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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 |
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#!/usr/bin/env python3 | |
# -*- coding: utf-8 -*- | |
# Copyright 2015 Lenna X. Peterson | |
# All rights reserved | |
import os | |
import socket | |
import subprocess | |
import sys |
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#!/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 |
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# 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 | |
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-- 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 |
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#!/usr/bin/env python | |
from __future__ import division | |
import argparse | |
import glob | |
import inspect | |
import logging | |
import os |
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# 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 | |
# |
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#!/usr/bin/python | |
import sys | |
import time | |
spinner = ["-", "\\", "|", "/"] | |
print "This is the header row" | |
try: | |
for i in range(10): |
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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: |
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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: |
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