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added GFF3 example of gene building
2009-09-02
Christop
h
er
L
ee
add
e
d G
F
F
3
example o
f
g
e
n
e
b
u
i
lding
commit
|
commitdiff
|
tree
2009-09-01
Christopher
Lee
Merge
c
omm
i
t
're
m
otes/mk
s
zuba/xmlrpc_tutoria
l
'
i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Christopher Lee
Mer
g
e co
m
mit 'rem
o
tes/ctb
/
doc_annotati
o
ns'
i
nto
t
utorial
commit
|
commitdiff
|
tree
2009-09-01
Chri
s
t
opher Lee
extracted material
fo
r
se
p
arate database tutor
i
al
commit
|
commitdiff
|
tree
2009-08-29
Ch
r
istopher Lee
remov
e
d
u
n
nec
e
ssa
r
y
s
tat and shutil i
m
port from setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
Ch
r
istopher
L
ee
f
i
xed easy_install bug
by protecting coordinator
.
R
es
o
ur
c
eFi
l
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
fixe
d
b
l
a
st_test: renamed test_seq_wi
t
hout_d
b
() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
ristopher
L
ee
Merge co
m
mit 'remotes/ctb/minor_fixes'
i
nto minor
_
fixes
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
fix port pa
s
sing
i
n
t
estutil
.
TestXMLRPCServer
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
use pair_
i
dentity_tuple
(
)
for bl
a
st_te
s
t for
m
atting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher
L
ee
added Bla
s
t
Base
.
tearDown()
t
o
c
los
e
seqdbs as th
e
y
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
hris
t
ophe
r
Lee
Merge
co
m
mit 'r
e
motes/mk
s
zuba/doc_make'
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
Merge commit 're
m
otes/mkszuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
Chr
i
stopher Lee
got ri
d
of Bl
a
s
t
M
app
i
ng
.
warn_about_self_matches()
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
changed NLMSA pai
r
wiseMode to allo
w
reporting of self
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christoph
e
r
Lee
Merge
commi
t
'
r
e
motes
/
mkszuba/debian'
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
retr
y
reading por
t
_
fi
l
e
in TestXMLRPCS
e
r
ver several
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher Lee
added comments to proces
s
_blas
t
(
)
commit
|
commitdiff
|
tree
2009-07-29
C
h
ristopher
Lee
fix probl
e
m int
r
oduce
d
in
p
rocess_blast() by commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
handle mi
s
sing WINDIR case on Windows
commit
|
commitdiff
|
tree
2009-07-28
C
h
r
istopher Lee
a
dde
d
SeqT
r
a
nslator
.
__repr__()
commit
|
commitdiff
|
tree
2009-07-28
Christoph
e
r Lee
Me
r
ge c
o
mm
i
t 'remotes/ctb/simplef
r
a
m
e_
f
ormat
d
b_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christop
h
er Lee
M
e
rg
e
br
a
nc
h
'master' i
n
to si
m
pleframe
commit
|
commitdiff
|
tree
2009-07-28
C
hristopher Lee
added SeqT
r
anslat
o
r
.
iter_frames()
m
ethod, used in BlastxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
C
h
ristophe
r
Lee
M
e
rge commit 'rem
o
tes/ctb/
s
impleframe_doc_ali
g
n' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
protect 2 more tests using blast_e
n
abled() check
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
fixed synt
a
x error
commit
|
commitdiff
|
tree
2009-07-27
Christopher Le
e
adde
d
python 2
.
3 code for F
i
leP
o
pen
to detect bad exit
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christo
p
h
er L
e
e
Merge branch 'no_
e
d
g
e
_
db'
commit
|
commitdiff
|
tree
2009-07-27
Christop
h
er Lee
Me
r
ge
branch 's
i
lencio
'
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
s
t
ophe
r
Lee
a
dded showFo
r
ma
t
dbMe
s
s
a
ge
s
option to BlastMapping
commit
|
commitdiff
|
tree
2009-07-25
C
hristopher
Lee
added s
u
p
port for no-edg
e
DB case in mapping
.
