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added GFF3 example of gene building
2009-09-02
Chri
s
t
opher Lee
added GFF3 example of g
e
ne building
commit
|
commitdiff
|
tree
2009-09-01
Ch
r
isto
p
h
e
r
Lee
Merge commi
t
'remot
e
s/mkszu
b
a/
x
mlrp
c
_tutorial' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Christopher Lee
Merge
c
ommit 'remotes/ctb
/
doc_annotat
i
ons
'
into tutorial
commit
|
commitdiff
|
tree
2009-09-01
Christ
o
pher Lee
e
x
tracted
m
ateri
a
l for sepa
r
at
e
database tutorial
commit
|
commitdiff
|
tree
2009-08-29
Christopher
L
ee
remov
e
d unneces
s
ary s
t
at and shutil impo
r
t
f
r
o
m setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
Christopher Lee
fixed easy_install b
u
g by protecting coo
r
dinator
.
Res
o
urceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
fixed blast
_
tes
t
:
renamed te
s
t
_
seq
_
without
_
db()
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
ristopher
L
ee
Merge commit 'r
e
motes/ctb/minor_
f
ixes'
i
nto minor_fixes
commit
|
commitdiff
|
tree
2009-08-04
C
h
r
istopher Lee
fix port passing in te
s
t
u
t
i
l
.
T
estX
M
LR
P
CServer
commit
|
commitdiff
|
tree
2009-08-04
C
hrist
o
pher
Lee
u
se
p
a
ir_identi
t
y_tuple() for blast_t
e
s
t formatting
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Lee
a
d
de
d
B
lastBase
.
tearD
o
w
n
()
to close seqdbs as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
stopher Lee
Me
r
ge commi
t
'rem
o
t
es/mkszuba/doc_make'
commit
|
commitdiff
|
tree
2009-08-04
Chri
s
to
p
her Le
e
Merge commit 'remotes/m
k
szuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
Chris
t
opher Le
e
go
t
rid o
f
BlastMapping
.
warn
_
about_
s
elf_
m
atches()
commit
|
commitdiff
|
tree
2009-07-29
C
hrist
o
pher Le
e
changed
N
LMSA pairw
i
seMo
d
e
t
o a
l
low re
p
or
t
ing of se
l
f
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher L
e
e
Me
r
ge commit
'
re
m
otes/mksz
u
ba/debian'
commit
|
commitdiff
|
tree
2009-07-29
Christopher L
e
e
retry reading p
o
rt_file in TestX
M
LRP
C
Server severa
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 problem introduced i
n
process_b
l
ast() by comm
i
t
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
i
st
o
pher
L
ee
handle m
i
ssing
W
INDI
R
case on Windows
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
added SeqTranslator
.
__repr__()
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
Merge comm
i
t
'
remotes/ctb
/
simpleframe
_
formatdb_cleanup
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Chri
s
toph
e
r Lee
Merge br
a
nch
'master' i
n
to simpleframe
commit
|
commitdiff
|
tree
2009-07-28
Christ
o
p
her Lee
added Seq
T
ranslator
.
iter_frames
(
)
method, used in Blastx
M
app
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
M
e
rge
c
ommi
t
'remo
t
es/ctb/s
i
mplefram
e
_
d
o
c_a
l
i
gn' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
p
r
otect
2
m
o
r
e
tes
t
s using
b
last_enabl
e
d()
check
commit
|
commitdiff
|
tree
2009-07-27
Christopher Lee
fixed syntax
e
rror
commit
|
commitdiff
|
tree
2009-07-27
C
h
r
i
s
t
opher
Lee
added py
t
hon 2
.
3 c
o
de for
F
ilePope
n
to detect bad exi
t
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher
L
ee
Merge branch 'n
o
_edg
e
_db
'
commit
|
commitdiff
|
tree
2009-07-27
Christopher L
e
e
Merg
e
branch 'silenc
i
o
'
commit
|
commitdiff
|
tree
2009-07-27
C
h
ristopher Lee
a
d
ded sh
o
wFormatdbMessages option to BlastMapping
commit
|
commitdiff
|
tree
2009-07-25
Chris
t
op
h
er
Lee
ad
d
ed support for
n
o
-
ed
g
eDB case in
mapping
.
G
r
aph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Christopher
L
ee
added option fo
r
l
atex
o
utput of the ref
e
re
n
ce manual
commit
|
commitdiff
|
tree
2009-07-16
Christopher
Lee
M
e
rge commit 're
m
o
t
es/ctb/blast_test_
r
c' into
simple
f
rame
commit
|
commitdiff
|
tree
2009-07-16
Christoph
e
r Lee
a
d
ded more docstrings fo
r
blast
.
p
y
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
removed old BlastxMapping
c
o
d
e
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
o
pher Lee
new, greatly simp
l
ifie
d
Bla
s
tx
M
appin
g
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
t
o
pher Lee
s
w
i
tched
test_
b
l
a
stx_serve
r
t
o use
n
ew
TranslationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
C
h
r
i
stopher Lee
a
dded r
e
ad_blas
t
_
a
lignm
e
nt() translateDest option
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher Lee
a
d
ded NLM
S
A
.
edges() me
t
h
o
d
commit
|
commitdiff
|
tree
2009-07-16
Christophe
r
Lee
switc
h
ed t
e
st_tb
l
astn_pars
e
r
t
o u
s
e
new T
r
anslation
D
B
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
C
h
ristopher Lee
switch tblastn
to
u
se new Tran
s
lationDB approach
commit
|
commitdiff
|
tree
2009-07-15
Christopher Le
e
ad
d
ed trans
l
ationDB
.
p
y
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher
L
e
e
mov
e
d
d
b
name default in
t
o get_bound_s
u
bclas
s
()
commit
|
commitdiff
|
tree
2009-07-15
Christopher L
e
e
mak
e
C
o
o
rdsToInterval
s
/ get_interval() use seq
.
a
b
solute_sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher Lee
clean
e
d
u
p SeqPath
.
class
y
Slice(
)
commit
|
commitdiff
|
tree
2009-07-15
C
h
ristopher Lee
M
erg
e
commit
'remotes
/
mkszuba/
n
lmsa
_
no_verbose' in
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Ch
r
istopher L
e
e
Me
r
ge
c
o
mmit 'remote
s
/mkszuba/c
n
e
s
ted
l
ist_notic
e
' in
t
o
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
incomp
l
ete new code for T
r
anslationDB
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
stopher Lee
cleaned up reversePath cons
t
r
u
cti
o
n
commit
|
commitdiff
|
tree
2009-07-15
Chris
t
opher
L
ee
add abs
o
lut
e
_slice(
)
m
ethod
t
o SeqPath
commit
|
commitdiff
|
tree
2009-07-14
Christopher Lee
M
erge
com
m
i
t 'remotes/mkszub
a
/cne
s
tedlist
_
logger' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Mar
e
k
S
zuba
Given
exi
s
ting isol
a
tio
n
problems be
t
ween tests run
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Ch
r
istophe
r
L
e
e
M
e
rge branch
'mas
t
er'
into meg
a
tests
commit
|
commitdiff
|
tree
2009-07-03
Chri
s
to
p
her L
e
e
M
e
r
ge br
a
nch 'formatdb_f
a
il'
commit
|
commitdiff
|
tree
2009-07-03
Christopher Lee
imp
r
ove
d
whitespace path war
n
i
n
g
commit
|
commitdiff
|
tree
2009-07-03
Chris
t
op
h
er Lee
add
e
d warning f
o
r whitespace i
n
path
commit
|
commitdiff
|
tree
2009-07-01
Christopher L
e
e
Merge commit '
r
emot
e
s/mkszuba/me
g
atests'
commit
|
commitdiff
|
tree
2009-07-01
Chris
t
oph
e
r Lee
use glob
.
glob() instead of
o
s
.
listdir(); cleane
d
up
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christopher
Le
e
Merge commit 'remo
t
es/
m
k
szuba/mimetext'
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
Merg
e
commit 'remotes/mksz
u
ba
/
docfixes'
commit
|
commitdiff
|
tree
2009-07-01
C
h
risto
p
her Le
e
Merge c
o
mmit 're
m
ote
s
/mkszuba/hashlib'
commit
|
commitdiff
|
tree
2009-06-26
Christophe
r
Lee
fixed caching bug introduced in commit 8d
9
9
6
6 in PrefixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Chr
i
stopher Lee
de
p
r
ecated
c
urs
o
r argu
m
ent to SQ
L
Table
commit
|
commitdiff
|
tree
2009-06-20
Christopher Le
e
f
i
xed issue
99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
added t
e
st fo
r
i
ssue 99
commit
|
commitdiff
|
tree
2009-06-20
Chri
s
topher Lee
c
l
e
a
ned up SQLi
t
eServerIn
f
o
commit
|
commitdiff
|
tree
2009-06-20
C
h
ri
s
t
o
p
her Lee
a
d
d
ed
D
B
ServerInfo
.
ne
w
_cursor() meth
o
d
commit
|
commitdiff
|
tree
2009-06-13
Christ
o
phe
r
L
ee
M
erge commit 'remot
e
s
/mkszuba
/
iss
u
e97
_
test' into
i
ssue97_test
commit
|
commitdiff
|
tree
2009-06-13
Chri
s
topher Lee
re
m
o
v
ed redundant and buggy
rstrip("
.
p
y") call from
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Christop
h
er Lee
fix issu
e
9
7
commit
|
commitdiff
|
tree
2009-06-12
Chri
s
toph
e
r Lee
ra
i
sed
m
inimum ident
i
ty for relaxed bla
s
t t
e
sts to 60%
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
replaced a
f
ew remaining r
e
fs in
t
he docs
to pygr
.
