noticed that could be problems are:

• Missing residues (-) are treated as the 21st character, which may result in the overestimation of number of clusters.
• Clustering is performed using scipy's hierarchical clustering function. Not sure if it's the desired way.

The actual code is very simple and can be compressed in five lines. The reason I created so many functions is because I guess other parts of the program may want to call some of these functions.

[coveralls]

Coverage increased (+0.3%) to 94.573% when pulling 89f44f4847c282997d9fac5e5f7a34f69a3a044a on qiyunzhu:process into 2410216bc2f4adcf51e1efc5b17fe0d9a2805281 on biocore:master.

[coveralls]

Coverage increased (+0.3%) to 94.595% when pulling 301b22907c576c2d6c8ec9d33a1d27c53e7020e0 on qiyunzhu:process into 2410216bc2f4adcf51e1efc5b17fe0d9a2805281 on biocore:master.

[tkosciol]

Looks good to me! @sjanssen2 any comments? In the interest of time I want to leave it with Hamming distance for now and I'll keep an issue open, so that we know to upgrade this script later.

[sjanssen2]

That's fine to me :thumbsup:

[qiyunzhu]

Thank you guys! @tkosciol @sjanssen2