nargs=1,
type=int,
dest='first')
parser.add_argument('-N',
'--count',
metavar='rows',
help='how many reads',
nargs=1,
type=int,
dest='count')
parser.add_argument('--split', help='split spot', action='store_true')
args = parser.parse_args()
try:
#open a manager in read-mode ( dflt-mode )
mgr = vdb.manager()
for acc in args.accession:
#detect path-type ( database or table or anything-else )
pt = mgr.PathType(acc)
if pt == vdb.PathType.Database:
#object is a database
fastq_from_tbl(args, mgr.OpenDB(acc).OpenTable("SEQUENCE"))
elif pt == vdb.PathType.Table:
#object is a table
fastq_from_tbl(args, mgr.OpenTable(acc))
else:
print("%s is not an SRA-object" % (acc))
except vdb.vdb_error as e:
print(e)
except KeyboardInterrupt:
f.write("%d, line # %d\n" % (i, i))
f.close()
def csv_to_vdb(mgr, csv_file, spec, vdb_table):
with open(csv_file, 'r') as f:
spec = 'CSVTAB'
tbl_wr = mgr.CreateTable(mgr.MakeSchema(schematxt), spec, vdb_table)
cur = tbl_wr.CreateCursor(vdb.OpenMode.Write)
cols = cur.OpenColumns(["C1", "C2"])
for row in csv.reader(f):
cur.OpenRow()
cols["C1"].write([int(row[0])])
cols["C2"].write(row[1].strip())
cur.CommitRow()
cur.CloseRow()
cur.Commit()
if __name__ == '__main__':
csv_file = 'data.txt'
write_csv(csv_file, 10)
try:
mgr = vdb.manager(vdb.OpenMode.Write)
spec = 'CSVTAB'
csv_to_vdb(mgr, csv_file, spec, 'L8')
mgr.OpenTable('L8').print_rows()
except vdb.vdb_error as e:
print(e)
os.remove(csv_file)
f.write("%d, line # %d\n" % (i, i))
f.close()
def csv_to_vdb(mgr, csv_file, spec, vdb_table):
with open(csv_file, 'r') as f:
spec = 'CSVTAB'
tbl_wr = mgr.CreateTable(mgr.MakeSchema(schematxt), spec, vdb_table)
cur = tbl_wr.CreateCursor(vdb.OpenMode.Write)
cols = cur.OpenColumns(["C1", "C2"])
for row in csv.reader(f):
cur.OpenRow()
cols["C1"].write([int(row[0])])
cols["C2"].write(row[1].strip())
cur.CommitRow()
cur.CloseRow()
cur.Commit()
if __name__ == '__main__':
csv_file = 'data.txt'
write_csv(csv_file, 10)
try:
mgr = vdb.manager(vdb.OpenMode.Write, "./2.8.0/libncbi-wvdb.so.2.8.0")
spec = 'CSVTAB'
csv_to_vdb(mgr, csv_file, spec, 'L8')
mgr.OpenTable(spec).print_rows()
except vdb.vdb_error as e:
print(e)
os.remove(csv_file)
for row in xrange( first, first + count ) :
read = c_read.Read( row )
print( fastq.format( acc, c_name.Read( row ), len( read ), read, c_qual.Read( row ) ) )
if __name__ == '__main__' :
parser = argparse.ArgumentParser()
parser.add_argument( 'accession', nargs='*' )
parser.add_argument( '-X', '--first', metavar='row-id', help='first row-id', nargs=1, type=int, dest='first' )
parser.add_argument( '-N', '--count', metavar='rows', help='how many reads', nargs=1, type=int, dest='count' )
parser.add_argument( '--split', help='split spot', action='store_true' )
args = parser.parse_args()
try :
#open a manager in read-mode ( dflt-mode )
mgr = vdb.manager()
for acc in args.accession :
#detect path-type ( database or table or anything-else )
pt = mgr.PathType( acc )
if pt == vdb.PathType.Database :
#object is a database
fastq_from_tbl( args, mgr.OpenDB( acc ).OpenTable( "SEQUENCE" ) )
elif pt == vdb.PathType.Table :
#object is a table
fastq_from_tbl( args, mgr.OpenTable( acc ) )
else :
print( "%s is not an SRA-object"%( acc ) )
except vdb.vdb_error as e :
print( e )
except KeyboardInterrupt :
help='schema',
type=str,
dest='schema')
parser.add_argument('-F',
'--freq',
metavar='number',
help='progress freq',
type=int,
dest='freq',
default=2000)
args = parser.parse_args()
try:
print("making a copy of : {}".format(args.accession))
#open 2 managers:
rd_mgr = vdb.manager(vdb.OpenMode.Read, args.readlib)
wr_mgr = vdb.manager(vdb.OpenMode.Write, args.writelib)
rd_tbl = None
pt = rd_mgr.PathType(
args.accession
) #detect path-type ( database or table or anything-else )
if pt == vdb.PathType.Database:
rd_tbl = rd_mgr.OpenDB(args.accession).OpenTable(
"SEQUENCE") #object is a database
elif pt == vdb.PathType.Table:
rd_tbl = rd_mgr.OpenTable(args.accession) #object is a table
else:
print("%s is not an SRA-object" % (args.accession))
if rd_tbl != None:
with open( filename, 'w' ) as f :
for i in range( 1, rowcount ) :
f.write( "%d, line # %d\n"%( i, i ) )
f.close()
def csv_to_vdb( mgr, csv_file, spec, vdb_table ) :
with open( csv_file, 'r' ) as f :
spec = 'CSVTAB'
tbl_wr = mgr.CreateTable( mgr.MakeSchema( schematxt ), spec, vdb_table )
cur = tbl_wr.CreateCursor( vdb.OpenMode.Write )
cols = cur.OpenColumns( [ "C1", "C2" ] )
for row in csv.reader( f ) :
cur.OpenRow()
cols[ "C1" ].write( [ int( row[ 0 ] ) ] )
cols[ "C2" ].write( row[ 1 ].strip() );
cur.CommitRow()
cur.CloseRow()
cur.Commit()
if __name__ == '__main__':
csv_file = 'data.txt'
write_csv( csv_file, 10 )
try :
mgr = vdb.manager( vdb.OpenMode.Write, "./2.8.0/libncbi-wvdb.so.2.8.0" )
spec = 'CSVTAB'
csv_to_vdb( mgr, csv_file, spec, 'L8' )
mgr.OpenTable( spec ).print_rows()
except vdb.vdb_error as e :
print( e )
os.remove( csv_file )