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moved schema material to worldbase2.rst tutorial
2009-09-04
Chri
s
toph
e
r
Lee
moved s
c
hema mate
r
ial to worldb
a
s
e2
.
rst
t
utorial
commit
|
commitdiff
|
tree
2009-09-03
Christophe
r
Lee
added
w
orldbase security warni
n
g
commit
|
commitdiff
|
tree
2009-09-03
Christopher Le
e
mor
e
rev
i
sion
s
ab
o
ut downloading tut
o
rial
commit
|
commitdiff
|
tree
2009-09-03
Chri
s
topher Lee
r
e
v
isions to
downl
o
ad=Tr
u
e sect
i
o
n
commit
|
commitdiff
|
tree
2009-09-03
C
h
ristopher L
e
e
adde
d
d
e
pe
n
d
e
n
c
y
sectio
n
in worldbase
.
rst tu
t
orial
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istop
h
e
r Lee
added worldbase
.
dir() tut
o
ria
l
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
opher Lee
added i
n
tro section
t
o worldbase
.
r
s
t
t
uto
r
ia
l
commit
|
commitdiff
|
tree
2009-09-03
C
h
r
i
s
topher
Lee
added Purpose to alignment
.
r
s
t
commit
|
commitdiff
|
tree
2009-09-03
C
h
r
istopher Lee
more little
change
s
to annotati
o
n
2
.
r
st
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er Lee
adde
d
Purpose and intro t
o
annotations2
.
r
st
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istopher
Lee
m
oved new
b
a
si
c
tut
o
rials to top of guide
l
ist
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
o
p
her Lee
minor fix to db_basic
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er Le
e
upda
t
e
s
to reference/sq
l
gr
a
ph
.
rst docs
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istopher Lee
added SQL
sa
v
ing s
e
ction to db
tu
t
o
r
ial
commit
|
commitdiff
|
tree
2009-09-03
C
h
r
is
t
o
p
h
e
r
Lee
basic da
t
abase tutorial
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istopher Lee
add
e
d back __l
e
n__() to
S
QLT
a
bleBase
.
How
i
n heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istopher Lee
add
e
d sect
i
on on Pre
f
ixUnionDict
commit
|
commitdiff
|
tree
2009-09-02
Chris
t
o
p
her Lee
added section o
n
p
lug
g
i
ng in
y
our o
w
n
s
equence
p
arser
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristopher Lee
move
d
old material out to c
o
mp
g
eno
m
ics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
som
e
minor
sequence tu
t
orial
r
evisions
commit
|
commitdiff
|
tree
2009-09-02
C
h
r
i
s
topher
Le
e
a
d
d
e
d tutorial sect
i
o
n
on accessing sequence d
a
t
a
base
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
split up bullet points to integrate into th
e
code
e
xample
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
stopher L
e
e
r
e
vi
s
ed sequence tutorial intro (
f
irst part)
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
Merge commi
t
'remotes/
c
tb/
x
mlrpc
_
tutorial' into t
u
t
or
i
al
commit
|
commitdiff
|
tree
2009-09-02
Christopher
Lee
Me
r
ge commit 'remote
s
/
c
t
b/doc_alignmen
t
' in
t
o
t
uto
r
ial
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
r
evised gff3
co
d
e
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher Lee
a
dded GF
F
3 example of gen
e
building
commit
|
commitdiff
|
tree
2009-09-01
Christ
o
phe
r
Lee
Merge commit 'r
e
m
otes/
m
kszu
b
a
/xmlrpc_tutorial' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Chris
t
op
h
e
r Lee
Merge commit 'remotes/c
t
b/
d
oc_annotations' into tutorial
commit
|
commitdiff
|
tree
2009-09-01
Christ
o
pher Lee
extrac
t
ed
m
aterial f
o
r separ
a
te
database tutoria
l
commit
|
commitdiff
|
tree
2009-08-29
Christoph
e
r Lee
remov
e
d unnecess
a
ry
sta
t
and shutil import from setup
.
p
y
commit
|
commitdiff
|
tree
2009-08-14
Christo
p
h
e
r Lee
fixed easy_install bug
b
y protecting
coordinator
.
ResourceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
hri
s
t
opher Lee
f
i
xed b
l
a
s
t
_test: renamed tes
t
_
s
eq_wi
t
hout_db(
)
to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christop
h
er Lee
Merg
e
commit 'rem
o
t
es/ctb/
m
in
o
r_f
i
x
e
s
'
into minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
Chri
s
t
o
p
h
er
Lee
fix
port passing
i
n
testutil
.
TestXMLRPCServe
r
commit
|
commitdiff
|
tree
2009-08-04
Christoph
e
r Lee
u
s
e p
a
ir_identity_tuple() for blast_test formatting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
ist
o
pher Le
e
add
e
d BlastBase
.
tea
r
Down() to
close seqdbs as
t
h
e
y
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
i
s
t
o
p
h
er Lee
Merge commit 'remotes/mkszuba/doc_make'
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Merge
c
ommit
'r
e
motes/mkszu
b
a
/rpm'
commit
|
commitdiff
|
tree
2009-07-29
C
hristo
p
her Lee
g
o
t rid of BlastMapping
.
war
n
_about_sel
f
_matc
h
es()
commit
|
commitdiff
|
tree
2009-07-29
Christo
p
her Lee
c
hanged NLMSA pairwiseMod
e
to allow rep
o
rting of sel
f
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Ch
r
ist
o
pher Lee
M
e
rge comm
i
t 'remotes/mkszuba/debian'
commit
|
commitdiff
|
tree
2009-07-29
Christop
h
er Le
e
retry
r
ead
i
ng
p
ort_file in T
e
s
t
X
M
LRPCServer several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Chr
i
st
o
pher Lee
added comments to pro
c
ess_bla
s
t(
)
commit
|
commitdiff
|
tree
2009-07-29
Christo
p
her Lee
fix problem introduced i
n
pro
c
ess_
b
l
a
s
t
()
b
y
commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
hristo
p
her Lee
h
andl
e
mi
s
sing W
I
NDIR
case on Windo
w
s
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
adde
d
SeqTra
n
slator
.
__
r
e
pr__(
)
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristoph
e
r Lee
Mer
g
e
com
m
it 'remotes/c
t
b/si
m
pleframe_formatd
b
_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
hristophe
r
L
ee
Merge branch 'mast
e
r'
i
nto
s
i
m
pleframe
commit
|
commitdiff
|
tree
2009-07-28
Chris
t
opher Lee
added SeqTranslator
.
i
t
er_fram
e
s(
)
met
h
od, used in BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christop
h
er Lee
Merge commit '
r
emotes/ctb/simplefram
e
_d
o
c_al
i
gn
'
into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher
L
ee
protect 2 m
o
r
e
tests using
b
last_enabled()
check
commit
|
commitdiff
|
tree
2009-07-27
Christophe
r
Lee
fixed syntax erro
r
commit
|
commitdiff
|
tree
2009-07-27
C
hrist
o
pher Lee
adde
d
python 2
.
3
code
f
or FilePopen to det
e
ct bad e
x
it
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
Me
r
ge branch 'no_edge_db
'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
Merge
b
ranch
'silencio'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
added showFormatdbMessages
o
p
t
ion
t
o BlastMapping
commit
|
commitdiff
|
tree
2009-07-25
Christopher Le
e
added support for no-edgeDB case in mapping
.
G
r
aph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Chris
t
opher Le
e
a
d
ded option
for lat
e
x out
p
ut of t
h
e refere
n
ce manu
a
l
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
Merge commit 'remote
s
/
c
tb/bla
s
t
_
t
e
st
_
rc' into s
i
m
p
leframe
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristop
h
er Lee
added more docst
r
ings for blast
.
p
y
commit
|
commitdiff
|
tree
2009-07-16
C
hristopher
Lee
rem
o
v
ed
old BlastxMapping co
d
e
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
new, greatly simplified Bla
s
txMapping
commit
|
commitdiff
|
tree
2009-07-16
Christopher
Lee
switched test_bla
s
t
x_se
r
ver to use new Translat
i
o
n
DB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
i
stopher Lee
added read_b
l
ast_ali
g
n
m
e
n
t
() translateDe
s
t option
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher Lee
added N
L
MSA
.
e
d
ges
(
) method
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
i
stoph
e
r Lee
switc
h
ed test_tblastn_
p
arser to use new Tra
n
slationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher L
e
e
swit
c
h tblastn to use n
e
w TranslationDB appro
a
c
h
commit
|
commitdiff
|
tree
2009-07-15
Christopher
Lee
a
d
ded
t
r
a
n
s
lationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christo
p
h
e
r
L
e
e
move
d
dbname default into
g
e
t
_
bound_subclass()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
make CoordsToIntervals / get_int
e
rval() use
s
e
q
.
