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basic database tutorial
2009-09-03
Christ
o
pher Lee
basic database tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christopher Lee
added
b
ack __len
_
_
(
)
to
S
QLTableBase
.
How in heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Christ
o
pher Lee
added section on PrefixUnionDi
c
t
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
added section on
plugging
in your o
w
n sequence parser
commit
|
commitdiff
|
tree
2009-09-02
Christo
p
her Lee
moved o
l
d material
ou
t
to compgenomics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
C
hristopher Le
e
som
e
m
inor sequence t
u
tori
a
l revisio
n
s
commit
|
commitdiff
|
tree
2009-09-02
Christo
p
her Lee
added tut
o
rial section on accessing
s
equence database
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Ch
r
istopher
L
ee
s
plit up bullet
point
s
to integrat
e
into the c
o
de
e
xamp
l
e
commit
|
commitdiff
|
tree
2009-09-02
C
hri
s
toph
e
r
Lee
revised seque
n
ce tutorial intro (
f
irst part)
commit
|
commitdiff
|
tree
2009-09-02
Christopher Le
e
Merge commit 'remotes/ct
b
/xmlrpc_tutorial'
into tutorial
commit
|
commitdiff
|
tree
2009-09-02
Christopher Le
e
M
erge c
o
m
mit
'
remotes
/
ctb
/
doc
_
alignment' in
t
o tu
t
or
i
al
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
stophe
r
L
ee
revised gff3 code
commit
|
commitdiff
|
tree
2009-09-02
Christ
o
pher Lee
a
d
ded GFF
3
example of gene
b
uilding
commit
|
commitdiff
|
tree
2009-09-01
Christopher
Lee
Merge co
m
mit 'remotes/mkszuba/xmlrpc
_
t
u
torial'
i
nto
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
C
hristopher Lee
M
erg
e
commit 'remotes/ctb/
d
oc_annotations' into
t
utoria
l
commit
|
commitdiff
|
tree
2009-09-01
Christ
o
pher Lee
extra
c
ted mate
r
i
al
f
or separate data
b
ase tutori
a
l
commit
|
commitdiff
|
tree
2009-08-29
Christopher Lee
removed unn
e
cessar
y
stat and shutil impor
t
from se
t
up
.
py
commit
|
commitdiff
|
tree
2009-08-14
Christ
o
pher Lee
fixe
d
easy
_
install
bug by
prot
e
ctin
g
coordinator
.
R
e
sourceFi
l
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
istoph
e
r
Le
e
fixed blast_t
e
st:
r
enam
e
d test_se
q
_
withou
t
_db()
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christoph
e
r
L
ee
Mer
g
e commit 'rem
o
tes/ctb/minor_fixes' into minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
Chris
t
op
h
er Lee
f
ix port p
a
ssing i
n
t
estutil
.
TestXMLRPCSe
r
v
er
commit
|
commitdiff
|
tree
2009-08-04
Chri
s
toph
e
r L
e
e
use pa
i
r_
i
dentity_tuple() fo
r
b
l
a
s
t
_t
e
s
t
fo
r
m
a
tting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christ
o
p
her
Lee
a
d
d
ed BlastB
a
se
.
tearDown() to close seqdbs as t
h
e
y
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
istop
h
e
r Lee
Merge c
o
mmit
'remotes/mkszuba/doc_make
'
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Merge com
m
i
t '
r
emot
e
s/mkszuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
Christophe
r
Lee
got rid of
BlastMa
p
p
ing
.
warn_about_self_matche
s
()
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
c
h
anged N
L
MSA pairw
i
seMode t
o
allow reporti
n
g of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Ch
r
isto
p
her Lee
M
e
rge commit 'remotes/
m
kszuba/
d
ebi
a
n'
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
retry reading port_fi
l
e in
Tes
t
XMLRPCServer
s
e
ve
r
a
l
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Chr
i
st
o
ph
e
r Lee
add
e
d c
o
mments to pro
c
ess_
b
last()
commit
|
commitdiff
|
tree
2009-07-29
Christopher L
e
e
fix problem introduced in pr
o
ces
s
_blast(
)
b
y c
o
mmit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Chris
t
op
h
er Lee
ha
n
d
l
e mi
s
sing
W
INDI
R
case on
Windows
commit
|
commitdiff
|
tree
2009-07-28
Christoph
e
r Lee
a
dded SeqTranslato
r
.
