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moved schema material to worldbase2.rst tutorial
2009-09-04
C
h
risto
p
her Lee
move
d
schema materi
a
l
to w
o
rldbase2
.
rst tutori
a
l
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
o
p
her Lee
added worldbase security warning
commit
|
commitdiff
|
tree
2009-09-03
Christoph
e
r Lee
more rev
i
sions abou
t
downlo
a
di
n
g tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christophe
r
L
e
e
revisions to download=Tr
u
e secti
o
n
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
i
s
topher Lee
added dep
e
nde
n
c
y
se
c
t
ion in
w
o
rldbase
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
isto
p
h
er Lee
add
e
d worldbase
.
dir() tu
t
orial
commit
|
commitdiff
|
tree
2009-09-03
Christophe
r
Lee
added i
n
t
r
o section t
o
w
orld
b
as
e
.
r
st tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christ
o
p
h
er Lee
added Purpose to
a
lignment
.
r
st
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stopher Lee
more little c
h
anges t
o
annotation2
.
rs
t
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added P
u
rpose and i
n
tro to a
n
notations2
.
r
s
t
commit
|
commitdiff
|
tree
2009-09-03
Christopher
L
ee
moved new basic tutorial
s
to to
p
of guide
list
commit
|
commitdiff
|
tree
2009-09-03
Christophe
r
Lee
minor fix to db_basic
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
updates to
r
eference/sqlgraph
.
rst
d
ocs
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
o
pher Lee
added SQ
L
s
a
v
ing s
e
c
t
i
on to db tutoria
l
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er
L
e
e
basic database
tut
o
rial
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
i
s
tophe
r
Lee
adde
d
back __
l
en__() to SQLTa
b
l
eBase
.
How
i
n hec
k
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added s
e
ct
i
on on
PrefixUni
o
nDict
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
a
dded section on plu
g
ging
in your
o
wn s
e
quence parser
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
stopher Lee
moved old materia
l
ou
t
to compgenomics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher Lee
som
e
mi
n
or
s
e
q
u
ence t
u
torial revi
s
ions
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher
L
ee
added
tutori
a
l sec
t
ion
o
n acc
e
ssing
s
e
quence data
b
ase
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
e
r
Le
e
split up bullet
po
i
nts to i
n
t
egrate i
n
to the c
o
d
e example
commit
|
commitdiff
|
tree
2009-09-02
Chris
t
opher Lee
revise
d
sequence tutorial i
n
tro (first part)
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er
L
ee
Merge co
m
mit 'rem
o
tes/ctb/x
m
lrp
c
_tutorial' int
o
tut
o
rial
commit
|
commitdiff
|
tree
2009-09-02
C
h
r
i
stopher Lee
Merge commit 'remo
t
es
/
ctb/doc
_
alignment' into
tutorial
commit
|
commitdiff
|
tree
2009-09-02
C
hristopher Lee
revised
g
ff3 code
commit
|
commitdiff
|
tree
2009-09-02
C
hristo
p
her
Lee
ad
d
ed GFF3 examp
l
e of
g
ene
building
commit
|
commitdiff
|
tree
2009-09-01
Christoph
e
r Lee
M
e
r
g
e
c
ommit
'remotes/mkszuba/xmlrpc_tutori
a
l
'
int
o
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Christopher Le
e
Merge
com
m
it 'remotes/ctb/doc_ann
o
tation
s
'
into t
u
tor
i
a
l
commit
|
commitdiff
|
tree
2009-09-01
Ch
r
istopher Lee
e
xtracted materia
l
for separate d
a
ta
b
ase
tutoria
l
commit
|
commitdiff
|
tree
2009-08-29
C
hrist
o
p
h
e
r Lee
remove
d
unnecessary sta
t
and shutil i
m
po
r
t from setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
Christo
p
her L
e
e
f
i
xed easy_ins
t
a
l
l bug by protec
t
ing coordinator
.
Resour
c
eFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
istop
h
er Lee
fi
x
ed
b
last_test: rena
m
ed test_
s
e
q_
w
it
h
o
ut_db(
)
to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chris
t
opher Lee
Merge commi
t
'rem
o
t
e
s
/
ctb/m
i
nor_fix
e
s' into mi
n
o
r_fixes
commit
|
commitdiff
|
tree
2009-08-04
C
hristopher
L
ee
fix port pas
s
ing
in testuti
l
.
