os.makedirs("Results")
outfile_name = "Results/" + 'exon_sequence_in_' + genome
# The steps below are taken if the user provides genomic location input in correct format.
# Using the location input, exon sequence, upstream and downstream regions
# are extracted from the whole genome information
if parsed_data['type'] == '2':
if re.match('chr\d+\:\d+\.\.\d+', location):
print "User has provided genomic location as input data."
if mode == 'batch':
mode_response = raw_input('USER HAS PROVIDED BATCH MODE WITH A SINGLE LOCATION...PRESS ENTER TO CONTINUE PROGRAM OR PRESS 2 TO CHANGE MODE : ')
if mode_response == '2':
mode = 'single'
exon_start, exon_end = PredictExon.extract_exon(location, strand)
seq_start = location.split(':')[1].split('..')[0]
seq_end = location.split(':')[1].split('..')[1]
chr_num = location.split(':')[0]
file_path = 'data/' + genome + '/' + chr_num + '.fa'
if exon_start == 0 or exon_end == 0:
exon_start = int(seq_start)
exon_end = int(seq_end)
# This checks to make sure the complete genome file exists in the current directory.
# If not present, program will terminate with a message
try:
file_handle = open(file_path, 'r')
except IOError:
def parse(mode, query_start, query_end, chr_num, genome, base_count, strand):
exon_sequence = ""
upstream_seq = ""
downstream_seq = ""
sequence = ""
alt_query_start = ""
alt_query_end = ""
file_path = 'data/' + genome + '/' + chr_num + '.fa'
if query_start == '' or query_end == '' or chr_num == '':
print "The input sequence could not be mapped to any genomic sequence data"
sys.exit(1)
if mode == 'batch':
if query_start > query_end:
strand = '-'
else:
strand = '+'
else:
if query_start > query_end:
if strand == '+':
print "USER SUPPLIED SEQUENCE IS PRESENT ON THE OPPOSITE STRAND (-)."
print "Changing strand information....."
#response = raw_input("Enter 2 to change strand : ")
#if response == '2':
strand = '-'
else:
if strand == '-':
print "USER SUPPLIED SEQUENCE IS PRESENT ON THE OPPOSITE STRAND (+)."
print "Changing strand information....."
#response = raw_input("Enter 2 to change strand : ")
#if response == '2':
strand = '+'
if strand == '+':
alt_query_start = query_start
alt_query_end = query_end
elif strand == '-':
alt_query_start = query_end
alt_query_end = query_start
try:
file_handle = open(file_path, 'r')
except IOError:
print "The genome is not available in the current directory."
sys.exit(1)
for lines in file_handle:
if lines.startswith('>'):
continue
sequence += lines.rstrip().lower()
file_handle.close()
location = chr_num + ':' + alt_query_start + '..' + alt_query_end
exon_start, exon_end = PredictExon.extract_exon(location, strand)
if exon_start == 0 or exon_end == 0:
exon_start = int(alt_query_start)
exon_end = int(alt_query_end)
upstream_seq, exon_sequence, downstream_seq = extractSequence.extract_single(
sequence, strand, exon_start, exon_end, base_count)
sequence = ""
if exon_sequence == '' or upstream_seq == '' or downstream_seq == '':
print "The specified coordinates are unable to extract any sequence."
sys.exit(1)
return upstream_seq, exon_sequence, downstream_seq, strand
def parse(mode, query_start, query_end, chr_num, genome, base_count, strand):
exon_sequence = ""
upstream_seq = ""
downstream_seq = ""
sequence = ""
alt_query_start = ""
alt_query_end = ""
file_path = 'data/' + genome + '/' + chr_num + '.fa'
if query_start == '' or query_end == '' or chr_num == '':
print "The input sequence could not be mapped to any genomic sequence data"
sys.exit(1)
if mode == 'batch':
if query_start > query_end:
strand = '-'
else:
strand = '+'
else:
if query_start > query_end:
if strand == '+' :
print "USER SUPPLIED SEQUENCE IS PRESENT ON THE OPPOSITE STRAND (-)."
print "Changing strand information....."
#response = raw_input("Enter 2 to change strand : ")
#if response == '2':
strand = '-'
else:
if strand == '-':
print "USER SUPPLIED SEQUENCE IS PRESENT ON THE OPPOSITE STRAND (+)."
print "Changing strand information....."
#response = raw_input("Enter 2 to change strand : ")
#if response == '2':
strand = '+'
if strand == '+':
alt_query_start = query_start
alt_query_end = query_end
elif strand == '-':
alt_query_start = query_end
alt_query_end = query_start
try:
file_handle = open(file_path, 'r')
except IOError:
print "The genome is not available in the current directory."
sys.exit(1)
for lines in file_handle:
if lines.startswith('>'):
continue
sequence += lines.rstrip().lower()
file_handle.close()
location = chr_num + ':' + alt_query_start + '..' + alt_query_end
exon_start, exon_end = PredictExon.extract_exon(location, strand)
if exon_start == 0 or exon_end == 0:
exon_start = int(alt_query_start)
exon_end = int(alt_query_end)
upstream_seq, exon_sequence, downstream_seq = extractSequence.extract_single(sequence, strand, exon_start, exon_end, base_count)
sequence = ""
if exon_sequence == '' or upstream_seq == '' or downstream_seq == '':
print "The specified coordinates are unable to extract any sequence."
sys.exit(1)
return upstream_seq, exon_sequence, downstream_seq, strand
outfile_name = "Results/" + 'exon_sequence_in_' + genome
# The steps below are taken if the user provides genomic location input in correct format.
# Using the location input, exon sequence, upstream and downstream regions
# are extracted from the whole genome information
if parsed_data['type'] == '2':
if re.match('chr\d+\:\d+\.\.\d+', location):
print "User has provided genomic location as input data."
if mode == 'batch':
mode_response = raw_input(
'USER HAS PROVIDED BATCH MODE WITH A SINGLE LOCATION...PRESS ENTER TO CONTINUE PROGRAM OR PRESS 2 TO CHANGE MODE : '
)
if mode_response == '2':
mode = 'single'
exon_start, exon_end = PredictExon.extract_exon(location, strand)
seq_start = location.split(':')[1].split('..')[0]
seq_end = location.split(':')[1].split('..')[1]
chr_num = location.split(':')[0]
file_path = 'data/' + genome + '/' + chr_num + '.fa'
if exon_start == 0 or exon_end == 0:
exon_start = int(seq_start)
exon_end = int(seq_end)
# This checks to make sure the complete genome file exists in the current directory.
# If not present, program will terminate with a message
try:
file_handle = open(file_path, 'r')
except IOError: