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#!python3
import sys
if __name__ != '__main__':
sys.exit(0)
if sys.platform != 'linux' and sys.platform != 'darwin':
sys.exit(0)
import os
import random
import re
saveSysPath = sys.path
sys.path.append(os.path.abspath('../../../ncbi-vdb/py_vdb'))
from vdb import *
sys.path = saveSysPath
output = 'test-data' if len(sys.argv) < 2 else sys.argv[1]
def findLibrary(what):
paths = []
try:
paths = os.environ['VDB_LIBRARY_PATH'].split(':')
except:
pass
for path in paths:
results = []
for file in os.listdir(path):
if re.search(what, file) == None:
continue
if os.path.isfile(os.path.join(path, file)):
results.append(file)
if len(results) != 0:
return os.path.realpath(os.path.join(path, sorted(results)[-1]))
print('fatal: Can not find ncbi-wvdb dynamic library, try setting VDB_LIBRARY_PATH')
exit(1)
def randomRead(length:int):
y = []
while len(y) <= length:
y += ['A', 'C', 'G', 'T']
# y is ACGT repeated enough times that there are at least length elements
return ''.join(random.sample(y, k=length))
def phred33(x:int):
return chr(x+33)
# NOTE: Rules for filtering
# Quote:
# Reads that have more than half of quality score values <20 will be
# flagged ‘reject’.
# Reads that begin or end with a run of more than 10 quality scores <20
# are also flagged ‘reject’.
#
def randomQuality(length:int, type:str, good):
y = []
if type == 'low':
while len(y) <= length // 2:
y.append(random.randrange(2, 20))
while good and len(y) * 2 > length:
y.pop()
while len(y) < length:
y.append(random.randrange(20,41))
random.shuffle(y)
elif type == 'front' or type == 'back':
limit = 10 if good else 11
while len(y) < limit:
y.append(random.randrange(2, 20))
while len(y) < length:
y.append(random.randrange(20,41))
if type == 'back':
y = reversed(y)
else:
# some values will <20, but never enough to have a chance to trigger any
# of the other rules, regardless of how they are arranged
while len(y) * 4 <= length and len(y) < 9:
y.append(random.randrange(2, 20))
while len(y) < length:
y.append(random.randrange(20,41))
random.shuffle(y)
return ''.join(map(phred33, y))[0:length]
cursDef = {
'READ_FILTER': {
'expression': '(U8)READ_FILTER',
},
'READ_TYPE': {
'expression': '(U8)READ_TYPE',
'default': [1, 1],
},
'NAME': {
'expression': '(ascii)NAME',
},
'READ_START': {
'expression': '(INSDC:coord:zero)READ_START',
},
'READ_LEN': {
'expression': '(INSDC:coord:len)READ_LEN',
},
'READ': {
'expression': '(INSDC:dna:text)READ',
},
'QUALITY': {
'expression': '(INSDC:quality:text:phred_33)QUALITY',
},
}
wvdb = findLibrary(r'ncbi-wvdb')
#print(wvdb);sys.exit(0)
mgr = manager(OpenMode.Write, wvdb)
print('info: loaded VDBManager', mgr.Version(), 'from', wvdb)
schema = mgr.MakeSchema()
schema.AddIncludePath(os.path.abspath('../../../ncbi-vdb/interfaces'))
schema.ParseFile('sra/generic-fastq.vschema')
db = mgr.CreateDB(schema, 'NCBI:SRA:GenericFastq:db', output)
schema = None
mgr = None
tbl = db.CreateTable('SEQUENCE')
db = None
curs = tbl.CreateCursor(OpenMode.Write)
tbl = None
cols = {}
for name, define in cursDef.items():
cols[name] = curs.AddColumn(define['expression'])
curs.Open()
for col in cols.values():
col._update()
for name, define in cursDef.items():
if 'default' in define:
cols[name].set_default(define['default'])
def writeTestData(name:str):
curs.OpenRow()
cols['NAME'].write(name)
type = ''
length = ''
good = ''
if name.startswith('good'):
cols['READ_FILTER'].write([ 0, 0 ])
name = name[4:]
else:
cols['READ_FILTER'].write([ 1, 1 ])
name = name[3:]
if name.startswith('good'):
good = True
name = name[4:]
else:
good = False
name = name[3:]
if name.startswith('lq'):
type = 'low'
length = int(name[2:])
elif name.startswith('f'):
type = 'front'
length = int(name[1:])
elif name.startswith('b'):
type = 'back'
length = int(name[1:])
else:
type = 'good'
length = int(name)
cols['READ_START'].write([0, length])
cols['READ_LEN'].write([length, length])
cols['READ'].write(randomRead(length) + randomRead(length))
cols['QUALITY'].write(randomQuality(length, type, good) + randomQuality(length, type, good))
curs.CommitRow()
curs.CloseRow()
return True
good = all(map(writeTestData, [
'goodgood75' ,
'goodgood50' ,
'goodgoodlq75',
'goodgoodlq50',
'goodgoodf75' ,
'goodgoodf50' ,
'goodgoodb75' ,
'goodgoodb50' ,
'goodbadlq75' ,
'goodbadlq50' ,
'goodbadf75' ,
'goodbadf50' ,
'goodbadb75' ,
'goodbadb50' ,
'badgood75' ,
'badgood50' ,
'badgoodlq75' ,
'badgoodlq50' ,
'badgoodf75' ,
'badgoodf50' ,
'badgoodb75' ,
'badgoodb50' ,
'badbadlq75' ,
'badbadlq50' ,
'badbadf75' ,
'badbadf50' ,
'badbadb75' ,
'badbadb50' ,
]))
cols = None
curs.Commit()
curs = None
assert good
print(f'info: successfully generated test data to \'{output}\'')
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