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moved schema material to worldbase2.rst tutorial
2009-09-04
Ch
r
i
stopher Lee
moved
schema material
t
o w
o
rldbase2
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
C
h
ri
s
tophe
r
Le
e
a
d
ded wo
r
l
dbase securi
t
y warn
i
ng
commit
|
commitdiff
|
tree
2009-09-03
C
h
rist
o
pher Lee
m
o
re revisions
about downloading tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher L
e
e
r
e
v
i
s
ions to dow
n
l
o
ad=True secti
o
n
commit
|
commitdiff
|
tree
2009-09-03
C
h
ri
s
top
h
er Lee
a
dded d
e
pendency section in worldbase
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istopher Lee
added world
b
ase
.
dir
(
)
tutorial
commit
|
commitdiff
|
tree
2009-09-03
C
h
ris
t
opher Lee
added
intr
o
secti
o
n to
w
orldbase
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
C
hristopher Le
e
added Purpose to alignment
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
mo
r
e li
t
tle changes to
annotation2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christopher
Lee
added Pu
r
pose and intro to
a
nnotati
o
ns2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istopher Lee
m
oved new b
a
s
ic tutorials to top of guide
list
commit
|
commitdiff
|
tree
2009-09-03
Christopher
Lee
minor fix to d
b
_basic
.
rst
commit
|
commitdiff
|
tree
2009-09-03
C
hristopher L
e
e
u
p
dates to reference/sq
l
g
raph
.
r
st d
o
cs
commit
|
commitdiff
|
tree
2009-09-03
Christ
o
pher L
e
e
adde
d
SQL sav
i
ng section to db t
u
to
r
ial
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stopher Lee
basic da
t
ab
a
se tutor
i
al
commit
|
commitdiff
|
tree
2009-09-03
Christopher
Lee
a
d
ded back __len__() to SQLTableBase
.
How
i
n hec
k
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Christoph
e
r Le
e
a
dded section on PrefixUnionDict
commit
|
commitdiff
|
tree
2009-09-02
C
h
r
i
stoph
e
r L
e
e
added se
c
ti
o
n on plugging in your own sequence parser
commit
|
commitdiff
|
tree
2009-09-02
Christopher
L
ee
moved old material out
t
o compgenomics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
C
hr
i
stopher Lee
some minor sequence tutorial revis
i
ons
commit
|
commitdiff
|
tree
2009-09-02
C
hr
i
stopher
Lee
added tut
o
ria
l
section on acce
s
si
n
g sequen
c
e database
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
split up bulle
t
point
s
to integrate
i
n
t
o the c
o
de
e
xam
p
l
e
commit
|
commitdiff
|
tree
2009-09-02
Chri
s
topher
Lee
re
v
i
sed sequence tutorial intro (first part)
commit
|
commitdiff
|
tree
2009-09-02
Christopher
Lee
Mer
g
e commit 'remotes/c
t
b/xmlrpc_tutoria
l
'
i
nto
tutorial
commit
|
commitdiff
|
tree
2009-09-02
C
hristopher Lee
M
erge com
m
it 'remotes
/
c
t
b/d
o
c_alignm
e
nt' into tutori
a
l
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
revised
gff3 code
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er L
e
e
adde
d
GFF3 example of
gene b
u
i
l
di
n
g
commit
|
commitdiff
|
tree
2009-09-01
Christopher Lee
Merge com
m
it 'r
e
motes
/
mkszub
a
/xmlrpc_tutorial' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
C
h
r
i
s
toph
e
r L
e
e
Merge com
m
it 'remotes/ctb/doc_annotations' int
o
t
utoria
l
commit
|
commitdiff
|
tree
2009-09-01
Christopher Lee
extr
a
cted material
f
or sep
a
rat
e
database tuto
r
ia
l
commit
|
commitdiff
|
tree
2009-08-29
Ch
r
i
s
t
o
pher Lee
removed unneces
s
a
r
y stat and shutil imp
o
r
t from setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
Chr
i
stopher
L
e
e
fixed ea
s
y_ins
t
all bug by protect
i
ng co
o
rdi
n
a
tor
.
Resou
r
ceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chris
t
o
pher L
e
e
fixed bla
s
t_
t
est: rename
d
test_
s
eq_without_db()
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
hristop
h
er
Lee
Merge commit 'r
e
mot
e
s/c
t
b/m
i
no
r
_fi
x
es' into min
o
r_fixes
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
fix port p
a
ssing in testutil
.
