import sys
import os
from database_info_parameters import parser
parser.add_option("-a","--prefix", dest="prefix",
help = "Cluster files prefix")
(options, args) = parser.parse_args()
import time
for current_file in os.popen("ls %s*" %options.prefix):
current_file = current_file.strip()
shf = open(current_file+".sh",'w')
#shf.write("/bin/bash\n")
#shf.write("source /sbi/users/jgarcia/.bashrc\n")
shf.write("setenv PYTHONPATH \"/sbi/users/jgarcia/biana/src\"\n")
shf.write("cd /sbi/users/jgarcia/biana/scripts/administration\n")
shf.write("python blast_cd_hit_clusters.py -n %s -c %s -i %s -f %s.blast.gz -s 3729884308 -l 632558808656\n" %(options.dbname, options.dbhost, current_file, current_file))
shf.close()
#os.system("qsub -q sbi %s.sh" %current_file)
import biana.BianaDB
import sys
from database_info_parameters import parser
parser.add_option("-i",
"--input-file",
dest="input_file",
help="Sequence file",
default="")
(options, args) = parser.parse_args()
dbaccess = biana.BianaDB.BianaDBaccess(dbname=options.dbname,
dbuser=options.dbuser,
dbhost=options.dbhost,
dbpassword=options.dbpass,
lock_tables=True)
dbaccess._insert_blast_results_file(file_path=options.input_file)
dbaccess.close()
import os
import gzip
import sys
import re
from database_info_parameters import parser
import biana.BianaObjects
import biana.BianaDB
parser.add_option("-t","--type", dest="type",
help = "proteinsequence or nucleotidesequence", default="")
parser.add_option("--conserve-temporary-files", dest="temporaryfiles",
help = "If \"yes\", it does not delete temporary files")
(options, args) = parser.parse_args()
if options.type is None or options.dbname is None:
parser.print_help()
sys.exit(1)
temporal_all = "all_sequences.temp"
temporal_removed = "unique_sequences.temp.gz"
def remove_duplicated_sequences_from_file(input_file,output_file):
"""
Removes all duplicates in a sequence file with the format sequenceID Sequence
For duplicated sequences, it takes the smallest sequenceID
"""
from database_info_parameters import parser
import biana
parser.add_option("-d","--description", dest="description",
help = "BIANA database description", default="")
(options, args) = parser.parse_args()
if options.dbname is None:
parser.print_help()
else:
biana.administration.create_biana_database( dbname = options.dbname,
dbuser = options.dbuser,
dbhost = options.dbhost,
dbpassword = options.dbpass,
description = options.description )
from database_info_parameters import parser
import biana.BianaDB
import biana.BianaObjects.sequenceUtilities
import sys
import gzip
import os
TEMP_FASTA_FILE = "temp_sequences_file.fasta"
TEMP_CLSTR_PREFIX = "./temp_sequence_clusters"
TEMP_CLSTR_FILE = TEMP_CLSTR_PREFIX + ".clstr"
TEMP_BLAST_RESULTS_FILE = "./blast_results.txt.gz"
parser.add_option("-t",
"--type",
dest="type",
help="proteinsequence or nucleotidesequence",
default="")
parser.add_option("--cd-hit-identity-cluster",
dest="cdhit_threshold",
help="See CD-HIT documentation",
default="")
parser.add_option("--conserve-temporary-files",
dest="temporaryfiles",
help="If \"yes\", it does not delete temporary files")
(options, args) = parser.parse_args()
if options.type is None or options.dbname is None:
import biana.BianaDB
import sys
from database_info_parameters import parser
parser.add_option("-i","--input-file", dest="input_file",
help = "Sequence file", default="")
(options, args) = parser.parse_args()
dbaccess = biana.BianaDB.BianaDBaccess(dbname = options.dbname,
dbuser = options.dbuser,
dbhost = options.dbhost,
dbpassword = options.dbpass,
lock_tables = True)
dbaccess._insert_blast_results_file( file_path=options.input_file )
dbaccess.close()
from database_info_parameters import parser
import biana.BianaObjects
import biana.BianaDB
parser.add_option("-i",
"--input-file",
dest="input_file",
help="CD HIT clusters file",
default="")
(options, args) = parser.parse_args()
dbaccess = biana.BianaDB.BianaDBaccess(dbhost=options.dbhost,
dbuser=options.dbuser,
dbpassword=options.dbpass,
dbname=options.dbname,
lock_tables=True)
biana.BianaObjects.sequenceUtilities.insert_cd_hit_clusters_to_biana_database(
cd_hit_clusters_file=options.input_file, dbaccess=dbaccess)
dbaccess.close()
from database_info_parameters import parser
import biana.BianaObjects
import biana.BianaDB
parser.add_option("-i", "--input-file", dest="input_file", help="CD HIT clusters file", default="")
(options, args) = parser.parse_args()
dbaccess = biana.BianaDB.BianaDBaccess(
dbhost=options.dbhost, dbuser=options.dbuser, dbpassword=options.dbpass, dbname=options.dbname, lock_tables=True
)
biana.BianaObjects.sequenceUtilities.insert_cd_hit_clusters_to_biana_database(
cd_hit_clusters_file=options.input_file, dbaccess=dbaccess
)
dbaccess.close()
import os
import gzip
import sys
import re
from database_info_parameters import parser
import biana.BianaObjects
import biana.BianaDB
parser.add_option("-t", "--type", dest="type", help="proteinsequence or nucleotidesequence", default="")
parser.add_option(
"--conserve-temporary-files", dest="temporaryfiles", help='If "yes", it does not delete temporary files'
)
(options, args) = parser.parse_args()
if options.type is None or options.dbname is None:
parser.print_help()
sys.exit(1)
temporal_all = "all_sequences.temp"
temporal_removed = "unique_sequences.temp.gz"
def remove_duplicated_sequences_from_file(input_file, output_file):
"""
Removes all duplicates in a sequence file with the format sequenceID Sequence
For duplicated sequences, it takes the smallest sequenceID
"""
# It creates a formatted blast database with all protein sequences in the database
# CD Hit results are also inserted in database
from database_info_parameters import parser
import biana.BianaDB
import biana.BianaObjects.sequenceUtilities
import sys
import gzip
import os
TEMP_FASTA_FILE = "temp_sequences_file.fasta"
TEMP_CLSTR_PREFIX = "./temp_sequence_clusters"
TEMP_CLSTR_FILE = TEMP_CLSTR_PREFIX+".clstr"
TEMP_BLAST_RESULTS_FILE = "./blast_results.txt.gz"
parser.add_option("-t","--type", dest="type",
help = "proteinsequence or nucleotidesequence", default="")
parser.add_option("--cd-hit-identity-cluster", dest="cdhit_threshold",
help = "See CD-HIT documentation", default="")
parser.add_option("--conserve-temporary-files", dest="temporaryfiles",
help = "If \"yes\", it does not delete temporary files")
(options, args) = parser.parse_args()
if options.type is None or options.dbname is None:
parser.print_help()
sys.exit(1)
# First, gets FASTA file