_
_
repr__()
commit
|
commitdiff
|
tree
2009-07-28
Chri
s
t
o
pher Lee
Merge commit 'remotes/ctb/simplef
r
ame_f
o
rmatdb_c
l
ean
u
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
Merge branch 'master' into simpleframe
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
is
t
ophe
r
Lee
added Seq
T
ranslator
.
iter_frames
(
) method,
used i
n
B
l
a
s
txMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
M
erge c
o
mmit 'remotes/ctb/simplef
r
ame
_
d
o
c_alig
n
' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher
L
ee
pro
t
ect 2 more te
s
ts using
b
l
ast_enabled() check
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stophe
r
Lee
fixed syntax
e
rror
commit
|
commitdiff
|
tree
2009-07-27
Christophe
r
Lee
added pyt
h
o
n
2
.
3 code for FilePopen t
o
d
etect bad
e
x
i
t
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher Le
e
Me
r
ge branch
'
no_edge_db'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
Merge branc
h
'
silencio'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
added s
h
owF
o
rmatdbMessages
o
ption to
Bl
a
stMa
p
p
i
ng
commit
|
commitdiff
|
tree
2009-07-25
C
hristopher L
e
e
a
d
ded support
for no-edgeDB ca
s
e
i
n ma
p
ping
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Chri
s
topher Lee
added o
p
tion for latex
o
utput of the r
e
f
eren
c
e
m
anual
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r L
e
e
M
erge commit
'
remotes/ctb/bl
a
st_test_rc'
into simpleframe
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
sto
p
he
r
Lee
added more docs
t
ring
s
for blast
.
py
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
i
stophe
r
Lee
removed old
B
l
as
t
xMa
p
ping co
d
e
commit
|
commitdiff
|
tree
2009-07-16
Christopher Le
e
new,
greatly simpli
f
ied BlastxMap
p
ing
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
swi
t
ched test_blastx_ser
v
er to use new Tran
s
lationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
h
e
r Lee
added
r
ead_blast_a
l
ignment() tran
s
lateD
e
st option
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
t
opher Lee
a
dd
e
d
NLMS
A
.
edges() method
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher L
e
e
swit
c
hed test_tb
l
astn_parser t
o
use new Transl
a
tionDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher Lee
switch tblastn to us
e
new TranslationDB appr
o
ach
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
a
dde
d
trans
l
at
i
onDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
i
stopher Lee
moved db
n
ame default i
n
to get_bound_
s
ubclass(
)
commit
|
commitdiff
|
tree
2009-07-15
Christopher L
e
e
m
a
ke
C
oordsTo
I
nter
v
als / get_interv
a
l()
use
seq
.
absolute_sl
i
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christop
h
er Lee
cleane
d
u
p
SeqPath
.
classy
S
lice()
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
Me
r
g
e commit
'
r
e
m
otes/m
k
szuba/nlmsa_
n
o
_verbose' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christop
h
er Le
e
Mer
g
e comm
i
t
'
remote
s
/mkszuba/
c
nestedlist_n
o
ti
c
e' i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
inc
o
mplete
ne
w
code for Tr
a
ns
l
ationDB
commit
|
commitdiff
|
tree
2009-07-15
C
hristop
h
e
r Le
e
clean
e
d up
r
eversePath construc
t
i
o
n
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
s
topher Lee
add
a
bsolute_slice() method to S
e
q
Path
commit
|
commitdiff
|
tree
2009-07-14
Christopher Lee
Merge commit
're
m
otes/mks
z
ub
a
/cne
s
tedlist_logger' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Marek Szuba
Given existing isolatio
n
problems betwe
e
n tests run
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christopher L
e
e
Merge
branch
'
master'
i
nto
megat
e
sts
commit
|
commitdiff
|
tree
2009-07-03
Christop
h
er Lee
Merge b
r
a
nc
h
'formatdb_fai
l
'
commit
|
commitdiff
|
tree
2009-07-03
Christopher L
e
e
improved whitesp
a
ce path
w
a
r
ning
commit
|
commitdiff
|
tree
2009-07-03
C
h
ri
s
topher Lee
a
d
ded warning for
w
hitespace in p
a
th
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
M
e
rge
commit '
r
em
o
tes/mkszuba/megatests'
commit
|
commitdiff
|
tree
2009-07-01
C
h
ri
s
topher Lee
u
s
e g
l
ob
.