TestXM
L
RPCS
e
rver
commit
|
commitdiff
|
tree
2009-08-04
Christop
h
er
L
ee
use pair_i
d
entity_t
u
ple() for
b
la
s
t
_
test formatting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christ
o
pher Lee
added BlastBase
.
t
e
arD
o
w
n
() to cl
o
se se
q
d
b
s
as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
M
erge commit
'
re
m
o
tes/mkszuba
/
doc
_
m
ake'
commit
|
commitdiff
|
tree
2009-08-04
C
h
risto
p
her Le
e
Merge
c
o
m
m
it 'remote
s
/mkszuba/rp
m
'
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
got
r
i
d
of BlastMapp
i
n
g
.
warn_about_self_matche
s
()
commit
|
commitdiff
|
tree
2009-07-29
C
hri
s
topher
L
ee
changed NLMSA pairwiseMode t
o
allow reporting o
f
self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
Merge comm
i
t 'r
e
mo
t
es/mkszuba/debian'
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
re
t
ry reading port_file in Test
X
MLRPCS
e
rver several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
C
hristophe
r
Lee
a
d
ded comments to
p
rocess
_
blast()
commit
|
commitdiff
|
tree
2009-07-29
Christoph
e
r Lee
fix problem introduced i
n
process
_
blast() by commi
t
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Chr
i
stopher Lee
handl
e
missing WIND
I
R case on Windows
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
add
e
d
S
eqTra
n
slat
o
r
.
__repr__(
)
commit
|
commitdiff
|
tree
2009-07-28
C
hristopher
L
ee
Merge commit 'remotes/ctb/
s
impleframe_formatdb_clea
n
up
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christo
p
he
r
Lee
Merge bran
c
h 'mast
e
r' into si
m
p
l
eframe
commit
|
commitdiff
|
tree
2009-07-28
Christophe
r
L
e
e
a
d
ded SeqTransla
t
or
.
iter_frames() method, u
s
ed in BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christo
p
her Lee
M
erge commi
t
'remotes/c
t
b/simpleframe_doc_align
'
into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher
L
e
e
p
r
o
tect
2
more t
e
s
t
s using blas
t
_enabled()
c
h
e
ck
commit
|
commitdiff
|
tree
2009-07-27
Christo
p
h
e
r
Lee
fixed
syntax error
commit
|
commitdiff
|
tree
2009-07-27
Chri
s
toph
e
r Le
e
a
d
d
ed
pyt
h
on 2
.
3 code fo
r
FilePo
p
en to detec
t
bad exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
st
o
pher Lee
Mer
g
e branch 'no_edge_db'
commit
|
commitdiff
|
tree
2009-07-27
Christop
h
er
Lee
Merge branch '
s
ilencio'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
ad
d
e
d
showFormatdbMessages o
p
tion to Bl
a
stMappi
n
g
commit
|
commitdiff
|
tree
2009-07-25
C
hristopher Lee
added sup
p
ort for no-edgeDB
c
ase i
n
mapp
i
ng
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christopher Lee
a
dd
e
d opti
o
n for l
a
te
x
o
utput of the re
f
e
r
ence
m
anual
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
her Lee
M
e
rge comm
i
t
'remot
e
s
/ct
b
/
b
la
s
t_
t
est_rc
'
into simple
f
rame
commit
|
commitdiff
|
tree
2009-07-16
Christopher L
e
e
a
dde
d
more docstr
i
ngs for blast
.
py
commit
|
commitdiff
|
tree
2009-07-16
Christopher Le
e
r
e
m
o
ved old BlastxMapping c
o
de
commit
|
commitdiff
|
tree
2009-07-16
C
h
r
istopher Lee
n
e
w, greatly simpl
i
fied Blas
t
xMappin
g
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
sto
p
her Lee
sw
i
tched test_bl
a
stx_
s
e
rver
t
o use new Tran
s
lationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christop
h
er
Lee
added read_bla
s
t_ali
g
nment() translateDest op
t
ion
commit
|
commitdiff
|
tree
2009-07-16
Christopher
L
ee
ad
d
ed NLMS
A
.
