# Created: August 26th 2019 """ import argparse from argparse import RawTextHelpFormatter from Bio import AlignIO import os import bcelldb_init as binit import collections import math from math import * ##usage -> todb_consensus_sequences.pl -aln <musclealign> [-h] ##get configuartion for scireptor config_scireptor = binit.get_config() if __name__ == "__main__": parser = argparse.ArgumentParser(description=__doc__, formatter_class=RawTextHelpFormatter) parser.add_argument('-aln', '--alignment', required=True, help="define input file") args = parser.parse_args() align = args.alignment ### 1. Prepare database for insertion of sequence conn = binit.connect() ##create a cursor object cursor = conn.cursor() ###prepare insert command
""" bcelldb_plotting.py Module that contains standard funtions for plotting data from the igdb. """ import bcelldb_init as bcelldb import matplotlib as mpl mpl.use('Agg') import numpy as np import numpy.random as random import sys import colorsys from datetime import datetime as dt conf = bcelldb.get_config() # Get log information for a plot # date, user, database, software version # config file variables def plot_log (object_name, args, db, short='T'): """ Arguments: - args: sys.args - verbose Return string for logging how plot was generated. Short: For titles in PDF. Long: also logging script that was executed to generate the plot """
required=True, help="where VDJ info will be written. Can be reads_VDJ_segments or VDJ_\ segments according to where the sequences in the IgBLAST analysis came from." ) parser.add_argument( "-ut", "--updatetable", required=True, help="Table that will be updated according to what was found\ by IgBLAST (orientation, locus). Can be reads or sequences." ) args = parser.parse_args() ### 0. Logging information (TBD) # get configuration using bcelldb_init conf = binit.get_config() db = binit.connect() cursor = db.cursor() ### 1. Open IgBLAST output file try: in_igblast = open(args.igblastoutput, "r") except FileNotFoundError: print('\n\tBLAST output {} not found\n').format(args.igblastoutput) # ### 2. Set up database handles for inserting to VDJ table and updating position ins_VDJ_sth = ( 'INSERT IGNORE INTO {}.{} (seq_id, type, locus,'
import matplotlib.colorbar as cbar import MySQLdb as mysql from datetime import datetime as dt import bcelldb_init as bcelldb # get command line arguments experiment_id = sys.argv[1] runname = sys.argv[2] try: greyscale = sys.argv[3] except IndexError: greyscale = '' # get configuration using bcelldb_init conf = bcelldb.get_config() # connect to database via ~/.my.conf settings db = mysql.connect(db=conf['database'], read_default_file="~/.my.cnf", read_default_group=conf['db_group_auth']) cursor = db.cursor() # defining common variables project = conf['database'] ncols, nrows = map(int, conf['matrix'].split('_')) nrows_per_plate = int(conf['nrows_per_plate']) ncols_per_plate = int(conf['ncols_per_plate']) loci = ['B', 'A']