Gr
a
ph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Ch
r
i
s
topher
Le
e
adde
d
option for latex output o
f
the reference manu
a
l
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stopher Lee
Mer
g
e commit
'remotes/ctb/blast
_
test_rc' int
o
sim
p
leframe
commit
|
commitdiff
|
tree
2009-07-16
Christopher
Lee
added more
docstrings for
b
las
t
.
py
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
phe
r
Lee
r
e
moved old Bl
a
stxMapping code
commit
|
commitdiff
|
tree
2009-07-16
Christ
o
p
her
Lee
new
,
greatly simplifi
e
d
B
lastxMap
p
ing
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r Lee
switched
test_blastx_
s
e
r
ver
t
o use new Tra
n
sla
t
ionDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
opher Lee
added read_blast_alignmen
t
(
)
translateDest option
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r
Lee
a
d
ded NLMSA
.
edges() meth
o
d
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher
Lee
s
witched t
e
st_tbla
s
tn_parser to use new Translation
D
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
switc
h
tbl
a
stn to use new TranslationDB approach
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
to
p
her
Lee
added translationDB
.
py
commit
|
commitdiff
|
tree
2009-07-15
C
hristopher Lee
moved dbname default int
o
get
_
bound_s
u
bcl
a
ss()
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
opher
L
ee
m
ake CoordsToIntervals / get_interval
(
) use seq
.
absolute_sl
i
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
istopher Lee
cleaned up SeqPath
.
clas
s
yS
l
i
c
e()
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
tophe
r
Lee
M
erge commit 'remot
e
s/mksz
u
ba/nlmsa_no_verbo
s
e' in
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher L
e
e
Merge c
o
mmit 're
m
ot
e
s/mkszuba/
c
nestedlist_
n
ot
i
ce'
into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
istoph
e
r Lee
i
n
c
o
mplet
e
n
ew
code for TranslationDB
commit
|
commitdiff
|
tree
2009-07-15
C
h
ristopher
Lee
cl
e
an
e
d up r
e
v
e
rsePat
h
construction
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
a
d
d absolu
t
e
_
slice(
)
method to SeqPa
t
h
commit
|
commitdiff
|
tree
2009-07-14
Christ
o
pher
Lee
Merge commit
'remotes/mks
z
uba
/
cnest
e
dlist_lo
g
ger' i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Marek Szuba
G
iven existing
i
solati
o
n prob
l
e
ms between te
s
ts run
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Christopher Le
e
Merge branch 'master' in
t
o megates
t
s
commit
|
commitdiff
|
tree
2009-07-03
Christ
o
phe
r
L
e
e
Merge
branch
'
f
ormatd
b
_fail'
commit
|
commitdiff
|
tree
2009-07-03
Christop
h
er Lee
imp
r
oved whites
p
ace path warning
commit
|
commitdiff
|
tree
2009-07-03
C
h
ristop
h
er Lee
a
dded warning
f
or w
h
itespace in path
commit
|
commitdiff
|
tree
2009-07-01
C
hristopher Le
e
Merg
e
c
o
mmit 'r
e
motes/m
k
s
z
u
b
a/me
g
atests
'
commit
|
commitdiff
|
tree
2009-07-01
Christopher L
e
e
use glob
.
glob() instead of os
.
lis
t
dir(); cleaned up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christopher
L
e
e
Merge commit
'
remotes/mkszuba/mi
m
etext'
commit
|
commitdiff
|
tree
2009-07-01
Christop
h
er
Lee
Merge commit 'remotes/mksz
u
ba/docfixes'
commit
|
commitdiff
|
tree
2009-07-01
C
hristop
h
e
r
Lee
M
erge commit 'rem
o
tes/mk
s
zuba/
h
ashlib'
commit
|
commitdiff
|
tree
2009-06-26
C
h
ristopher Lee
f
i
x
ed cachi
n
g bug introduced
i
n commit 8d9
9
6
6
i
n Pref
i
xUnio
n
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christo
p
her Lee
deprecated cur
s
or argument to SQLTable
commit
|
commitdiff
|
tree
2009-06-20
Christopher
L
e
e
fixed i
s
sue
99
commit
|
commitdiff
|
tree
2009-06-20
Chri
s
topher Lee
a
dded te
s
t for issue 99
commit
|
commitdiff
|
tree
2009-06-20
C
hristopher Lee
cleane
d
up
S
Q
Lite
S
erver
I
nfo
commit
|
commitdiff
|
tree
2009-06-20
C
hri
s
topher Lee
added DB
S
erverIn
f
o
.
new
_
cursor() metho
d
commit
|
commitdiff
|
tree
2009-06-13
Christopher
L
e
e
Merge
commit 're
m
otes/mksz
u
ba/is
s
ue97_test'
i
nto
issu
e
97
_
test
commit
|
commitdiff
|
tree
2009-06-13
Chris
t
opher Lee
remov
e
d
redun
d
a
n
t and buggy rstrip("
.
py
"
) call from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Christoph
e
r Lee
f
i
x
py
r
ex
c
def
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
f
i
x
issue
9
7
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
r
aised min
i
mum identity
fo
r
r
elaxed blast tests
to 6
0
%
commit
|
commitdiff
|
tree
2009-06-09
Christopher
L
ee
replaced
a
few remaining r
e
f
s
in
t
h
e doc
s
to pygr
.