glob(
)
inste
a
d
of os
.
listdir(); cleaned up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christophe
r
Lee
Mer
g
e commit 'remotes/mkszuba/mimetext
'
commit
|
commitdiff
|
tree
2009-07-01
Christoph
e
r Lee
Merg
e
commi
t
're
m
o
t
e
s/mkszuba/
d
ocfixes'
commit
|
commitdiff
|
tree
2009-07-01
Chr
i
s
t
ophe
r
Lee
Merge
c
ommit 'remotes/
m
k
s
z
ub
a
/hashlib'
commit
|
commitdiff
|
tree
2009-06-26
Christop
h
e
r Lee
f
ixed cac
h
ing bug introdu
c
ed i
n
com
m
it 8d9966 in PrefixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
deprecated cursor
argum
e
nt to SQLTable
commit
|
commitdiff
|
tree
2009-06-20
Ch
r
is
t
opher Lee
fixed issue 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
a
d
ded test for
i
s
s
ue 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
cleaned up SQLiteServe
r
I
nfo
commit
|
commitdiff
|
tree
2009-06-20
Christ
o
pher Lee
added DBServerI
n
fo
.
new_curso
r
() method
commit
|
commitdiff
|
tree
2009-06-13
C
h
ristop
h
er Lee
Merge c
o
mmit 'r
e
motes/mks
z
u
b
a
/
i
ssue
9
7_test' into i
s
sue
9
7_test
commit
|
commitdiff
|
tree
2009-06-13
Christopher Lee
removed redun
d
an
t
and buggy rstrip("
.
p
y
") call from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
fix
issue97
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
raised minimum ide
n
tity for rela
x
ed b
l
ast tests
to 60%
commit
|
commitdiff
|
tree
2009-06-09
C
hris
t
opher Lee
replac
e
d
a few remainin
g
r
e
fs in the doc
s
to pygr
.
D
a
ta
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
M
erge comm
i
t
'rem
o
tes/mkszu
b
a/deb'
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
M
e
rge
c
ommit 'remotes/mkszub
a
/renames'
commit
|
commitdiff
|
tree
2009-06-09
Christ
o
pher Lee
Mer
g
e bra
n
ch
'
interval_filters
'
i
n
t
o
bl
a
st_tests
commit
|
commitdiff
|
tree
2009-06-09
C
hristopher Lee
relaxed-
t
e
s
ts had a bug that made them p
a
ss
t
h
e com
p
arison
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christo
p
her
Lee
mus
t
close F
i
lePopen object before exi
t
ing BlastxMap
p
ing
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher Le
e
merged in
c
t
b/bla
s
tx_databa
s
e
commit
|
commitdiff
|
tree
2009-06-04
Chr
i
stopher Lee
Merge com
m
it 'remot
e
s
/ctb
/
b
l
a
stx_generator' into ctb_t
m
p
commit
|
commitdiff
|
tree
2009-06-04
Christo
p
her Lee
PEP8 and whitespac
e
fi
x
es to nlmsa_utils
.
py; no fu
n
c
t
ionalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christ
o
pher Lee
co
n
v
e
rted add_aligned_intervals function
a
lity into
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
hristopher Lee
clean up AttributeInte
r
face according to
T
itus
s
ug
g
estions
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
Merge c
o
mm
i
t '
r
emotes/ctb/ctb_intervals' int
o
interval_filters
commit
|
commitdiff
|
tree
2009-06-03
C
hristopher Lee
M
erge co
m
mi
t
'remotes/ctb/c
t
b
_
blast2' in
t
o ctb
_
tmp
commit
|
commitdiff
|
tree
2009-06-03
Chris
t
opher L
e
e
Merge commit 'remotes/ctb/minor_doc_fixes
'
into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Christopher
L
ee
merged
i
n
ctb/annotation
commit
|
commitdiff
|
tree
2009-06-03
C
hri
s
tophe
r
Le
e
merged in ctb
/
blast_skip con
f
lict wi
t
h c
t
b
/b
l
ast_cache
commit
|
commitdiff
|
tree
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