def run(args):
logging.basicConfig(level=logging.DEBUG)
db_filename=args.translator
t_name,t_ext=splitext(args.translator)
'''
test if it is db file
generate db file if it doesn't exists.
'''
if t_ext!="db":
#possible_db=args.translator.strip("\\.gz")+".db"
possible_db=args.translator+".db"
print(possible_db)
if os.path.exists(possible_db):
db_filename=possible_db
else:
_generate_db(args.translator,possible_db,args.table_name)
db_filename=possible_db
'''
query db file
'''
out=IO.fopen(args.output,"w")
with sqlite3.connect(db_filename) as conn:
conn.row_factory=lambda conn,x: Bed12._make(Bed12._types(x[1:]))
cursor=conn.cursor()
for i in TableIO.parse(IO.fopen(args.input,"r"),"bed"):
s=template.substitute({"table_name":args.table_name,"name":i.chr.strip()})
print(s)
cursor.execute(s)
gene=None
try:
gene=cursor.fetchone()
logging.debug(i)
logging.debug(i.cdna_length())
logging.debug(gene)
logging.debug(gene.cdna_length())
except:
raise
logging.warning("can't find gene %s"%i.chr)
continue
assert gene.cdna_length() > i.cdna_length()
print(reverse_translate(gene,i),file=out)
def iterate(fin):
buf = fin.next()
x = buf.split("\t")[1:]
qr = BED12._make(BED12._types(x))
hits = []
overlap = []
i = 0
for x in TableIO.parse(fin):
if x[0] == "QR":
if i % 100 == 0:
logging.info("processing " + str(i) + " genes")
i += 1
yield qr, hits, overlap
qr = BED12._make(BED12._types(x[1:]))
hits = []
overlap = []
elif x[0] == "HT":
hits.append(BED12._make(BED12._types(x[1:])))
elif x[0] == "OP":
overlap.append(BED12._make(BED12._types(x[1:])))
yield qr, hits, overlap
""")
bed3_insert_template=string.Template("""insert into $table_name (chr,start,stop)
values (?,?,?)
""")
schema_templates={
"bed12":bed12_schema_template,
"bed6":bed6_schema_template,
"bed3":bed3_schema_template,
}
insert_templates={
"bed12":bed12_insert_template,
"bed6":bed6_insert_template,
"bed3":bed3_insert_template,
}
factories = {
"bed12":lambda c,r:BED12._make(BED12._types(r[1:])),
"bed6":lambda c,r:BED6._make(BED6._types(r[1:])),
"bed3":lambda c,r:BED3._make(BED3._types(r[1:])),
}
select_template=string.Template("""select * from $table_name where name=\"$name\"""")