tbrittoborges

def reverse_complement(sequence):    
     tab = str.maketrans("ACGT", "TGCA")
     return sequence.translate(tab)[::-1]

def apply_rc(row):
     if row['strand'] == '-':
         row['seq'] = reverse_complement(row['seq'])
    
     return row
        

tbrittoborges

# run this in you bash command line
# list all r3 packages installed with conda:
conda list | grep r3 | awk '{print $1}')

# remove all pakages r3
for i in $(conda list | grep r3 | awk '{print $1}'); do conda remove -y $i; done

# finally, remove R
conda remove r-essentials

tbrittoborges

\documentclass{article}
\usepackage{tikz}
\usepackage{array}
\usepackage{siunitx}

\usetikzlibrary{shapes.geometric, shapes.misc, arrows, fit, calc}

\newcommand\addvmargin[1]{
  \node[fit=(current bounding box),inner ysep=#1,inner xsep=0]{};
}

tbrittoborges

df['new'] = df['new'].str.split('/') # example how to listfy a column of strings
temp = pd.DataFrame(df['new'].dropna().tolist())

temp = temp.stack()
temp.index = temp.index.droplevel(1) # index need to be coherent with the original dataframe
temp.name = 'new_colum' # name of the new column in the original dataframe

df = df.join(temp)

tbrittoborges

def better_table(table, caption, name):
    
    start = r"""
\begin{{table}}[!htb]
\sisetup{{round-mode=places, round-precision=2}}
\caption{{{}}}\label{{table:{}}}
\centering
""".format(caption, name)
    
    end = r"\end{table}"

tbrittoborges

#
import operator
sequence = "ACGACTGATCGATCGATCGATGCATCGATCGACGAT"
random_positions = random.sample(xrange(len(sequence)), 30)
get_positions = operator.itemgetter(*random_positions)
get_positions(sequence)
('T', 'C', 'G', 'C', 'A', 'C', 'C', 'T', 'A', 'T', 'G', 'T', 'A', 'T', 'C', 'C', 'T', 'T', 'A', 'G', 'T', 'A', 'A', 'A', 'C', 'G', 'G', 'C', 'G', 'A')

from itertools import groupby

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

tbrittoborges

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

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

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)