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basic database tutorial
2009-09-03
Chri
s
topher
Lee
basic d
a
tabase tutorial
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
opher Lee
a
d
ded
back __l
e
n__() to SQLTableBa
s
e
.
How in heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
i
s
t
oph
e
r
L
ee
added section on Prefix
U
nionDict
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristoph
e
r Lee
added section on plugging in
yo
u
r o
w
n sequence
p
arser
commit
|
commitdiff
|
tree
2009-09-02
C
hrist
o
p
h
er Lee
moved
old mater
i
al out to compgeno
m
i
c
s
.
r
st
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristophe
r
Lee
so
m
e minor sequence tuto
r
i
al
r
evisions
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristopher Lee
added tut
o
rial
sec
t
ion on accessing s
e
quence data
b
ase
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
isto
p
her Lee
spl
i
t up bulle
t
p
oi
n
ts
to integrate int
o
th
e
cod
e
examp
l
e
commit
|
commitdiff
|
tree
2009-09-02
Christo
p
her Lee
revised sequen
c
e
t
utori
a
l int
r
o
(first pa
r
t)
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
Merge comm
i
t 'remotes/ctb/xm
l
rpc_tutorial
'
i
nto t
u
torial
commit
|
commitdiff
|
tree
2009-09-02
Christ
o
p
her Lee
M
er
g
e commit 'remotes/ctb/doc_a
l
i
g
nme
n
t' int
o
tutorial
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
revised
g
ff3 co
d
e
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher Lee
a
dded GFF3 example of gene buil
d
i
n
g
commit
|
commitdiff
|
tree
2009-09-01
Chris
t
o
p
her Lee
M
e
rge co
m
mit 'remot
e
s/mkszuba/x
m
lrpc_tut
o
r
ial' i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Christop
h
er
L
ee
Merge
commit '
r
e
mote
s
/ctb/doc_annotat
i
on
s
' i
n
to
t
utorial
commit
|
commitdiff
|
tree
2009-09-01
Christophe
r
Lee
ex
t
racted material for separate dat
a
base tuto
r
i
al
commit
|
commitdiff
|
tree
2009-08-29
Chr
i
stoph
e
r Lee
r
e
moved unnece
s
sary stat and shutil
import from setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
C
hristop
h
er L
e
e
fixed easy_ins
t
all bug
by p
r
otecting co
o
rdinator
.
ResourceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christ
o
pher
Lee
f
i
xed bl
a
st_test: renamed
test_seq_wi
t
h
o
u
t_
d
b
(
)
to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
istopher Le
e
Merge commi
t
'remotes/ctb/minor_fixes'
into minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
fix port passing in testutil
.
Test
X
MLRPCServer
commit
|
commitdiff
|
tree
2009-08-04
Christopher Le
e
use pair_identity_tupl
e
()
for blast
_
te
s
t
formatti
n
g
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
st
o
p
her Lee
ad
d
e
d
BlastBase
.
tearDown() to c
l
ose s
e
qdbs as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher
Lee
M
erge commit 'remotes/mksz
u
ba/doc_make'
commit
|
commitdiff
|
tree
2009-08-04
Chri
s
topher Lee
Mer
g
e
c
ommi
t
'r
e
mote
s
/mkszuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
C
h
rist
o
pher
L
e
e
got rid of Blast
M
apping
.
warn_about_sel
f
_m
a
t
c
hes()
commit
|
commitdiff
|
tree
2009-07-29
Chr
i
sto
p
her Lee
changed NL
M
SA pair
w
iseMode to allow reportin
g
o
f self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher
L
ee
Mer
g
e comm
i
t
're
m
otes/mksz
u
ba/debian'
commit
|
commitdiff
|
tree
2009-07-29
Christop
h
er Lee
retry reading port_file
i
n
TestXMLRPCServer sev
e
r
a
l
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher
Lee
added
comments to process_blast
(
)
commit
|
commitdiff
|
tree
2009-07-29
C
hristop
h
e
r Lee
f
i
x
pr
o
blem
i
ntroduced in
process_bla
s
t() by commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
ha
n
dle missing WINDIR case on Windows
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
istopher Lee
adde
d
SeqTrans
l
at
o
r
.