absol
u
te_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
p
he
r
Lee
cleane
d
up
SeqPath
.
cl
a
ssySlice()
commit
|
commitdiff
|
tree
2009-07-15
Christopher L
e
e
Merg
e
commit
'
re
m
otes
/
mkszuba/nl
m
sa_no_verbose
'
i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
hr
i
stopher Lee
Mer
g
e commit 'remo
t
es/
m
k
szuba
/
cnestedlist_no
t
i
c
e' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher L
e
e
inc
o
m
plete new code for TranslationDB
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
oph
e
r
Lee
cleaned up
reversePa
t
h con
s
tr
u
cti
o
n
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher L
e
e
add ab
s
o
l
ute_
s
l
i
ce
(
) method to Seq
P
ath
commit
|
commitdiff
|
tree
2009-07-14
Chris
t
opher L
e
e
Merge commit 'remotes/mkszuba/cnestedlist_l
o
gger' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christo
p
her Lee
Merge branch
'master' int
o
m
egatests
commit
|
commitdiff
|
tree
2009-07-03
Ch
r
istophe
r
Lee
Merg
e
branch 'format
d
b
_fail'
commit
|
commitdiff
|
tree
2009-07-03
Christ
o
pher
L
e
e
i
mprov
e
d whitespace
p
ath warning
commit
|
commitdiff
|
tree
2009-07-03
Ch
r
ist
o
pher Lee
added warnin
g
for whitespace in path
commit
|
commitdiff
|
tree
2009-07-01
C
hristophe
r
Lee
Me
r
ge commit
'
re
m
otes/
m
kszuba/mega
t
e
s
ts'
commit
|
commitdiff
|
tree
2009-07-01
Christophe
r
Lee
use glob
.
glob() ins
t
ea
d
of os
.
listdir(); clea
n
ed
u
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
C
hr
i
s
t
opher Le
e
M
erge c
o
m
m
it '
r
emotes/mkszuba/mimetext'
commit
|
commitdiff
|
tree
2009-07-01
Christo
p
her
L
ee
Merge commit
'
remotes/mkszub
a
/docfixes'
commit
|
commitdiff
|
tree
2009-07-01
C
h
r
istopher Lee
Merge
c
om
m
i
t
'remotes/mkszuba/has
h
lib'
commit
|
commitdiff
|
tree
2009-06-26
Chris
t
opher L
e
e
fixed
c
achi
n
g bug
int
r
oduced in c
o
mmit 8d9966 in
PrefixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Chr
i
s
topher
Lee
d
e
preca
t
ed
c
ursor a
r
gument to S
Q
LTab
l
e
commit
|
commitdiff
|
tree
2009-06-20
Chris
t
oph
e
r Le
e
fix
e
d issue 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher L
e
e
added test for is
s
ue 99
commit
|
commitdiff
|
tree
2009-06-20
Ch
r
istopher Lee
c
l
eaned
u
p
SQLiteServerInfo
commit
|
commitdiff
|
tree
2009-06-20
Ch
r
istopher Lee
added DBServerInfo
.
new_
c
u
r
s
o
r
(
)
metho
d
commit
|
commitdiff
|
tree
2009-06-13
Christoph
e
r
Lee
Merge
c
ommit
'
r
emot
e
s/mkszuba/issue97_tes
t
' into issue97_t
e
st
commit
|
commitdiff
|
tree
2009-06-13
Christopher Lee
re
m
oved
r
e
d
u
ndant
a
n
d
b
uggy rstrip("
.
py") ca
l
l f
r
o
m
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Christo
p
her
L
ee
fix pyrex
c
def
commit
|
commitdiff
|
tree
2009-06-12
Chr
i
sto
p
her Lee
fix issu
e
97
commit
|
commitdiff
|
tree
2009-06-12
C
h
rist
o
pher L
e
e
ra
i
s
e
d
minimum
i
dentity for rel
a
xed blast test
s
to 60%
commit
|
commitdiff
|
tree
2009-06-09
Christophe
r
L
e
e
replaced a few
rem
a
in
i
ng refs in the docs
to
pygr
.
Data
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
istopher
L
ee
M
e
rge
c
ommit 're
m
o
te
s
/mksz
u
ba/deb
'
commit
|
commitdiff
|
tree
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