tbrittoborges

def is_prime(N):
    for x in xrange(2, N):
        if N % x == 0:
            return False
    return True
    
def sum_prime(N):
    return sum(x for x in xrange(N) if is_prime(x))

tbrittoborges

import matplotlib
matplotlib.use("Agg")
import pyplot as plt
plt.plot([1, 2, 3])
plt.savefig("something.png")

tbrittoborges

_ref = "10.1371/journal.pone.0038772"
norm_vdw_volume = {'A': 1.00, 'M': 4.43, 'C': 2.43, 'N': 2.95, 'D': 2.78, 'P': 2.72, 'E': 3.78, 'Q': 3.95, 'F': 5.89, 'R': 6.13,
 'G': 0.00, 'S': 1.60, 'H': 4.66, 'T': 2.60, 'I': 4.00, 'V': 3.00, 'K': 4.77, 'W': 8.08, 'L': 4.00, 'Y': 6.47}

tbrittoborges

def remove_description_from_fasta(input, output, regex):
    with open(input,) as input_stream, open(output , 'w') as output_stream:
        for line in input_stream:                                                         
    if line.startswith('>'):
        if regex in line:
            output_stream.write(line)
            write = True 
        else:
            write = False
    elif write:

tbrittoborges

#!/usr/bin/env python
import requests
import sys
import utils

__author__ = 'tbrittoborges'
"""
Created on 14:45 04/11/2014 2014 
Given a list of UniProt accession id, return all missense variants.
All variants means:

tbrittoborges

def get_url_or_retry(url, retry_in=(), wait=1, json=False, header={}, **params):
    """
    Fetch an url using Requests or retry fetching it if the server is
     complaining with retry_in error.
    :param url: url to be fetched as a string
    :param wait: sleeping between tries in seconds
    :param params: request.get kwargs.
    :return: url content or url content in json data structure.
    """
    if json:

tbrittoborges

import pandas as pd
colspecs = [(0, 6), (6, 11), (12, 16), (16, 17), (17, 20), (21, 22), (22, 26),
            (26, 27), (30, 38), (38, 46), (46, 54), (54, 60), (60, 66), (76, 78),
            (78, 80)]

names = ['ATOM', 'serial', 'name', 'altloc', 'resname', 'chainid', 'resseq',
         'icode', 'x', 'y', 'z', 'occupancy', 'tempfactor', 'element', 'charge']

pdb = pd.read_fwf(pdb_path, names=names, colspecs=colspecs)

tbrittoborges

import requests

data = {"title": "Found a bug", # str
        "body": "I'm having a problem with this.", # str
        "assignee": None, # username str or None
        "milestone": 1, # int
        "labels": ['label1']} # list of str

def submit_github_issue(data, token, username, repo):
    headers = {'Content-Type':'application/json',

tbrittoborges

print '>\n' + '\n> \n'.join(list(df.query(...).sequence_column))

tbrittoborges

from urlparse import parse_qs

import pandas as pd

def _fetch_uniprot_gff(identifier):
    """
    Retrieve UniProt data from the GFF file

    :param identifier: UniProt accession identifier
    :type identifier: str