T
estXMLRPCSe
r
v
e
r
commit
|
commitdiff
|
tree
2009-08-04
C
hr
i
stopher
L
ee
us
e
pair_id
e
ntity_tuple() for blast_t
e
st
formattin
g
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christ
o
p
h
er Lee
added
Blas
t
Base
.
tearDown() to close seqdbs as
they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
r
i
stopher L
e
e
Merge commit 'remote
s
/
mkszuba
/
doc_mak
e
'
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
ist
o
pher Lee
M
erge
c
ommit
'
rem
o
tes
/
mkszuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
C
h
ristopher Lee
got rid of BlastMap
p
i
n
g
.
warn_ab
o
u
t
_self_matches()
commit
|
commitdiff
|
tree
2009-07-29
C
h
ristopher Lee
cha
n
ged NLMSA pairw
i
seMode to allow re
p
orting of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Chri
s
tophe
r
Lee
Me
r
ge
commit 'remo
t
es/mks
z
uba/deb
i
an'
commit
|
commitdiff
|
tree
2009-07-29
Chri
s
topher Le
e
retry rea
d
ing por
t
_fi
l
e
i
n
TestX
M
LRPCServer se
v
eral
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Ch
r
istopher Lee
added c
o
mm
e
nts
t
o
proc
e
ss_blast()
commit
|
commitdiff
|
tree
2009-07-29
Christophe
r
Lee
fix problem introduced in proc
e
ss_
b
last
(
) by
c
om
m
it
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christoph
e
r L
e
e
handle missing WINDIR cas
e
on Windows
commit
|
commitdiff
|
tree
2009-07-28
Christoph
e
r
Lee
add
e
d S
e
qTranslator
.
_
_repr__()
commit
|
commitdiff
|
tree
2009-07-28
Christophe
r
Lee
Merge commit 'r
e
motes/ctb/s
i
mp
l
efra
m
e_formatdb_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Chr
i
stophe
r
Lee
Merge b
r
anch 'master'
i
nto simpl
e
f
ra
m
e
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
add
e
d SeqTran
s
la
t
or
.
iter_f
r
ames()
meth
o
d,
u
sed in BlastxMap
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
hrist
o
pher Le
e
Merge commit 'remotes/ctb/simp
l
eframe_
d
oc
_
align' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher
L
ee
protect
2
more
t
ests using blast_
e
nable
d
() check
commit
|
commitdiff
|
tree
2009-07-27
Christopher
L
e
e
fixed
syntax error
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
added python 2
.
3 code for FilePopen to detect bad exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christoph
e
r Lee
Merge branch 'no
_
edge_db'
commit
|
commitdiff
|
tree
2009-07-27
C
h
r
istopher Lee
M
e
r
g
e branch 'silencio'
commit
|
commitdiff
|
tree
2009-07-27
Ch
r
istopher Lee
added showFormatdbMessages option to BlastM
a
pping
commit
|
commitdiff
|
tree
2009-07-25
Christophe
r
Lee
a
d
d
ed support for n
o
-edgeD
B
case in mapping
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christo
p
h
e
r Lee
add
e
d opt
i
on for l
a
tex output
of the
r
e
ference manual
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
Merge commit 're
m
o
t
es/ctb/blast_test_
r
c
' in
t
o simpl
e
frame
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
opher Lee
a
dde
d
m
o
r
e docstrings for blast
.
py
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher
Le
e
remov
e
d old Bl
a
stxMapping
c
o
de
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r Lee
new, greatly simplified BlastxMapping
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
ph
e
r Lee
switche
d
t
es
t
_blas
t
x_server to use new
T
r
a
ns
l
ationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
a
d
d
e
d read
_
blas
t
_
al
i
gnment() translateDest opt
i
on
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
t
o
pher
L
ee
added NL
M
SA
.
edges() method
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
her L
e
e
s
w
itched tes
t
_
t
blastn_pars
e
r to use new Translat
i
o
nDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
switch tblastn t
o
use
n
e
w Translat
i
on
D
B
a
pproach
commit
|
commitdiff
|
tree
2009-07-15
Christoph
e
r Lee
added translationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
s
t
op
h
er Le
e
mo
v
ed dbname default into
g
e
t_boun
d
_subclass()
commit
|
commitdiff
|
tree
2009-07-15
Christopher
L
ee
make Coo
r
dsToIntervals / g
e
t_int
e
r
v
al() use seq
.
absolute_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
cleaned up
S
e
qPath
.
classyS
l
ice()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
Me
r
ge commit '
r
em
o
tes/mk
s
zuba/
n
lmsa
_
n
o_ve
r
bos
e
' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher
Lee
Merge commit 're
m
otes/mkszuba/cnestedli
s
t_n
o
tice' in
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christo
p
her Lee
inc
o
mplete ne
w
code for Translatio
n
DB
commit
|
commitdiff
|
tree
2009-07-15
C
hri
s
topher Lee
c
l
eaned up reversePath construction
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
add a
b
solute_slice()
m
eth
o
d to SeqPath
commit
|
commitdiff
|
tree
2009-07-14
Chri
s
to
p
her Lee
Merge commit 'r
e
motes/mks
z
uba/cnestedlist_logger'
into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Chris
t
opher Lee
Merge branch 'master' into meg
a
tests
commit
|
commitdiff
|
tree
2009-07-03
Chri
s
top
h
e
r
Lee
M
e
rge branch 'format
d
b
_fail
'
commit
|
commitdiff
|
tree
2009-07-03
Christopher Lee
improved whitespace path
w
a
rning
commit
|
commitdiff
|
tree
2009-07-03
C
h
ristopher Le
e
added w
a
r
n
i
n
g for wh
i
tespace in path
commit
|
commitdiff
|
tree
2009-07-01
Christophe
r
Lee
Me
r
ge commit '
r
emotes/mksz
u
ba/meg
a
te
s
ts'
commit
|
commitdiff
|
tree
2009-07-01
C
hri
s
topher Lee
use glob
.
glob(
)
instead of
os
.
listdir(); cleane
d
up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
C
hristophe
r
Lee
Merge
c
o
m
mit '
r
em
o
t
es/mkszuba/
m
imetext
'
commit
|
commitdiff
|
tree
2009-07-01
Christopher
L
ee
Me
r
ge commit 'remotes
/
mkszub
a
/docfixe
s
'
commit
|
commitdiff
|
tree
2009-07-01
Christoph
e
r Lee
Me
r
g
e
c
o
mmit 'remo
t
es/mkszuba/h
a
s
h
lib'
commit
|
commitdiff
|
tree
2009-06-26
C
h
ristopher L
e
e
f
ixed ca
c
h
i
ng
bug i
n
trodu
c
ed in
c
omm
i
t
8
d9966 in Pre
f
ixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christopher
Lee
d
e
p
r
e
cated cu
r
sor argument
to SQLTabl
e
commit
|
commitdiff
|
tree
2009-06-20
C
h
ristopher Lee
f
ix
e
d issue
9
9
commit
|
commitdiff
|
tree
2009-06-20
C
hristopher Lee
added te
s
t for is
s
ue 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
cleaned up SQLiteServerInfo
commit
|
commitdiff
|
tree
2009-06-20
Chr
i
stoph
e
r Lee
a
d
ded DBSe
r
verInfo
.
new_cursor(
)
method
commit
|
commitdiff
|
tree
2009-06-13
Christophe
r
Lee
Mer
g
e
c
om
m
i
t
'remotes/mkszuba/issue97_test' into iss
u
e97_test
commit
|
commitdiff
|
tree
2009-06-13
C
h
ris
t
opher Lee
rem
o
v
e
d redundant a
n
d b
u
ggy rs
t
rip(
"
.
py") call from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
C
h
r
i
stopher
Lee
fix pyrex
c
de
f
commit
|
commitdiff
|
tree
2009-06-12
C
hristop
h
er
L
ee
fix
iss
u
e97
commit
|
commitdiff
|
tree
2009-06-12
C
h
rist
o
pher
L
e
e
r
a
ised minimum identity for
relaxe
d
blast tests t
o
60
%
commit
|
commitdiff
|
tree
2009-06-09
Chris
t
o
p
her Lee
r
epl
a
ced a few remaining
r
efs in the do
c
s to pygr
.
Da
t
a
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
Merg
e
commit 're
m
otes/
m
kszu
b
a/
d
eb'
commit
|
commitdiff
|
tree
next