Data
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
istopher Lee
Merge
commit 'remotes/mkszuba/
d
eb'
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
is
t
opher Lee
Merge commit 're
m
otes
/
m
ks
z
uba/renam
e
s'
commit
|
commitdiff
|
tree
2009-06-09
Christop
h
er Lee
Merg
e
bra
n
ch 'inte
r
val_filters' int
o
b
l
ast_tests
commit
|
commitdiff
|
tree
2009-06-09
Ch
r
i
stophe
r
Lee
relaxed-tests
had a bug that ma
d
e
the
m
pass
t
he comparison
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christo
p
he
r
Lee
must close Fil
e
Popen ob
j
ect befo
r
e e
x
iting BlastxMappi
n
g
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
hr
i
sto
p
he
r
Lee
mer
g
ed in ctb/b
l
astx
_
d
atab
a
se
commit
|
commitdiff
|
tree
2009-06-04
Christo
p
h
er Le
e
Merg
e
co
m
mit 'r
e
motes
/
c
t
b/blastx_gen
e
r
a
t
or
'
into
ct
b
_tmp
commit
|
commitdiff
|
tree
2009-06-04
Christoph
e
r Lee
PEP8 an
d
whi
t
es
p
ace fixes to nlmsa_utils
.
py; no f
u
nctionalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
h
rist
o
p
he
r
Le
e
conve
r
te
d
add
_
aligned
_
int
e
rval
s
functiona
l
ity i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Ch
r
i
s
topher Lee
clean up
A
t
tributeI
n
terf
a
ce accordi
n
g to Titus sug
g
estions
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
M
erge co
m
m
i
t
'
remotes/c
t
b/ctb_inte
r
v
a
ls'
into
i
n
terval_filters
commit
|
commitdiff
|
tree
2009-06-03
Christopher Lee
Merg
e
c
ommit 'remo
t
e
s
/
c
tb/ct
b
_b
l
as
t
2' into ctb_tm
p
commit
|
commitdiff
|
tree
2009-06-03
C
hristopher Lee
Mer
g
e
c
ommit
'
remotes/ct
b
/mino
r
_
d
o
c
_f
i
xes' int
o
ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Christ
o
ph
e
r Lee
me
r
ged in
c
tb/annotation
commit
|
commitdiff
|
tree
2009-06-03
Chr
i
stopher
L
ee
m
erged in ctb/bl
a
st_ski
p
c
onflict
w
i
t
h ctb/blast_cac
h
e
commit
|
commitdiff
|
tree
2009-06-03
Christ
o
p
h
e
r
Le
e
Merge commit 'remotes/
c
tb/blast_ca
c
h
e
'
into ctb_tmp
commit
|
commitdiff
|
tree
2009-05-29
Chr
i
s
t
opher
Lee
Merge commi
t
'
remotes/ctb/nlmsa_iter_repr'
commit
|
commitdiff
|
tree
2009-05-29
Christop
h
er Lee
remov
e
d unnecessary
i
mport
commit
|
commitdiff
|
tree
2009-05-29
C
hri
s
topher Lee
converted tes
t
_
mu
l
tiblast_single(
)
back to test ag
a
inst
.
.
.
commit
|
commitdiff
|
tree
2009-05-29
Christopher L
e
e
rename to avoid fal
s
e i
m
plication
this test involves
.
.
.
commit
|
commitdiff
|
tree
2009-05-28
Titus Br
o
w
n
f
ixed t
y
p
o
i
n
cnestedlist:
MaskEnd =
>
m
a
skEnd
commit
|
commitdiff
|
tree
2009-05-27
Chri
s
t
opher
Lee
Merge commit 'rem
o
tes/mkszu
b
a/trove' into m
a
rek_tmp
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
added comparis
o
n with si
n
gle se
q
bla
s
t in test_m
u
lt
i
blast
commit
|
commitdiff
|
tree
2009-05-27
Chri
s
topher
L
ee
added text fil
e
for che
c
king l
o
ng parser
results
commit
|
commitdiff
|
tree
2009-05-27
Chr
i
stopher Lee
put close() within try-
f
inally as
always
commit
|
commitdiff
|
tree
2009-05-27
Christopher
L
ee
M
e
rge commit 're
m
otes/
m
ks
z
uba/blast_test' into marek_tmp
commit
|
commitdiff
|
tree
next