assembly_alignment
Preliminary assembly-assembly alignment analysis
Currently supports:
- creating a stats table with 1 row per assembly sequence with numbers per alignment discrepancy type
- if the assembly has chromosomes, make graphs.
- Creates per assembly bed files for each discrepancy type
To do:
- update stats to add the top ten by size for each even type
To run: Create a config file specifying path to files and files to create
Dependencies:
- from future import division
- import csv
- from collections import defaultdict
- import collections
- import pybedtools
- from pybedtools import BedTool
- import subprocess
- import numpy as np
- import matplotlib.pylab as plt
- import seaborn as sns
- import os
- import logging
- import logging.handlers
- from logging import config
- import datetime
- import yaml
- import errno
- import argparse