def main():
#command line arguments
parser = argparse.ArgumentParser(
description=
'Convert RefGene Genbank protein files to tab-delimited database files',
epilog=
'pypeline.refgene2db version 1.0β1 ©2011-2012 Michael Yourshaw all rights reserved'
)
parser.add_argument('--ref',
'-r',
required=True,
help='path to gene_RefSeqGene file')
parser.add_argument('--input',
'-i',
nargs='+',
help='downloaded refseqgeneN.genomic.gbff.gz files')
parser.add_argument('--output', '-o', required=True, help='output file')
args = parser.parse_args()
locus2gene = {}
with open(args.ref) as ref:
for r in ref:
if r.startswith('#'):
continue
r = r.rstrip('\n').split('\t')
locus2gene[r[3].split('.')[0]] = r[2]
inputs = my.unglob(args.input)
locus2comment = {}
locus_count = 0
refseq_re = re.compile(r"\s*\[provided by RefSeq.*\]", re.I)
for input in inputs:
f = my.open_gz_or_text(input)
in_comment = False
for line in f:
if line[0:5] == "LOCUS":
locus = line.split()[1]
comment = ""
locus_count += 1
elif line[0:7] == "COMMENT":
in_comment = True
comment += line.split(" ")[1].replace("\n", " ")
elif line[0:7] == "PRIMARY":
in_comment = False
try:
summary = comment.split(
"Summary:"
)[1] #.strip().split('[provided by RefSeq].')[0].rstrip()
except:
summary = comment #.strip().split('[provided by RefSeq].')[0].rstrip()
locus2comment[locus] = refseq_re.split(summary)[0]
elif in_comment:
comment += line.split(" ")[1].replace("\n", " ")
with open(args.output, 'w') as output:
output.write('#NG_ID\tGeneSymbol\tSUMMARY\n')
for locus in sorted(locus2comment):
output.write('{}\t{}\t{}\n'.format(locus,
locus2gene.get(locus, ''),
locus2comment[locus]))
def main():
#command line arguments
parser = argparse.ArgumentParser(
description = 'Convert RefGene Genbank protein files to tab-delimited database files',
epilog = 'pypeline.refgene2db version 1.0β1 ©2011-2012 Michael Yourshaw all rights reserved')
parser.add_argument('--ref', '-r', required=True,
help='path to gene_RefSeqGene file')
parser.add_argument('--input', '-i', nargs='+',
help='downloaded refseqgeneN.genomic.gbff.gz files')
parser.add_argument('--output', '-o', required=True,
help='output file')
args = parser.parse_args()
locus2gene = {}
with open(args.ref) as ref:
for r in ref:
if r.startswith('#'):
continue
r = r.rstrip('\n').split('\t')
locus2gene[r[3].split('.')[0]] = r[2]
inputs = my.unglob(args.input)
locus2comment = {}
locus_count = 0
refseq_re = re.compile(r"\s*\[provided by RefSeq.*\]",re.I)
for input in inputs:
f = my.open_gz_or_text(input)
in_comment=False
for line in f:
if line[0:5] == "LOCUS":
locus = line.split()[1]
comment = ""
locus_count += 1
elif line[0:7] == "COMMENT":
in_comment=True
comment += line.split(" ")[1].replace("\n", " ")
elif line[0:7] == "PRIMARY":
in_comment = False
try:
summary = comment.split("Summary:")[1]#.strip().split('[provided by RefSeq].')[0].rstrip()
except:
summary = comment#.strip().split('[provided by RefSeq].')[0].rstrip()
locus2comment[locus] = refseq_re.split(summary)[0]
elif in_comment:
comment += line.split(" ")[1].replace("\n", " ")
with open(args.output,'w') as output:
output.write('#NG_ID\tGeneSymbol\tSUMMARY\n')
for locus in sorted(locus2comment):
output.write('{}\t{}\t{}\n'.format(locus, locus2gene.get(locus,''), locus2comment[locus]))
def run(input, table=None, skip=None, header_line='#', column_names=None, no_column_names=False):
header_line_number = int(header_line) if my.is_int(header_line) and int(header_line) > 0 else None
header_chars = header_line if not my.is_int(header_line) else None
output = os.path.join(os.path.dirname(input),table+'.mysql') if table else input+'.table.mysql'
with my.open_gz_or_text(input) as input_file, open(output, 'w') as mysql:
column_widths = {}
column_names = {}
column_names_list = None
line_count = 0
first_data_line = None
header_found = False if header_line_number or header_chars else True
if column_names:
header_found = True
column_names_list = column_names
column_names = {i:column_names_list[i] for i in range(len(column_names_list))}
sql_column_spec = my.get_sql_column_spec(column_names_list)
for line in input_file:
line_count += 1
line = line.rstrip('\n')
if not bool(line.strip()):
continue
if not header_found:
if no_column_names:
header_found = True
column_names_list = ['col'+str(i+1) for i in range(len(line.split('\t')))]
column_names = {i:column_names_list[i] for i in range(len(column_names_list))}
sql_column_spec = my.get_sql_column_spec(column_names_list)
elif (header_line_number and header_line_number == line_count) or (header_chars and header_chars != '#' and line.startswith(header_chars)) or (header_chars and header_chars == '#' and line.startswith(header_chars) and line[1] != '#'):
header_found = True
column_names_list = line.split('\t')
column_names = {i:column_names_list[i] for i in range(len(column_names_list))}
sql_column_spec = my.get_sql_column_spec(column_names_list)
continue
elif skip and line.startswith(skip):
continue
else: #data line
if first_data_line == None:
first_data_line = line_count
fields = line.split('\t')
indices = [i for i in range(len(fields))]
column_widths = {i: max(len(fields[i]),column_widths.setdefault(i,0)) for i in indices}
sql_data_dict = my.get_sql_data_dict(column_names, fields)
my.update_sql_column_spec(sql_column_spec, sql_data_dict)
pass
#output.write('col_number\tcol_name\tcol_width\n')
#output.write(''.join(['{}\t{}\t{}\n'.format(col+1, column_names[col], column_widths[col]) for col in sorted(column_widths)]))
if not (column_names_list and sql_column_spec):
raise SqlColumnsError('Could not identify columns. Try using --column_names or --no_column_names.')
mysql_scripts = my.get_mysql_scripts(
table_name=table if table else os.path.basename(input).replace('.','_')[:64],
index_base_name=os.path.basename(input).replace('.','_')[:16],
indices=[],
columns_out=column_names_list,
columns_out_spec=sql_column_spec,
rows_to_delete=first_data_line-1
)
mysql.write(mysql_scripts[0])
