lennax

sbjct_aln = "C-GGLK-GAPFLAC"
query_aln = "CHG--KTGASFLQC"

gap = "-"

sbjct_idx = -1
query_idx = -1
for sbjct_resn, query_resn in zip(sbjct_aln, query_aln):

    # Check for gaps

lennax

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2015 Lenna X. Peterson
# All rights reserved

import os
import socket
import subprocess
import sys

lennax

#!/usr/bin/env python
# Copyright (c) 2014 Lenna X. Peterson, all rights reserved
# [email protected]

import argparse
import csv
import glob
import logging
import math
import os

lennax

# Copyright 2012-2014 Lenna X. Peterson
# [email protected]

# 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
 

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

#!/usr/bin/env python

from __future__ import division

import argparse
import glob
import inspect
import logging
import os

lennax

# CoordinateMapper -- map between genomic, cds, and protein coordinates
# AUTHOR: Reece Hart <[email protected]>
# Modifications: Lenna X. Peterson <[email protected]>
# LICENSE: BioPython

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

lennax

#!/usr/bin/python

import sys
import time

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

try:
    for i in range(10):

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

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: