def gtf2chain(chain_file, input_file, output_file, chain_genes=False):
"""
:param chain_file:
:param input_file:
:param output_file:
:param chain_genes:
:return:
"""
start = time.time()
LOG.info("Execution complete: {0}".format(format_time(start, time.time())))
chain_file = g2g_fu.check_file(chain_file)
input_file = g2g_fu.check_file(input_file)
output_file = g2g_fu.check_file(output_file, 'w')
output_file_dir = os.path.dirname(output_file)
LOG.info("GTF FILE: {0}".format(input_file))
LOG.info("FROM CHAIN FILE: {0}".format(chain_file))
LOG.info("TO CHAIN FILE: {0}".format(output_file))
temp_db = g2g_fu.gen_file_name("_g2gtempfile", output_file_dir, ".db3")
gtf2db(input_file, temp_db)
db2chain(chain_file, temp_db, output_file, chain_genes)
g2g_fu.delete_file(temp_db)
LOG.info("Execution complete: {0}".format(format_time(start, time.time())))
def gtf2chain(chain_file, input_file, output_file, chain_genes=False):
"""
:param chain_file:
:param input_file:
:param output_file:
:param chain_genes:
:return:
"""
start = time.time()
LOG.info("Execution complete: {0}".format(format_time(start, time.time())))
chain_file = g2g_fu.check_file(chain_file)
input_file = g2g_fu.check_file(input_file)
output_file = g2g_fu.check_file(output_file, 'w')
output_file_dir = os.path.dirname(output_file)
LOG.info("GTF FILE: {0}".format(input_file))
LOG.info("FROM CHAIN FILE: {0}".format(chain_file))
LOG.info("TO CHAIN FILE: {0}".format(output_file))
temp_db = g2g_fu.gen_file_name("_g2gtempfile", output_file_dir, ".db3")
gtf2db(input_file, temp_db)
db2chain(chain_file, temp_db, output_file, chain_genes)
g2g_fu.delete_file(temp_db)
LOG.info("Execution complete: {0}".format(format_time(start, time.time())))
def offset2chain(from_file, to_file, output_file):
"""
Convert Seqnature offset files to new chain file.
:param from_file: from Chromosome File (see docs)
:param to_file: to Chromosome File (see docs)
:param output_file: the output chain file
"""
start = time.time()
from_file = g2g_fu.check_file(from_file)
to_file = g2g_fu.check_file(to_file)
output_file_name = g2g_fu.check_file(output_file, 'w')
g2g_fu.delete_file(output_file_name)
LOG.info("FROM FILE: {0}".format(from_file))
LOG.info("TO FILE: {0}".format(to_file))
LOG.info("CHAIN FILE: {0}".format(output_file_name))
LOG.info("Generating chain file...")
try:
chromosomes = offset_parse_chromosomes(from_file, to_file)
for c, chromosome in chromosomes.iteritems():
LOG.debug('Examining chromosome: {0}'.format(chromosome))
if chromosome['file_path']:
offset_chromosome_to_chain(chromosome, output_file)
else:
LOG.debug("No file for {0}, so skipping".format(chromosome))
LOG.info("Chain file created")
except Exception, e:
raise G2GChainFileError("Unable to generate chain file")
def offset2chain(from_file, to_file, output_file):
"""
Convert Seqnature offset files to new chain file.
:param from_file: from Chromosome File (see docs)
:param to_file: to Chromosome File (see docs)
:param output_file: the output chain file
"""
start = time.time()
from_file = g2g_fu.check_file(from_file)
to_file = g2g_fu.check_file(to_file)
output_file_name = g2g_fu.check_file(output_file, 'w')
g2g_fu.delete_file(output_file_name)
LOG.info("FROM FILE: {0}".format(from_file))
LOG.info("TO FILE: {0}".format(to_file))
LOG.info("CHAIN FILE: {0}".format(output_file_name))
LOG.info("Generating chain file...")
try:
chromosomes = offset_parse_chromosomes(from_file, to_file)
for c, chromosome in chromosomes.iteritems():
LOG.debug('Examining chromosome: {0}'.format(chromosome))
if chromosome['file_path']:
offset_chromosome_to_chain(chromosome, output_file)
else:
LOG.debug("No file for {0}, so skipping".format(chromosome))
LOG.info("Chain file created")
except Exception, e:
raise G2GChainFileError("Unable to generate chain file")
for seqid in tb.contigs:
processed_seqids[seqid] = False
left = VCFtoChainInfo()
right = VCFtoChainInfo()
chain_info = {}
if diploid:
left.output_file = g2g_fu.prepend_before_extension(output_file, 'left')
right.output_file = g2g_fu.prepend_before_extension(
output_file, 'right')
chain_info['left'] = left
chain_info['right'] = right
g2g_fu.delete_file(left.output_file)
g2g_fu.delete_file(right.output_file)
else:
left.output_file = output_file
chain_info['left'] = left
g2g_fu.delete_file(left.output_file)
try:
all_chrom = [c for c in fasta_file.references]
all_chrom_length = [n for n in fasta_file.lengths]
all_vcffiles = [input_file] * len(all_chrom)
all_sample_index = [sample_index] * len(all_chrom)
all_chain_info = [chain_info] * len(all_chrom)
all_diploid = [diploid] * len(all_chrom)
all_passed = [passed] * len(all_chrom)
def fasta_transform(fasta_file, chain_file, locations, output_file, bgzip=False, reverse=False):
"""
:param fasta_file:
:param chain_file:
:param locations:
:param output_file:
:param bgzip:
:param reverse:
:return:
"""
start = time.time()
if not isinstance(fasta_file, FastaFile):
fasta_file = g2g_fu.check_file(fasta_file)
if not isinstance(chain_file, ChainIter):
chain_file = g2g_fu.check_file(chain_file)
output_file = g2g_fu.check_file(output_file, 'w')
g2g_fu.delete_file(output_file)
g2g_fu.delete_index_files(output_file)
LOG.info("FASTA FILE: {0}".format(fasta_file))
LOG.info("CHAIN FILE: {0}".format(chain_file))
LOG.info("OUTPUT FILE: {0}".format(output_file))
LOG.info("BGZIP: {0}".format(bgzip))
LOG.info("REVERSE: {0}".format(reverse))
if isinstance(fasta_file, FastaFile):
fasta = fasta_file
else:
fasta = FastaFile(fasta_file)
if not isinstance(chain_file, ChainIter):
chain_file = ChainIter(chain_file, reverse=reverse)
seq_ids = []
if locations:
LOG.debug("Have locations")
new_locations = []
for l in locations:
if isinstance(l, Location):
new_locations.append(l)
else:
new_locations.append(parse_location(l))
seq_ids.append(new_locations[-1].seqid)
locations = new_locations
else:
LOG.debug("Calculating locations")
locations = [parse_location("{0}:1-{1}".format(a, fasta.get_reference_length(a)), 1) for a in fasta.references]
seq_ids = [a for a in fasta.references]
temp_output_file = output_file
if bgzip:
if g2g_fu.get_extension(output_file) != 'gz':
output_file = "{0}.gz".format(output_file)
else:
temp_output_file = temp_output_file[:-3]
fasta_out = open(temp_output_file, "w")
LOG.info("Transforming...")
chr_info = {}
try:
# will need a better way, but for now...
LOG.info("Parsing chain file...")
for line in chain_file:
if len(line) > 7:
LOG.debug("Adding chromosome {0}".format(chain_file.current_chain_header[1]))
chr_info[chain_file.current_chain_header[1]] = {'from_size': line[2], 'from_start': line[4], 'from_end': line[5],
'to_size': line[7], 'to_start': line[9], 'to_end': line[10],
'header_chain':chain_file.current_chain_header, 'lines': []}
else:
chr_info[chain_file.current_chain_header[1]]['lines'].append(line)
LOG.info("Chain file parsed")
insertion_bases = 0
deletion_bases = 0
for location in locations:
LOG.info("Processing chromosome={0}".format(location.seqid))
LOG.debug("Location: {0}".format(location))
chrom_size_from = chr_info[location.seqid]['from_size']
chrom_size_to = chr_info[location.seqid]['to_size']
last_pos = chr_info[location.seqid]['from_start']
new_sequence = StringIO()
chain_file.reset()
for chain_line in chr_info[location.seqid]['lines']:
LOG.debug("\nLINE: {0} : {1}".format(chain_file.line_no, chain_line))
if len(chain_line) == 1:
# last line
fragment = chain_line[0]
partial_seq = fasta.fetch(location.seqid, last_pos, last_pos + fragment)
new_sequence.write(str(partial_seq))
if len(new_sequence.getvalue()) < chrom_size_to:
LOG.warn("Length's do not match, chromosome length in chain: {0}, sequence length: {1}".format(chrom_size_to, len(new_sequence.getvalue())))
fasta_out.write(">{0} {1}:{2}-{3}\n".format(location.seqid, location.seqid, chr_info[location.seqid]['from_start'] + 1, chrom_size_to))
for l in wrap_sequence(new_sequence.getvalue()):
fasta_out.write(l.strip())
fasta_out.write('\n')
break
else:
# fragment_size dt_size dq_size same_bases dt_bases dq_bases
fragment = chain_line[0]
dt = chain_line[1 if not reverse else 2]
dq = chain_line[2 if not reverse else 1]
same = chain_line[3]
dt_bases = chain_line[4 if not reverse else 5]
dq_bases = chain_line[5 if not reverse else 4]
partial_seq = fasta.fetch(location.seqid, last_pos, last_pos + fragment)
new_sequence.write(partial_seq)
if dq > 0:
# insertion
LOG.debug("INSERTION")
new_sequence.write(dq_bases)
LOG.debug("{0}:{1}-{2} (Length: {3})".format(location.seqid, last_pos, last_pos + fragment, len(partial_seq)))
if len(partial_seq) > 100:
LOG.debug("{0}...{1}".format(partial_seq[:10], partial_seq[-10:]))
else:
LOG.debug(partial_seq)
LOG.debug("Adding {0}".format(dq_bases))
LOG.debug("SAME={0}, {1}".format(same, partial_seq[-(len(same)):]))
insertion_bases += dq
if dt > 0:
# deletion
LOG.debug("DELETION")
last_pos += dt
LOG.debug("skipping ahead {0} bases".format(dt))
deletion_bases += dt
last_pos += fragment
LOG.debug("LAST_POS={0}, INSERTIONS={1}, DELETIONS={2}, DIFF={3}".format(last_pos, insertion_bases, deletion_bases, (insertion_bases - deletion_bases)))
# bgzip and index
if bgzip:
LOG.info("Compressing and indexing...")
g2g_fu.bgzip_index(temp_output_file, output_file, 'fa')
except G2GLocationError, le:
LOG.debug("Unable to parse location, {0}".format(le.message))
raise le
def fasta_transform(fasta_file,
chain_file,
locations,
output_file,
bgzip=False,
reverse=False):
"""
:param fasta_file:
:param chain_file:
:param locations:
:param output_file:
:param bgzip:
:param reverse:
:return:
"""
start = time.time()
if not isinstance(fasta_file, FastaFile):
fasta_file = g2g_fu.check_file(fasta_file)
if not isinstance(chain_file, ChainIter):
chain_file = g2g_fu.check_file(chain_file)
output_file = g2g_fu.check_file(output_file, 'w')
g2g_fu.delete_file(output_file)
g2g_fu.delete_index_files(output_file)
LOG.info("FASTA FILE: {0}".format(fasta_file))
LOG.info("CHAIN FILE: {0}".format(chain_file))
LOG.info("OUTPUT FILE: {0}".format(output_file))
LOG.info("BGZIP: {0}".format(bgzip))
LOG.info("REVERSE: {0}".format(reverse))
if isinstance(fasta_file, FastaFile):
fasta = fasta_file
else:
fasta = FastaFile(fasta_file)
if not isinstance(chain_file, ChainIter):
chain_file = ChainIter(chain_file, reverse=reverse)
seq_ids = []
if locations:
LOG.debug("Have locations")
new_locations = []
for l in locations:
if isinstance(l, Location):
new_locations.append(l)
else:
new_locations.append(parse_location(l))
seq_ids.append(new_locations[-1].seqid)
locations = new_locations
else:
LOG.debug("Calculating locations")
locations = [
parse_location(
"{0}:1-{1}".format(a, fasta.get_reference_length(a)), 1)
for a in fasta.references
]
seq_ids = [a for a in fasta.references]
temp_output_file = output_file
if bgzip:
if g2g_fu.get_extension(output_file) != 'gz':
output_file = "{0}.gz".format(output_file)
else:
temp_output_file = temp_output_file[:-3]
fasta_out = open(temp_output_file, "w")
LOG.info("Transforming...")
chr_info = {}
try:
# will need a better way, but for now...
LOG.info("Parsing chain file...")
for line in chain_file:
if len(line) > 7:
LOG.debug("Adding chromosome {0}".format(
chain_file.current_chain_header[1]))
chr_info[chain_file.current_chain_header[1]] = {
'from_size': line[2],
'from_start': line[4],
'from_end': line[5],
'to_size': line[7],
'to_start': line[9],
'to_end': line[10],
'header_chain': chain_file.current_chain_header,
'lines': []
}
else:
chr_info[chain_file.current_chain_header[1]]['lines'].append(
line)
LOG.info("Chain file parsed")
insertion_bases = 0
deletion_bases = 0
for location in locations:
LOG.info("Processing chromosome={0}".format(location.seqid))
LOG.debug("Location: {0}".format(location))
chrom_size_from = chr_info[location.seqid]['from_size']
chrom_size_to = chr_info[location.seqid]['to_size']
last_pos = chr_info[location.seqid]['from_start']
new_sequence = StringIO()
chain_file.reset()
for chain_line in chr_info[location.seqid]['lines']:
LOG.debug("\nLINE: {0} : {1}".format(chain_file.line_no,
chain_line))
if len(chain_line) == 1:
# last line
fragment = chain_line[0]
partial_seq = fasta.fetch(location.seqid, last_pos,
last_pos + fragment)
new_sequence.write(str(partial_seq))
if len(new_sequence.getvalue()) < chrom_size_to:
LOG.warn(
"Length's do not match, chromosome length in chain: {0}, sequence length: {1}"
.format(chrom_size_to,
len(new_sequence.getvalue())))
fasta_out.write(">{0} {1}:{2}-{3}\n".format(
location.seqid, location.seqid,
chr_info[location.seqid]['from_start'] + 1,
chrom_size_to))
for l in wrap_sequence(new_sequence.getvalue()):
fasta_out.write(l.strip())
fasta_out.write('\n')
break
else:
# fragment_size dt_size dq_size same_bases dt_bases dq_bases
fragment = chain_line[0]
dt = chain_line[1 if not reverse else 2]
dq = chain_line[2 if not reverse else 1]
same = chain_line[3]
dt_bases = chain_line[4 if not reverse else 5]
dq_bases = chain_line[5 if not reverse else 4]
partial_seq = fasta.fetch(location.seqid, last_pos,
last_pos + fragment)
new_sequence.write(partial_seq)
if dq > 0:
# insertion
LOG.debug("INSERTION")
new_sequence.write(dq_bases)
LOG.debug("{0}:{1}-{2} (Length: {3})".format(
location.seqid, last_pos, last_pos + fragment,
len(partial_seq)))
if len(partial_seq) > 100:
LOG.debug("{0}...{1}".format(
partial_seq[:10], partial_seq[-10:]))
else:
LOG.debug(partial_seq)
LOG.debug("Adding {0}".format(dq_bases))
LOG.debug("SAME={0}, {1}".format(
same, partial_seq[-(len(same)):]))
insertion_bases += dq
if dt > 0:
# deletion
LOG.debug("DELETION")
last_pos += dt
LOG.debug("skipping ahead {0} bases".format(dt))
deletion_bases += dt
last_pos += fragment
LOG.debug(
"LAST_POS={0}, INSERTIONS={1}, DELETIONS={2}, DIFF={3}"
.format(last_pos, insertion_bases, deletion_bases,
(insertion_bases - deletion_bases)))
# bgzip and index
if bgzip:
LOG.info("Compressing and indexing...")
g2g_fu.bgzip_index(temp_output_file, output_file, 'fa')
except G2GLocationError, le:
LOG.debug("Unable to parse location, {0}".format(le.message))
raise le
def gtf2db(input_file, output_file):
"""
Convert a GTF file into SQLite
:param input_file: the GTF file to convert
:param output_file: The generated database file
"""
start = time.time()
input_file = g2g_fu.check_file(input_file, 'r')
output_file = g2g_fu.check_file(output_file, 'w')
g2g_fu.delete_file(output_file)
LOG.info("GTF FILE: {0}".format(input_file))
LOG.info("DB File: {0}".format(output_file))
conn = sqlite3.connect(output_file)
c = conn.cursor()
LOG.debug("Generating tables")
c.execute(SQL_CREATE_GTF_TABLE)
c.execute(SQL_CREATE_GTF_LOOKUP_TABLE)
c.execute(SQL_CREATE_GTF_SOURCES_TABLE)
c.execute(SQL_CREATE_GTF_TYPES_TABLE)
c.execute(SQL_CREATE_GTF_ATTRIBUTES_TABLE)
gtf_types = {}
gtf_sources = {}
gtf_attributes = {}
LOG.info("Parsing GTF file...")
gtf_file = GTF(input_file)
counter = 0
for record in gtf_file:
if counter and counter % 100000 == 0:
LOG.info("Processed {0:,} records".format(counter))
if record.type not in gtf_types:
_type_key = len(gtf_types.keys())
gtf_types[record.type] = _type_key
else:
_type_key = gtf_types[record.type]
if record.source not in gtf_sources:
_source_key = len(gtf_sources.keys())
gtf_sources[record.source] = _source_key
else:
_source_key = gtf_sources[record.source]
strand = 0
if record.strand in ['+', '-']:
strand = 1 if record.strand == '+' else -1
gene_id = record.attributes['gene_id']
transcript_id = record.attributes['transcript_id'] if 'transcript_id' in record.attributes else None
ensembl_id = None
if record.type == 'gene':
ensembl_id = record.attributes['gene_id']
elif record.type == 'transcript':
ensembl_id = record.attributes['transcript_id']
elif record.type == 'exon':
ensembl_id = record.attributes['exon_id']
else:
ensembl_id = record.attributes['protein_id'] if 'protein_id' in record.attributes else None
c.execute(SQL_INSERT_GTF_TABLE, (gene_id, transcript_id, ensembl_id, record.seqid, record.start, record.end, strand, record.score, _source_key, _type_key, record.frame))
gtf_key = c.lastrowid
for attribute, value in record.attributes.iteritems():
if attribute not in ['gene_id', 'transcript_id', 'exon_id']:
if attribute not in gtf_attributes:
_attribute_key = len(gtf_attributes.keys())
gtf_attributes[attribute] = _attribute_key
else:
_attribute_key = gtf_attributes[attribute]
c.execute(SQL_INSERT_GTF_LOOKUP_TABLE, (gtf_key, _attribute_key, value))
counter += 1
# save (commit) the changes
conn.commit()
for source, _key in gtf_sources.iteritems():
c.execute(SQL_INSERT_GTF_SOURCES_TABLE, (_key, source))
conn.commit()
for type, _key in gtf_types.iteritems():
c.execute(SQL_INSERT_GTF_TYPES_TABLE, (_key, type))
conn.commit()
for attribute, _key in gtf_attributes.iteritems():
c.execute(SQL_INSERT_GTF_ATTRIBUTES_TABLE, (_key, attribute))
conn.commit()
LOG.info("GTF File parsed")
LOG.info("Finalizing database...")
for sql in SQL_INDICES_GTF:
LOG.debug(sql)
c.execute(sql)
for sql in SQL_INDICES_GTF_LOOKUP:
LOG.debug(sql)
c.execute(sql)
for sql in SQL_INDICES_GTF_TYPES:
LOG.debug(sql)
c.execute(sql)
for sql in SQL_INDICES_GTF_SOURCES:
LOG.debug(sql)
c.execute(sql)
for sql in SQL_INDICES_GTF_ATTRIBUTES:
LOG.debug(sql)
c.execute(sql)
LOG.info("Database created")
# close connection
conn.close()
LOG.info("Execution complete: {0}".format(format_time(start, time.time())))
for seqid in tb.contigs:
processed_seqids[seqid] = False
left = VCFtoChainInfo()
right = VCFtoChainInfo()
chain_info = {}
if diploid:
left.output_file = g2g_fu.prepend_before_extension(output_file, 'left')
right.output_file = g2g_fu.prepend_before_extension(output_file, 'right')
chain_info['left'] = left
chain_info['right'] = right
g2g_fu.delete_file(left.output_file)
g2g_fu.delete_file(right.output_file)
else:
left.output_file = output_file
chain_info['left'] = left
g2g_fu.delete_file(left.output_file)
try:
all_chrom = [c for c in fasta_file.references]
all_chrom_length = [n for n in fasta_file.lengths]
all_vcffiles = [input_file] * len(all_chrom)
all_sample_index = [sample_index] * len(all_chrom)
all_chain_info = [chain_info] * len(all_chrom)
all_diploid = [diploid] * len(all_chrom)
all_passed = [passed] * len(all_chrom)
def gtf2db(input_file, output_file):
"""
Convert a GTF file into SQLite
:param input_file: the GTF file to convert
:param output_file: The generated database file
"""
start = time.time()
input_file = g2g_fu.check_file(input_file, 'r')
output_file = g2g_fu.check_file(output_file, 'w')
g2g_fu.delete_file(output_file)
LOG.info("GTF FILE: {0}".format(input_file))
LOG.info("DB File: {0}".format(output_file))
conn = sqlite3.connect(output_file)
c = conn.cursor()
LOG.debug("Generating tables")
c.execute(SQL_CREATE_GTF_TABLE)
c.execute(SQL_CREATE_GTF_LOOKUP_TABLE)
c.execute(SQL_CREATE_GTF_SOURCES_TABLE)
c.execute(SQL_CREATE_GTF_TYPES_TABLE)
c.execute(SQL_CREATE_GTF_ATTRIBUTES_TABLE)
gtf_types = {}
gtf_sources = {}
gtf_attributes = {}
LOG.info("Parsing GTF file...")
gtf_file = GTF(input_file)
counter = 0
for record in gtf_file:
if counter and counter % 100000 == 0:
LOG.info("Processed {0:,} records".format(counter))
if record.type not in gtf_types:
_type_key = len(gtf_types.keys())
gtf_types[record.type] = _type_key
else:
_type_key = gtf_types[record.type]
if record.source not in gtf_sources:
_source_key = len(gtf_sources.keys())
gtf_sources[record.source] = _source_key
else:
_source_key = gtf_sources[record.source]
strand = 0
if record.strand in ['+', '-']:
strand = 1 if record.strand == '+' else -1
gene_id = record.attributes['gene_id']
transcript_id = record.attributes[
'transcript_id'] if 'transcript_id' in record.attributes else None
ensembl_id = None
if record.type == 'gene':
ensembl_id = record.attributes['gene_id']
elif record.type == 'transcript':
ensembl_id = record.attributes['transcript_id']
elif record.type == 'exon':
ensembl_id = record.attributes['exon_id']
else:
ensembl_id = record.attributes[
'protein_id'] if 'protein_id' in record.attributes else None
c.execute(SQL_INSERT_GTF_TABLE,
(gene_id, transcript_id, ensembl_id, record.seqid,
record.start, record.end, strand, record.score, _source_key,
_type_key, record.frame))
gtf_key = c.lastrowid
for attribute, value in record.attributes.iteritems():
if attribute not in ['gene_id', 'transcript_id', 'exon_id']:
if attribute not in gtf_attributes:
_attribute_key = len(gtf_attributes.keys())
gtf_attributes[attribute] = _attribute_key
else:
_attribute_key = gtf_attributes[attribute]
c.execute(SQL_INSERT_GTF_LOOKUP_TABLE,
(gtf_key, _attribute_key, value))
counter += 1
# save (commit) the changes
conn.commit()
for source, _key in gtf_sources.iteritems():
c.execute(SQL_INSERT_GTF_SOURCES_TABLE, (_key, source))
conn.commit()
for type, _key in gtf_types.iteritems():
c.execute(SQL_INSERT_GTF_TYPES_TABLE, (_key, type))
conn.commit()
for attribute, _key in gtf_attributes.iteritems():
c.execute(SQL_INSERT_GTF_ATTRIBUTES_TABLE, (_key, attribute))
conn.commit()
LOG.info("GTF File parsed")
LOG.info("Finalizing database...")
for sql in SQL_INDICES_GTF:
LOG.debug(sql)
c.execute(sql)
for sql in SQL_INDICES_GTF_LOOKUP:
LOG.debug(sql)
c.execute(sql)
for sql in SQL_INDICES_GTF_TYPES:
LOG.debug(sql)
c.execute(sql)
for sql in SQL_INDICES_GTF_SOURCES:
LOG.debug(sql)
c.execute(sql)
for sql in SQL_INDICES_GTF_ATTRIBUTES:
LOG.debug(sql)
c.execute(sql)
LOG.info("Database created")
# close connection
conn.close()
LOG.info("Execution complete: {0}".format(format_time(start, time.time())))