etal

"""Find adjacent SNPs/MNPs in a VCF, and look in the BAM file to see if these
should be joined into a larger variant.

This script can only handle up to 2 internal compound ALT alleles for every
stretch of adjacent SNPs. This script is not designed to test all possible
combinations of internal joined SNPs for SNP stretches longer than 3.
This script also cannot handle multiallelic variants or indels.

"ALERT" will be added to VCF INFO columns for cases that are too complex.
"""

etal

#!/usr/bin/env python
from __future__ import print_function

import sys

import numpy as np
import pandas as pd

import cnvlib

etal

from __future__ import print_function

import sys

import numpy as np
import cnvlib
from cnvlib.metrics import biweight_location

cnr, cns = sys.argv[1:]

etal

#!/usr/bin/env python

"""Extract well-supported clades from a phylogenetic tree as sequence clusters."""

import os.path
import subprocess
import sys
import tempfile
from cStringIO import StringIO

etal

#!/usr/bin/env python
"""Benchmark several different operations."""

from time import time
from contextlib import contextmanager
try:
    from cStringIO import StringIO
    BytesIO = StringIO
except ImportError:
    # Python 3

etal

#!/usr/bin/env python

"""Demo for tasks.py."""

import os
import sys
from glob import glob
from Bio import SeqIO
from tasks import Task, ext, sh

etal

#!/usr/bin/env python
# -*- coding:utf-8 -*-

u"""Gō plot of residue-to-residue distances in a protein structure.

Usage:
    go1981.py <PDB_file> [<chain_ID>] [<junction_position> ...]

Example:
    ./go1981.py 3ONZ.pdb B 30 68 104

etal

Four score and seven years ago our fathers brought forth on this continent, a
new nation, conceived in Liberty, and dedicated to the proposition that all men
are created equal.

Now we are engaged in a great civil war, testing whether that nation, or any
nation so conceived and so dedicated, can long endure. We are met on a great
battle-field of that war. We have come to dedicate a portion of that field, as a
final resting place for those who here gave their lives that that nation might
live. It is altogether fitting and proper that we should do this.