vhoulbreque

Nteract tricks

To add a conda environment to the list of environments:

$ source activate thisenv
(thisenv) $ pip install ipykernel
(thisenv) $ python -m ipykernel install --user --name thisenv

marcelm

from pysam import AlignmentFile
from pyfaidx import Fasta

def has_mismatch_in_interval(reference, bamfile, chrom, start, end):
    """
    Return whether there is a mismatch in the interval (start, end) in any read mapping to the given chromosome.

    reference -- a pyfaidx.Fasta object or something that behaves similarly
    """
    for column in bamfile.pileup(chrom, start, end):

TomAugspurger

# see also https://github.com/wrobstory/pgshift

import gzip
from io import StringIO, BytesIO
from functools import wraps

import boto
from sqlalchemy import MetaData
from pandas import DataFrame
from pandas.io.sql import SQLTable, pandasSQL_builder