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moved schema material to worldbase2.rst tutorial
2009-09-04
Christop
h
e
r
Lee
mov
e
d schema ma
t
erial
to worldbase2
.
rst
t
utor
i
al
commit
|
commitdiff
|
tree
2009-09-03
Christ
o
pher
L
ee
added worldb
a
se se
c
urity warni
n
g
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
stophe
r
Lee
more revisions about downloading
tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher
Lee
re
v
isi
o
n
s to download=True section
commit
|
commitdiff
|
tree
2009-09-03
C
hris
t
opher Le
e
adde
d
dependen
c
y section i
n
worldbas
e
.
rst tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher L
e
e
a
dded worldb
a
se
.
dir() tutoria
l
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
ad
d
ed intro section to worldb
a
s
e
.
rst tu
t
orial
commit
|
commitdiff
|
tree
2009-09-03
Chris
t
op
h
e
r Lee
added Purpose
t
o
a
lignmen
t
.
rst
commit
|
commitdiff
|
tree
2009-09-03
C
h
ristopher Lee
m
o
r
e little changes to a
n
nota
t
ion2
.
rst
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
istopher L
e
e
adde
d
Purpose and intro
to annotations2
.
r
st
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
is
t
opher L
e
e
moved new basic tutorials
t
o
top of guide lis
t
commit
|
commitdiff
|
tree
2009-09-03
C
h
ristopher Lee
minor
fix to db_basic
.
rst
commit
|
commitdiff
|
tree
2009-09-03
C
h
ristoph
e
r
Lee
up
d
ates
t
o refer
e
nce/
s
qlgrap
h
.
rst docs
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
adde
d
SQ
L
saving section to db tu
t
o
r
ia
l
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
basic databas
e
tuto
r
ial
commit
|
commitdiff
|
tree
2009-09-03
Christopher
Lee
added
b
ack _
_
l
e
n__() to SQLTableBase
.
How
in he
c
k
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
C
h
ris
t
opher L
e
e
added section on Prefix
U
nionDict
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
added sec
t
ion
o
n plug
g
ing in your
own sequence
p
a
r
ser
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
moved old mate
r
ial ou
t
to
c
ompgenomics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
Christoph
e
r Lee
so
m
e
mino
r
sequence tutorial revisions
commit
|
commitdiff
|
tree
2009-09-02
C
h
r
istopher Lee
added tutorial se
c
tion on ac
c
essi
n
g sequence databa
s
e
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
s
p
lit up
b
ul
l
et points to integrate into the code examp
l
e
commit
|
commitdiff
|
tree
2009-09-02
C
hristopher Lee
re
v
ised sequence tutoria
l
intro (first
part)
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher Lee
Merge commit 're
m
ot
e
s/ctb/x
m
lrpc_
t
uto
r
ial' int
o
tu
t
orial
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
s
t
opher Lee
Merge commi
t
'
remotes/ctb/doc_alignment' into tutori
a
l
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
is
t
ophe
r
Lee
revi
s
e
d gff3 code
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristopher Lee
add
e
d GFF3
e
xample
o
f gene build
i
ng
commit
|
commitdiff
|
tree
2009-09-01
C
hristopher Lee
Mer
g
e commi
t
'
r
emo
t
es/mkszuba/xm
l
rp
c
_tutorial' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Christopher Lee
M
e
r
ge commit 'r
e
motes
/
ctb/doc_annotat
i
ons' into tutorial
commit
|
commitdiff
|
tree
2009-09-01
Ch
r
i
s
topher Lee
extrac
t
ed
m
aterial f
o
r separate database
t
utorial
commit
|
commitdiff
|
tree
2009-08-29
Christop
h
er Lee
rem
o
ved un
n
e
c
e
s
sar
y
s
t
at an
d
sh
u
ti
l
impor
t
from setup
.
p
y
commit
|
commitdiff
|
tree
2009-08-14
Christo
p
her Lee
fixed eas
y
_install
b
u
g
by pr
o
t
ecting coord
i
nato
r
.
ResourceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chri
s
topher L
e
e
fixed
b
last_test: r
e
named test_seq_without_db() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
ristopher
Lee
Merge com
m
it 'remot
e
s
/
ctb/minor_fixes' int
o
minor_f
i
xes
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
sto
p
her Lee
fix
p
ort passing
in testut
i
l
.
TestXMLRPCServer
commit
|
commitdiff
|
tree
2009-08-04
Christopher
L
ee
use pair_identity_tuple
(
) for blast_test
f
ormatt
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christophe
r
L
e
e
added BlastBase
.
tearDown() to close seqdbs as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chri
s
topher Lee
Merge commit 'remotes/mkszu
b
a
/
doc_make'
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
istopher Lee
Merge com
m
it 'remotes/m
k
szuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
Christoph
e
r Lee
got rid of Bla
s
tMa
p
ping
.
war
n
_about_self_m
a
tches()
commit
|
commitdiff
|
tree
2009-07-29
Christo
p
her Lee
changed N
L
MS
A
pairwiseMode to allo
w
reporting of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Ch
r
istopher Lee
Merge commit 'rem
o
tes/
m
kszuba/debian'
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
r
et
r
y read
i
ng
port_file
in Te
s
tXMLRPCServer sev
e
ra
l
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher
Lee
added comme
n
ts to process_blast()
commit
|
commitdiff
|
tree
2009-07-29
C
h
r
i
stopher Le
e
fix p
r
oblem i
n
tr
o
duced
i
n process_b
l
a
st() by commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christoph
e
r Lee
ha
n
dle missing W
I
NDIR c
a
se
o
n Windows
commit
|
commitdiff
|
tree
2009-07-28
Chris
t
opher Lee
ad
d
ed SeqTransla
t
or
.
__
r
e
p
r__()
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
istophe
r
Lee
M
erg
e
c
o
mmit 'remotes/ctb/simpleframe_
f
or
m
atdb_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
isto
p
he
r
Lee
M
e
rge
b
r
a
nch 'm
a
ster' in
t
o simplef
r
a
m
e
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
istopher Lee
a
d
ded Seq
T
ranslator
.
i
t
e
r_frames() method, used in BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher
L
ee
Merge commit 'remotes/ctb/s
i
mpleframe
_
doc_align' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christo
p
h
e
r Lee
prote
c
t 2 more te
s
ts using bla
s
t_
e
na
b
le
d
()
c
heck
commit
|
commitdiff
|
tree
2009-07-27
Christopher L
e
e
fixed s
y
ntax
e
rror
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
a
dded p
y
thon 2
.
3 code for File
P
open to
detect
bad exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
C
hristopher Lee
M
erg
e
branch
'
no_
e
dge_db'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
Me
r
ge branch
's
i
lencio'
commit
|
commitdiff
|
tree
2009-07-27
C
h
ristopher L
e
e
a
dded s
h
owFo
r
matdbMe
s
sages op
t
ion to BlastMapping
commit
|
commitdiff
|
tree
2009-07-25
Christop
h
er Lee
a
d
d
ed support
for no-edgeDB c
a
se in map
p
ing
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
C
h
rist
o
pher Lee
added option for la
t
e
x
out
p
ut of the r
e
ference manu
a
l
commit
|
commitdiff
|
tree
2009-07-16
Christop
h
er Lee
Me
r
ge
co
m
mit 'remot
e
s/ctb
/
blast_test_rc' in
t
o simpleframe
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
her Lee
ad
d
ed more docstri
n
gs
for
blast
.
p
y
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
opher Le
e
remove
d
old Bla
s
txMapping code
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
topher Lee
new, greatly si
m
plified
B
l
a
stxMapp
i
ng
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
istopher
L
e
e
switched test_blastx
_
server to use new Tr
a
nslationD
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
her Lee
a
d
ded read_blast_ali
g
nment() tr
a
nslat
e
Dest option
commit
|
commitdiff
|
tree
2009-07-16
Christophe
r
L
ee
added
NLMSA
.
e
d
g
es() met
h
od
commit
|
commitdiff
|
tree
2009-07-16
C
h
r
istophe
r
L
ee
s
w
itche
d
t
e
st_tblastn_parse
r
to use new Translat
i
o
n
DB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
s
witch tblastn
t
o use new Trans
l
ationDB
a
ppro
a
ch
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stopher Lee
a
d
ded translationD
B
.