edges() method
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
i
stopher Lee
s
w
itche
d
test_
t
blastn_pa
r
ser to use new Transl
a
tion
D
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
to
p
h
e
r
Lee
switch tblastn to
u
s
e new TranslationDB appr
o
ach
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
sto
p
her Le
e
added trans
l
ationD
B
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christo
p
h
e
r
Lee
mov
e
d dbname def
a
ult into g
e
t_bound_subcl
a
ss()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
ma
k
e
CoordsToInt
e
rvals / get_interval(
)
us
e
seq
.
absolute_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher Lee
cleaned up
S
eqPath
.
cl
a
ssySlice()
commit
|
commitdiff
|
tree
2009-07-15
C
h
ris
t
op
h
er L
e
e
Merge c
o
m
mit 'remotes
/
mkszu
b
a/nlmsa_n
o
_
verb
o
s
e' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
Merge commit 'remotes/mkszub
a
/c
n
est
e
dlist_notice
'
into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
i
n
c
omplete
n
ew c
o
de for TranslationDB
commit
|
commitdiff
|
tree
2009-07-15
Christopher Le
e
c
l
eaned up
re
v
ersePath constructio
n
commit
|
commitdiff
|
tree
2009-07-15
C
hrist
o
pher Lee
add absolute_slice() method to Se
q
Pa
t
h
commit
|
commitdiff
|
tree
2009-07-14
C
h
ristopher
L
ee
M
erge commit
'remotes/mkszub
a
/cnestedlist_l
o
gger' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christopher
L
e
e
Merg
e
branch 'ma
s
ter
'
into megatests
commit
|
commitdiff
|
tree
2009-07-03
Ch
r
istopher Lee
Merge branc
h
'formatdb_fa
i
l'
commit
|
commitdiff
|
tree
2009-07-03
C
h
ris
t
opher L
e
e
imp
r
oved
whites
p
a
ce pa
t
h warn
i
ng
commit
|
commitdiff
|
tree
2009-07-03
Christo
p
her
L
ee
added w
a
r
ning fo
r
whitespace in pa
t
h
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
Merg
e
co
m
mit 'remot
e
s/mkszuba/megatests'
commit
|
commitdiff
|
tree
2009-07-01
Christoph
e
r L
e
e
use glob
.
glob
(
)
i
n
stead of
os
.
listdir(); cl
e
aned u
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Chri
s
tophe
r
Le
e
Merge commit 'remot
e
s/mkszuba/mi
m
etex
t
'
commit
|
commitdiff
|
tree
2009-07-01
C
hristo
p
her Lee
Merge com
m
it 'remotes/mkszuba/docfixes'
commit
|
commitdiff
|
tree
2009-07-01
C
hristophe
r
Lee
Merge com
m
i
t
'
remotes
/
mkszuba/hashlib'
commit
|
commitdiff
|
tree
2009-06-26
Ch
r
ist
o
pher L
e
e
f
ixed
cachin
g
b
ug introdu
c
ed in commit 8d9966
i
n
PrefixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
C
hristophe
r
Lee
depr
e
cated cu
r
sor
a
r
gument to S
Q
LTable
commit
|
commitdiff
|
tree
2009-06-20
Christo
p
her Lee
fixed iss
u
e 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
added
test for iss
u
e 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
cleaned up SQLiteServe
r
Inf
o
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
added D
B
S
erver
I
n
f
o
.
new_c
u
rs
o
r
() method
commit
|
commitdiff
|
tree
2009-06-13
Chri
s
topher
L
ee
M
e
r
ge commit 'remotes/
m
kszuba/issue
9
7_tes
t
' into
i
ssue97
_
test
commit
|
commitdiff
|
tree
2009-06-13
Christopher
Lee
removed
redundant and bug
g
y rstrip
(
"
.
py") call from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Chri
s
toph
e
r Lee
fix issue97
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
raised
m
inimum identity for relaxed bl
a
st tests to 60%
commit
|
commitdiff
|
tree
2009-06-09
Chri
s
t
opher Lee
replace
d
a few remaini
n
g ref
s
in the
docs to p
y
gr
.
Data
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Christop
h
er Lee
Merge commit 'remotes/
m
kszub
a
/deb'
commit
|
commitdiff
|
tree
2009-06-09
Chr
i
stopher Lee
Merge c
o
m
mit '
r
e
motes
/
m
kszuba/rena
m
es'
commit
|
commitdiff
|
tree
next