daler

#!/usr/bin/env python

import os
import logging
from collections import Counter
import gffutils
from gffutils.create import logger
logger.setLevel(logging.INFO)

usage = """

daler

"""
Illustrates how to use pybedtools to count motifs along sliding windows 
of UTRs from a GFF file.

This uses example data shipped with pybedtools.
"""

import pybedtools

daler

# for pybedtools issue #99

import pybedtools

# make a demo list of chrom:start-stop strings from example data shipped with
# pybedtools
n_intervals = 20000
loc_list = []
for i, feature in enumerate(pybedtools.example_bedtool('x.bed')):
    if i >= n_intervals:

daler

"""
Demo pathfinding, with obstacles
"""

from matplotlib import pyplot as plt
import networkx as nx


GRID_SIZE = [100, 100]
G = nx.grid_graph(dim=GRID_SIZE)

daler

"""
Demonstration of getting the coding sequence for each alterative isoform of
each gene in a GFF file.

Uses pybedtools.BedTool.seq to extract sequences from a FASTA file.
"""
import gffutils
import pybedtools
from gffutils.helpers import asinterval

daler

import gffutils

# Import the GTF file into a sqlite3 database.
# This only ever has to be done once.
db = gffutils.create_db("example.gtf", dbfn='example.gtf.db')

# In other scripts, you can connect to the database like this:
db = gffutils.FeatureDB('example.gtf.db')

# Note that gene and transcript have been inferred

daler

#!/bin/bash


set -e

# Defaults ------------------------------------------------------
MINICONDA_DIR="${HOME}/miniconda"
INSTALL_DIR="$(pwd)/tools"
TO_INSTALL="bedtools,samtools,tabix,bigWigSummary"
INSTALL_MINICONDA=1

daler

#!/usr/bin/env python
import sys
import os
import errno
import argparse
import logging
from urllib2 import urlopen
from urllib2 import Request
from socket import error as SocketError

daler

#!/usr/bin/env python

import os
import sys
import platform
import argparse
import ftplib
import time
import netrc
from fnmatch import fnmatch

daler

import pybedtools
import pandas


def split_coverage(x):
    """
    Split a coverage file created using bedtools coverage -hist -- which will
    have trailing "all" hist lines -- into 1) a BedTool object with valid BED
    lines and 2) a pandas DataFrame of all coverage, parsed from the trailing
    "all" lines.