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basic database tutorial
2009-09-03
Christopher Lee
basic database tutorial
commit
|
commitdiff
|
tree
2009-09-03
Christo
p
her Lee
a
d
d
ed back _
_
len__() to SQLTableBase
.
How i
n
heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Christop
h
er Lee
a
d
d
e
d
section on PrefixUnionDic
t
commit
|
commitdiff
|
tree
2009-09-02
Christo
p
h
e
r
L
e
e
added se
c
tion on pl
u
gging i
n
y
our own sequence parse
r
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristopher Lee
moved old materi
a
l
out to compgenomics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
some minor seque
n
ce
t
utorial
r
e
visions
commit
|
commitdiff
|
tree
2009-09-02
C
hristophe
r
Lee
added tuto
r
i
a
l section on accessing sequence database
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christo
p
her
L
ee
sp
l
it up
b
ullet poi
n
ts to integrate in
t
o the co
d
e
e
x
am
p
le
commit
|
commitdiff
|
tree
2009-09-02
C
h
ri
s
topher Lee
revise
d
sequence tutor
i
a
l
i
ntro
(
first pa
r
t)
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
stoph
e
r Lee
Merge commit 'remotes/ctb/xmlrpc_tutorial' int
o
tutorial
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
Merge comm
i
t 'remotes/ct
b
/doc
_
alignment' int
o
tutorial
commit
|
commitdiff
|
tree
2009-09-02
Chri
s
topher Lee
revised gff
3
c
o
de
commit
|
commitdiff
|
tree
2009-09-02
Christopher
Lee
added GFF3 example of gene bu
i
lding
commit
|
commitdiff
|
tree
2009-09-01
Ch
r
istopher Lee
Mer
g
e comm
i
t
'
remotes/mkszuba/xmlrpc
_
tutorial' i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
C
hristop
h
er Le
e
Me
r
ge comm
i
t
'
r
emotes/c
t
b/doc_annotations' into tutorial
commit
|
commitdiff
|
tree
2009-09-01
Chri
s
tophe
r
L
e
e
e
x
tracted material
f
or se
p
a
r
ate database tut
o
rial
commit
|
commitdiff
|
tree
2009-08-29
Chris
t
opher L
e
e
rem
o
ved
unnecessary stat an
d
shuti
l
import fr
o
m setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
Christopher Lee
fixed eas
y
_inst
a
ll
bug by prot
e
cting coordin
a
t
o
r
.
R
es
o
urceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stophe
r
Lee
fixed blast_
t
est: renamed test_seq_without_db(
)
to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
rist
o
pher Lee
Merg
e
commit 'remotes/ctb/minor_fixes' in
t
o mi
n
or_
f
ixes
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
fix port
p
assing
in tes
t
util
.
TestXMLRPCServer
commit
|
commitdiff
|
tree
2009-08-04
Christopher L
e
e
u
se
p
air_identity_
t
uple(
)
for blast_t
e
st formatt
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christ
o
pher Lee
added Bla
s
tBas
e
.
tearDown() t
o
close seq
d
bs as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chris
t
opher Lee
Me
r
ge commit 'remotes/mksz
u
ba/doc_make
'
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Merge commit 'r
e
motes/m
k
szuba/rpm
'
commit
|
commitdiff
|
tree
2009-07-29
Ch
r
istoph
e
r
Lee
got
r
id of Blas
t
Mappi
n
g
.
warn_about_self_
m
atches()
commit
|
commitdiff
|
tree
2009-07-29
Christopher
L
ee
chan
g
ed
N
LMSA pairwi
s
eMode to allo
w
reporting of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
Merge co
m
mi
t
'
remotes/mk
s
zuba/
d
ebian'
commit
|
commitdiff
|
tree
2009-07-29
C
hristopher
Lee
retry
re
a
ding port_file in TestXMLRPC
S
erver several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
added com
m
ent
s
to
process_bla
s
t()
commit
|
commitdiff
|
tree
2009-07-29
Chr
i
sto
p
he
r
Lee
fix
p
roblem introduced in pro
c
ess_blast(
)
by commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
i
s
topher Lee
ha
n
dl
e
mis
s
ing WIN
D
IR ca
s
e on Windows
commit
|
commitdiff
|
tree
2009-07-28
C
h
ri
s
tophe
r
Lee
added SeqTra
n
s
l
ator
.
