def create_one_wormtable(schema_path, inp_file, out_file):
"""
Create a single wormtable database from the input file and an .xml schema.
"""
cachesize = '16G '
if WIN_PLATFORM_NONFREE:
cachesize = '4G ' # to deal with BDB error...
runargs = '-q --schema ' + schema_path + ' --cache-size=' + cachesize + \
inp_file + ' ' + out_file
#run vcf2wt as a library function, no system calls
try:
wt.vcf2wt_main(runargs.split())
except:
raise #return quietly
# add row index for this wormtable
# supersedes add_all_rowid_indexes() and add_one_rowid_index()
# doing it here means we avail of the thread/process that is already spawned
# sys.stderr.write('Indexing %s\n' % (out_file,))
runargs = 'add -q --cache-size=' + cachesize + out_file + ' row_id'
wt.wtadmin_main(runargs.split())
return
def create_one_wormtable(schema_path, inp_file, out_file):
"""
Create a single wormtable database from the input file and an .xml schema.
"""
cachesize = '16G '
if WIN_PLATFORM_NONFREE:
cachesize = '4G ' # to deal with BDB error...
runargs = '-q --schema ' + schema_path + ' --cache-size=' + cachesize + \
inp_file + ' ' + out_file
#run vcf2wt as a library function, no system calls
try:
wt.vcf2wt_main(runargs.split())
except:
raise #return quietly
# add row index for this wormtable
# supersedes add_all_rowid_indexes() and add_one_rowid_index()
# doing it here means we avail of the thread/process that is already spawned
# sys.stderr.write('Indexing %s\n' % (out_file,))
runargs = 'add -q --cache-size=' + cachesize + out_file + ' row_id'
wt.wtadmin_main(runargs.split())
return
def add_one_rowid_index(wt_path):
"""
Add the 'row_id' index to the wormtable wt_path.
"""
cachesize = '16G '
if WIN_PLATFORM_NONFREE:
cachesize = '4G ' # to deal with BDB error...
wt_path = wt_path.replace('\\', '\\\\')
# run wtadmin as a library function, no system calls
runargs = 'add -q --cache-size=' + cachesize + wt_path + ' row_id'
wt.wtadmin_main(runargs.split())
return
def add_one_rowid_index(wt_path):
"""
Add the 'row_id' index to the wormtable wt_path.
"""
cachesize = '16G '
if WIN_PLATFORM_NONFREE:
cachesize = '4G ' # to deal with BDB error...
wt_path = wt_path.replace('\\', '\\\\')
# run wtadmin as a library function, no system calls
runargs = 'add -q --cache-size=' + cachesize + wt_path + ' row_id'
wt.wtadmin_main(runargs.split())
return
def add_chrompos_index(out_folder):
"""
Add the 'CHROM+POS' index to the wormtable 'CHROM+POS.wt'.
"""
# Turning this off for now, since it's not much overhead
# and needs to be created the first time, which this check won't allow!
#if os.path.exists(os.path.join(out_folder, 'CHROM+POS.wt')):
# return
cachesize = '16G '
divider = '/'
if WIN_PLATFORM_NONFREE:
cachesize = '4G ' # to deal with BDB error...
out_folder = out_folder.replace('\\', '\\\\')
divider = '\\\\'
#run wtadmin as a library function, no system calls!
#for now, force this index to run each time...
runargs = 'add -q --force --cache-size=' + cachesize + out_folder + divider + \
'CHROM+POS.wt CHROM+POS'
wt.wtadmin_main(runargs.split())
return
def add_chrompos_index(out_folder):
"""
Add the 'CHROM+POS' index to the wormtable 'CHROM+POS.wt'.
"""
# Turning this off for now, since it's not much overhead
# and needs to be created the first time, which this check won't allow!
#if os.path.exists(os.path.join(out_folder, 'CHROM+POS.wt')):
# return
cachesize = '16G '
divider = '/'
if WIN_PLATFORM_NONFREE:
cachesize = '4G ' # to deal with BDB error...
out_folder = out_folder.replace('\\', '\\\\')
divider = '\\\\'
#run wtadmin as a library function, no system calls!
#for now, force this index to run each time...
runargs = 'add -q --force --cache-size=' + cachesize + out_folder + divider + \
'CHROM+POS.wt CHROM+POS'
wt.wtadmin_main(runargs.split())
return
import wormtable as wt
if __name__ == "__main__":
wt.wtadmin_main()