py
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stopher Lee
m
oved dbna
m
e default in
t
o get_boun
d
_subclass()
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
o
p
her Lee
make CoordsToIn
t
erva
l
s
/
get
_
i
n
t
erval() use se
q
.
a
b
solute_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher Lee
cl
e
aned up SeqPath
.
classySlice()
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
istophe
r
Lee
M
e
rge c
o
mmit 're
m
otes/mk
s
z
u
ba/nlmsa
_
no_verbose' i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
p
h
er Le
e
M
erge commit '
r
e
motes/mkszuba/cnestedlist_noti
c
e' in
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
L
e
e
incomplete new cod
e
for T
r
anslationDB
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
st
o
ph
e
r Lee
cleaned
u
p rev
e
rsePath con
s
t
r
uction
commit
|
commitdiff
|
tree
2009-07-15
C
hristopher Lee
a
dd absolute_slice() metho
d
to Seq
P
ath
commit
|
commitdiff
|
tree
2009-07-14
C
hri
s
to
p
her Le
e
Mer
g
e commit 'remo
t
es/mkszuba/cnestedl
i
st_logger'
into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Marek
S
z
uba
Given existing isola
t
ion problems between
t
ests
run
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christophe
r
Lee
M
erge branch 'mast
e
r' into m
e
gatests
commit
|
commitdiff
|
tree
2009-07-03
Chri
s
t
o
pher Lee
Merge bran
c
h 'formatdb_fail'
commit
|
commitdiff
|
tree
2009-07-03
C
h
ristopher Lee
improved whitespace p
a
th warning
commit
|
commitdiff
|
tree
2009-07-03
Christopher L
e
e
a
d
ded warning for whi
t
e
s
p
a
ce
i
n pa
t
h
commit
|
commitdiff
|
tree
2009-07-01
Chris
t
opher Lee
Merge
commit 're
m
otes/m
k
szuba/mega
t
ests'
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
use glob
.
glob() instead of
o
s
.
lis
t
dir(); cleaned up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christopher Le
e
Merge commit
'remot
e
s
/mkszuba/mime
t
e
xt'
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
Merge commit 'r
e
motes/mk
s
zuba/docfixes'
commit
|
commitdiff
|
tree
2009-07-01
Chri
s
topher
Lee
Me
r
ge
c
ommit 'remotes/mkszuba/hashlib
'
commit
|
commitdiff
|
tree
2009-06-26
Christopher Lee
f
i
xed
caching bug introduc
e
d in co
m
mit 8d9966 in PrefixUn
i
on
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christop
h
er
L
ee
d
eprecated cursor argument to SQLTable
commit
|
commitdiff
|
tree
2009-06-20
Chris
t
op
h
er Lee
fixed issue 99
commit
|
commitdiff
|
tree
2009-06-20
Chri
s
t
opher Lee
add
e
d test for
i
ssue 99
commit
|
commitdiff
|
tree
2009-06-20
Christ
o
p
h
er Lee
clea
n
ed up SQLiteServe
r
I
nfo
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
adde
d
DBSer
v
erInfo
.
new_cu
r
sor()
m
ethod
commit
|
commitdiff
|
tree
2009-06-13
Christo
p
her Lee
Merge commit 'r
e
m
otes/mkszuba/issue97_test'
i
nt
o
is
s
ue
9
7
_
t
e
s
t
commit
|
commitdiff
|
tree
2009-06-13
Chr
i
stopher
L
ee
removed redundant and buggy rstrip("
.
py") call from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Christop
h
er Lee
fix py
r
ex cde
f
commit
|
commitdiff
|
tree
2009-06-12
C
h
ristopher Lee
f
i
x issue97
commit
|
commitdiff
|
tree
2009-06-12
Christophe
r
Le
e
raised m
i
n
i
mum identity for relaxed blast tests
t
o 60%
commit
|
commitdiff
|
tree
2009-06-09
Chri
s
t
o
p
h
e
r
L
e
e
rep
l
aced a few rem
a
ining
r
efs in the docs to pygr
.
D
a
ta
.
.
.
commit
|
commitdiff
|
tree
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