_
_repr__(
)
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
Me
r
ge comm
i
t 're
m
otes/ctb/simpleframe_formatdb_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
hristopher Lee
Mer
g
e branch 'master
'
into simpl
e
frame
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
a
d
de
d
S
eqTran
s
l
ator
.
iter_f
r
am
e
s() metho
d
,
used in BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Chris
t
opher Le
e
Merge commit
'remotes/ctb/s
i
mple
f
r
a
me_doc_align'
int
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher
Lee
protect
2
more tests using blast_enabled() check
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
istopher L
e
e
fixed
synta
x
error
commit
|
commitdiff
|
tree
2009-07-27
Chri
s
topher
L
ee
added pyth
o
n 2
.
3 code
f
or FilePo
p
en to detect bad exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher Lee
Merge b
r
anch 'no_edge_db'
commit
|
commitdiff
|
tree
2009-07-27
Chri
s
topher L
e
e
M
erge branch
'
sil
e
n
cio
'
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher Lee
added showFormatdbMessages
option
to
BlastMapping
commit
|
commitdiff
|
tree
2009-07-25
Ch
r
isto
p
her Lee
added sup
p
ort for
n
o-edgeDB c
a
se
i
n
mapping
.
Graph
:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
C
hristopher Lee
added o
p
t
ion for
l
atex out
p
ut
of the reference manual
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
isto
p
her Lee
M
e
rg
e
commit 'r
e
motes/ctb
/
b
l
ast_test_rc' into
s
impleframe
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
istopher Lee
adde
d
m
o
re docstri
n
gs for blast
.
py
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher Lee
remo
v
ed old Blast
x
Mappi
n
g cod
e
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher Lee
new, greatly simpl
i
f
i
ed Bl
a
stxMapping
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
pher
Lee
s
witched t
e
st
_
blastx_server to use new Trans
l
ationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r
Lee
a
dde
d
read_
b
la
s
t_alignment()
translateDest option
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
topher Lee
added NLMSA
.
edges() m
e
tho
d
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
switc
h
ed
t
est_tbl
a
s
t
n_
p
a
r
ser
to use new Transl
a
tionD
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
topher Lee
switch
t
blastn to use new T
r
anslat
i
o
nDB appro
a
ch
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
added t
r
a
n
s
l
ation
D
B
.
p
y
commit
|
commitdiff
|
tree
2009-07-15
Christopher L
e
e
m
o
ved d
b
name de
f
ault in
t
o
get_bound_subcla
s
s()
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
opher Lee
m
a
k
e
C
oords
T
o
I
nter
v
als / get_interval() use seq
.
absolute_s
l
i
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stopher
L
e
e
cleaned u
p
SeqPath
.
classySlice()
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stopher Le
e
Merge commit '
r
emot
e
s/mkszuba
/
nlms
a
_no_v
e
rbose'
into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Le
e
Merge commit
'
re
m
ote
s
/mkszuba/cnestedlist
_
notice' in
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
h
r
i
stop
h
er Lee
incomp
l
ete new c
o
de
f
or
T
ransla
t
ionDB
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
cleaned up revers
e
Path construction
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
istopher Lee
ad
d
abs
o
lut
e
_slice(
)
method to S
e
qPath
commit
|
commitdiff
|
tree
2009-07-14
Christo
p
her Lee
Merge comm
i
t 'remotes/mkszuba/cnes
t
edlist_logger' i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Chr
i
stopher Lee
Merge branch
'master' into megatests
commit
|
commitdiff
|
tree
2009-07-03
Christopher Lee
Merge
bra
n
ch
'
for
m
atdb_fai
l
'
commit
|
commitdiff
|
tree
2009-07-03
Christopher
Lee
improved whitespace path warni
n
g
commit
|
commitdiff
|
tree
2009-07-03
Christo
p
her Lee
added war
n
ing for whitespac
e
in path
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
M
e
rge commi
t
'r
e
mote
s
/mkszub
a
/me
g
atests'
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
use
glob
.
glob() inst
e
ad o
f
o
s
.
