##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
# find out, whether it is 1. or 2. consensus
# select the row, col, locus and experiment_id and check, whether there is another one for that
#hash_ascii_phred = {"!": "0", '"' : "1", "#": "2", "$": "3", "%": "4", "&": "5","'": "6","(": "7",")":"8", "*": "9","+": "10",",":"11","-": "12", "." : "13","/":"14", "0":"15","1": "16","2": "17","3": "18", "4": "19", "5": "20", "6": "21","7":"22", "8": "23", "9":"24",":":"25",";": "26","<": "27","=": "28", ">" : "29", "?" : "30", "@" : "31", "A" : "32", "B" : "33", "C" :"34", "D" : "35", "E" : "36", "F" : "37", "G" : "38", "H" : "39", "I": "40"}
hash_phred_ascii = {
'0': '!',
'1': '"',
'2': '#',
'3': '$',
'4': '%',
'5': '&',
'6': "'",
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,'
' igblast_rank, name, eval, score, VDJ_id) VALUES (%s,%s,%s,%s,%s,%s,%s,%s);'
).format(conf['database'], args.targettable)