# 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']