_
_
repr__()
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristoph
e
r
L
e
e
Merge commit 'rem
o
t
e
s/ctb/simplefr
a
me_form
a
tdb_clea
n
up
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristoph
e
r Lee
Merge br
a
nch 'master'
i
nto si
m
pleframe
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
add
e
d
SeqTranslator
.
iter_frames() method, used in BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristop
h
er
L
ee
Merge
commit 'remotes
/
ct
b
/simpleframe_d
o
c_alig
n
' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher
Lee
prote
c
t 2 more tests usin
g
blast_enabled() ch
e
ck
commit
|
commitdiff
|
tree
2009-07-27
Christop
h
er Lee
fixe
d
syntax error
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
adde
d
python 2
.
3 code
f
or FilePopen
t
o detec
t
b
ad
e
xit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
Merge branch 'no_ed
g
e
_
db'
commit
|
commitdiff
|
tree
2009-07-27
Christop
h
er Lee
M
e
rge bran
c
h 'sile
n
cio
'
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
added showFormatdbMessages
op
t
i
on to Bla
s
tMapping
commit
|
commitdiff
|
tree
2009-07-25
Christo
p
h
er
Lee
added sup
p
ort fo
r
n
o-edgeDB case in mapping
.
Grap
h
:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christ
o
pher Lee
added option
for
la
t
ex ou
t
put of the reference manual
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
topher Lee
M
erge com
m
it
'remotes
/
ctb/blast_test_rc' into simpleframe
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
pher
L
ee
ad
d
ed
more
d
ocstrings for blast
.
py
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
ph
e
r Lee
re
m
o
v
ed ol
d
Bla
s
txMapping code
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher Lee
new,
g
reatly simplifi
e
d BlastxMapping
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
switched te
s
t
_
blastx_serv
e
r to use new TranslationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
added r
e
ad_blast_alignment() tra
n
slate
D
e
s
t option
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
her Lee
added
NLMSA
.
edges() method
commit
|
commitdiff
|
tree
2009-07-16
Christo
p
h
er Lee
switched test_t
b
la
s
t
n_parser to use new Tra
n
slationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Le
e
switch tblastn to use n
e
w Tra
n
slat
i
o
n
DB
appr
o
ach
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher Lee
a
dded tran
s
lationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
m
o
v
e
d dbname def
a
ult
i
nto
get_
b
ound_
s
ubcl
a
s
s()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
make Co
o
rdsToInt
e
rvals / get
_
interval()
u
se seq
.
absolute_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
h
ristopher Lee
clean
e
d up SeqPath
.
cl
a
s
s
ySlice(
)
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
Merge co
m
mit 'r
e
mot
e
s/m
k
szuba/
n
l
m
sa_no_ver
b
ose' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
hr
i
s
topher Lee
Merge com
m
it 'remotes/mkszuba/cnestedlist_notice' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
hristopher Lee
i
ncomp
l
et
e
n
ew code fo
r
TranslationDB
commit
|
commitdiff
|
tree
2009-07-15
Christo
p
her Lee
cleaned up reversePath c
o
n
struction
commit
|
commitdiff
|
tree
2009-07-15
C
h
r
i
stopher Lee
a
dd absolute_slice()
m
ethod to SeqPath
commit
|
commitdiff
|
tree
2009-07-14
Ch
r
i
stopher
Lee
M
erg
e
commit 'remotes/mkszuba
/
cnestedlist_logger
'
into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christ
o
pher Le
e
Merge branch
'master' into m
e
g
a
tests
commit
|
commitdiff
|
tree
2009-07-03
Christoph
e
r Lee
Merge b
r
anch 'f
o
rmatd
b
_
f
ail'
commit
|
commitdiff
|
tree
2009-07-03
Ch
r
istopher L
e
e
improved whitespace path warning
commit
|
commitdiff
|
tree
2009-07-03
Christopher Lee
added w
a
r
n
ing for
wh
i
tes
p
ace in path
commit
|
commitdiff
|
tree
2009-07-01
C
h
ristopher L
e
e
Merge
commit 'rem
o
te
s
/mkszub
a
/
me
g
a
tests'
commit
|
commitdiff
|
tree
2009-07-01
C
h
r
i
stopher
Lee
use glob
.
glob() i
n
stead
of os
.