listdir(); cleaned up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christopher
Le
e
Merge commit
'
remotes/m
k
szuba/mimetext'
commit
|
commitdiff
|
tree
2009-07-01
Christo
p
her Lee
Mer
g
e commit
'
remotes
/
m
k
s
z
uba/docfixes'
commit
|
commitdiff
|
tree
2009-07-01
Christo
p
her
L
e
e
Merge
c
om
m
it 'r
e
motes/
m
kszuba/hashlib'
commit
|
commitdiff
|
tree
2009-06-26
C
h
ristopher Lee
fixed caching
b
u
g introduced in c
o
mmit 8
d
9966
i
n
P
r
efixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christoph
e
r
Lee
depre
c
ated cursor a
r
gum
e
nt
to
SQLTable
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
fixed iss
u
e 99
commit
|
commitdiff
|
tree
2009-06-20
C
h
r
istopher Lee
a
dded
test for issue 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
cleane
d
u
p
SQL
i
teServerInfo
commit
|
commitdiff
|
tree
2009-06-20
Christop
h
er L
e
e
a
d
ded
D
BServerInfo
.
n
e
w
_cursor() met
h
od
commit
|
commitdiff
|
tree
2009-06-13
Ch
r
istopher Lee
Me
r
ge commit
'
rem
o
tes/mkszuba/issu
e
9
7
_test' into issue
9
7_t
e
s
t
commit
|
commitdiff
|
tree
2009-06-13
Chr
i
stoph
e
r Lee
r
emo
v
ed redundant and b
u
ggy rstrip("
.
py") call from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
C
h
r
i
stopher Lee
fix
p
yrex cdef
commit
|
commitdiff
|
tree
2009-06-12
Chris
t
opher Lee
fix i
s
sue97
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
r
a
ised minimum ident
i
ty
f
o
r relaxed blast tes
t
s to 60%
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
ist
o
pher Lee
replaced a few r
e
maining refs in the docs to p
y
gr
.
Data
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
istop
h
er Lee
Merg
e
c
o
mmit 'remotes/mkszuba/deb
'
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
isto
p
her Lee
Mer
g
e commit 'remotes
/
mkszuba/renames'
commit
|
commitdiff
|
tree
2009-06-09
Christ
o
pher Lee
Merge b
r
a
nch
'
interval_filter
s
' into bla
s
t
_tests
commit
|
commitdiff
|
tree
2009-06-09
Christopher
L
e
e
r
e
laxed-tests
had a bug that made th
e
m pass the comparison
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
hri
s
t
o
pher Lee
must close Fi
l
ePop
e
n object
b
efore exiting BlastxMapping
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
h
ristop
h
er Lee
merge
d
in ct
b
/blas
t
x_dat
a
base
commit
|
commitdiff
|
tree
2009-06-04
Chris
t
op
h
er Lee
Merg
e
commit '
r
emotes/ctb/blastx_ge
n
erator' in
t
o ctb_tm
p
commit
|
commitdiff
|
tree
2009-06-04
Christophe
r
L
ee
PEP
8
and
whitespace
fixes
t
o nlmsa_ut
i
ls
.
py; no fun
c
t
ionalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christop
h
er Lee
converted add
_
aligned_intervals functionality
i
nt
o
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chris
t
o
pher L
e
e
clean up AttributeInterface
accordi
n
g to Titus sugge
s
tions
commit
|
commitdiff
|
tree
2009-06-04
Christopher
Lee
Merge commit
'
remote
s
/ctb/
c
tb_interv
a
ls' into interval
_
fi
l
ters
commit
|
commitdiff
|
tree
2009-06-03
Chris
t
opher
L
ee
Me
r
ge commit 'r
e
mote
s
/ctb/ct
b
_blast2' into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Chris
t
opher Lee
Merge
c
ommit
'rem
o
tes/ct
b
/mi
n
or_
d
oc_f
i
xes' into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
C
hristopher Lee
merged in
c
tb
/
annotat
i
on
commit
|
commitdiff
|
tree
2009-06-03
Chris
t
opher Lee
mer
g
ed
i
n ctb/blast_skip conf
l
ict
w
ith ctb/blast_ca
c
he
commit
|
commitdiff
|
tree
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