lennax

import re

units = {
        'day': 'd',
        'hour': 'h',
        'minute': 'm',
        'second': 's',
        }

# Matches only valid data (I hope)

lennax

float_t = r"[+-]?(\d*\.\d+|\d+\.?)(e{1,2}[+-]?\d+)?"

lennax

"""
This is located inside a fake numpy, and could allow "import numpy" 
to work invisibly on both Python and PyPy.
Not quite sure how to get files to find it. 
In any case, NumPyPy is only a partial implementation of NumPy, 
so it's probably not ready for unintended/untested/automatic use. 
"""

import sys
# Delete current directory from module search path

lennax

class Variant(object):
    """This is the top level class for genomic variants"""
    def __init__(self, filename, filetype=None, gvfreader=None, vcfreader=None):
        """
        Uses the default parser Wrappers unless otherwise specified. 
        Currently supported arguments to filetype are "vcf" and "gvf".
        If filetype is not specified, guessed from file extension.
        """
        self.filename = filename
        if filetype is not None:

lennax

class _AltRecord(object):
    def __init__(self, alt_type, **kwargs):
        print "_AltRecord"
        super(_AltRecord, self).__init__(**kwargs)
        self.alt_type = alt_type

class _Substitution(_AltRecord):
    def __init__(self, sequence, **kwargs):
        print "_Substitution"
        if len(sequence) == 1:

lennax

#!/usr/bin/python

import sys
import time

spinner = ["-", "\\", "|", "/"]
print "This is the header row"

try:
    for i in range(10):

lennax

# CoordinateMapper -- map between genomic, cds, and protein coordinates
# AUTHOR: Reece Hart <reecehart@gmail.com>
# Modifications: Lenna X. Peterson <arklenna@gmail.com>
# LICENSE: BioPython

# Examples:
# AB026906.1:g.7872G>T
# AB026906.1:c.274G>T
# BA...:p.Asp92Tyr
#

lennax

#!/usr/bin/env python

from __future__ import division

import argparse
import glob
import inspect
import logging
import os

lennax

-- More than one chain is possible for each code
CREATE TABLE IF NOT EXISTS smallest
                  (
                      id INTEGER PRIMARY KEY NOT NULL,
                      code TEXT NOT NULL,
                      chain TEXT NOT NULL,
                      timestamp TEXT NOT NULL
                  );

CREATE TABLE IF NOT EXISTS ligands

lennax

# Copyright 2012-2014 Lenna X. Peterson
# arklenna@gmail.com

# The first step to using the mapper is to get the exons from a GenBank or similar file.
# The mapper will accept exons as a sequence of pairs, a SeqRecord with a CDS feature, or a CDS SeqFeature.
# The file used in this example is located in the Tests directory of the Biopython source code.

from Bio.SeqUtils.Mapper import CoordinateMapper
from Bio import SeqIO