listdir(); c
l
ea
n
ed up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christop
h
er Lee
Merg
e
c
ommit 'remotes/mkszu
b
a/mimete
x
t'
commit
|
commitdiff
|
tree
2009-07-01
Chris
t
op
h
er
L
ee
Merge com
m
it 'r
e
motes/mkszuba
/
docf
i
xes'
commit
|
commitdiff
|
tree
2009-07-01
Ch
r
i
st
o
pher Lee
M
erg
e
c
ommi
t
'remote
s
/mkszuba/hashli
b
'
commit
|
commitdiff
|
tree
2009-06-26
C
h
ristop
h
er Le
e
fixed caching
b
u
g
i
ntrodu
c
ed in
c
om
m
it 8d9966 in Pr
e
fixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christoph
e
r Le
e
deprecated cursor
argume
n
t t
o
SQL
T
able
commit
|
commitdiff
|
tree
2009-06-20
Christopher Le
e
fixed
i
ssu
e
99
commit
|
commitdiff
|
tree
2009-06-20
Chr
i
stopher
Lee
added test for issue
9
9
commit
|
commitdiff
|
tree
2009-06-20
Christoph
e
r Lee
cleaned up SQ
L
iteSer
v
erInfo
commit
|
commitdiff
|
tree
2009-06-20
Christopher
L
e
e
add
e
d
D
BServe
r
I
n
f
o
.
new_
c
ursor() method
commit
|
commitdiff
|
tree
2009-06-13
Christophe
r
L
ee
M
e
rge commit
'
rem
o
t
es/mkszuba/issue97_test' in
t
o issu
e
97_test
commit
|
commitdiff
|
tree
2009-06-13
C
hristoph
e
r
L
ee
r
e
moved redundan
t
and buggy
r
strip
(
"
.
py") call from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
fix
i
ssue97
commit
|
commitdiff
|
tree
2009-06-12
C
h
r
istopher
Lee
r
aised
m
i
nimum iden
t
ity fo
r
relaxed blast tests to 60
%
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
replaced
a
few re
m
ain
i
ng
refs in
t
he docs to p
y
gr
.
D
ata
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
M
erg
e
commit 'remotes/mkszu
b
a
/
d
eb'
commit
|
commitdiff
|
tree
2009-06-09
Christop
h
er Lee
Merge com
m
it 'remotes/mkszuba/renames'
commit
|
commitdiff
|
tree
2009-06-09
Christoph
e
r Lee
Merge
branch 'interval_filte
r
s' i
n
t
o b
l
ast_tests
commit
|
commitdiff
|
tree
2009-06-09
Chri
s
topher Lee
r
elaxed-tes
t
s had a bug t
h
at made them pass the compar
i
son
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
m
u
st
close
Fil
e
Popen
o
bject before
exiting BlastxMapping
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
m
erged in ct
b
/blastx_da
t
ab
a
se
commit
|
commitdiff
|
tree
2009-06-04
C
h
r
istop
h
er Le
e
Merge commit 'r
e
m
o
t
e
s/ctb/bla
s
tx_generator'
into ctb
_
tmp
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
P
EP
8
and whi
t
espace fi
x
es to n
l
msa_
u
tils
.
p
y
;
no f
u
nctionalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
hrist
o
pher Lee
converted add_aligned_interv
a
ls functionalit
y
into
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher
L
ee
cle
a
n up AttributeInterface according to Ti
t
u
s s
u
ggestions
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
Merge
c
om
m
it 'remotes/ctb/ctb_intervals' into int
e
rval_filters
commit
|
commitdiff
|
tree
2009-06-03
Christopher L
e
e
M
e
rge
commit 'rem
o
tes/ctb/ct
b
_blast2' into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Christopher
Lee
Merge comm
i
t 're
m
ot
e
s/ctb/mi
n
or_doc
_
fi
x
e
s' into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Christopher Lee
merged in ctb/annot
a
tion
commit
|
commitdiff
|
tree
2009-06-03
Chri
s
topher
L
e
e
m
e
rged i
n
c
t
b/
b
last_
s
kip conflic
t
with ctb/b
l
a
s
t_cac
h
e
commit
|
commitdiff
|
tree
2009-06-03
Christopher L
e
e
Me
r
ge
commi
t
'remote
s
/
ctb/blast_c
a
che
'
into
ctb_t
m
p
commit
|
commitdiff
|
tree
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