Da
t
a
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
C
h
r
i
sto
p
h
e
r
Lee
Mer
g
e
com
m
it 'remo
t
es
/
mksz
u
b
a/
d
eb'
commit
|
commitdiff
|
tree
2009-06-09
Chris
t
opher Lee
Merg
e
commit 'remot
e
s/mkszuba/renames'
commit
|
commitdiff
|
tree
2009-06-09
Christopher
L
ee
Merge branch 'interval_filters' i
n
to blast_tes
t
s
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
relaxed-te
s
ts had a bug tha
t
made
t
hem pass the comparison
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chri
s
topher Lee
must
close Fi
l
e
Popen object before exiting BlastxM
a
pping
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chri
s
topher Le
e
merged in ctb/blastx_database
commit
|
commitdiff
|
tree
2009-06-04
Christo
p
h
e
r Lee
Merge comm
i
t
'r
e
motes/ctb/
b
lastx_
g
enerat
o
r
'
into ctb_t
m
p
commit
|
commitdiff
|
tree
2009-06-04
Christop
h
e
r Lee
PE
P
8 a
n
d whitespace
f
ixes to nlms
a
_u
t
ils
.
py; no
functionalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher Le
e
converted
add_aligned
_
in
t
e
r
vals func
t
iona
l
ity into
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chr
i
stopher Lee
clean up AttributeInterface according
to Titu
s
suggestions
commit
|
commitdiff
|
tree
2009-06-04
Chris
t
ophe
r
Lee
Merge
commit 're
m
ote
s
/ctb/ctb_int
e
rvals' into
interval_filters
commit
|
commitdiff
|
tree
2009-06-03
Chris
t
oph
e
r Lee
Merge commit 'remot
e
s/ctb/c
t
b_blast2' into
ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Chris
t
opher Lee
Merge
c
ommit '
r
emotes/ctb/minor_doc_fixes' in
t
o
c
tb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Chri
s
topher Lee
m
erge
d
in
c
tb/annota
t
ion
commit
|
commitdiff
|
tree
2009-06-03
C
hri
s
tophe
r
Lee
merged in ctb/bl
a
st_skip con
f
li
c
t with ctb/blas
t
_cache
commit
|
commitdiff
|
tree
2009-06-03
Christ
o
phe
r
Lee
Me
r
ge commit 'r
e
motes/ctb/blast_c
a
che' into
c
tb_tm
p
commit
|
commitdiff
|
tree
2009-05-29
Christoph
e
r Lee
M
erge co
m
mit 'rem
o
tes/ctb/nlmsa_iter_repr'
commit
|
commitdiff
|
tree
2009-05-29
Christ
o
phe
r
Lee
remo
v
ed unnecessary import
commit
|
commitdiff
|
tree
2009-05-29
Christopher Lee
convert
e
d test_mu
l
t
i
blast_s
i
ng
l
e() back t
o
test
against
.
.
.
commit
|
commitdiff
|
tree
2009-05-29
Ch
r
istopher Lee
r
e
name to avoid false implica
t
ion this test invo
l
ves
.
.
.
commit
|
commitdiff
|
tree
2009-05-28
Titus Brown
fixed
t
ypo i
n
cnestedlist:
MaskEn
d
=> mask
E
nd
commit
|
commitdiff
|
tree
2009-05-27
C
h
rist
o
pher
L
ee
M
e
rge commit '
r
emotes/mkszuba/
t
r
ove' i
n
t
o
marek_tmp
commit
|
commitdiff
|
tree
2009-05-27
Christopher
L
e
e
added
com
p
ari
s
on with single seq b
l
a
s
t
in test_multiblast
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
added text file fo
r
checking l
o
ng parser result
s
commit
|
commitdiff
|
tree
2009-05-27
Ch
r
i
stopher Lee
put close() withi
n
try-finally as always
commit
|
commitdiff
|
tree
2009-05-27
Christopher Lee
Merge commit 'remotes/mkszuba/blast_test' into ma
r
ek_t
m
p
commit
|
commitdiff
|
tree
2009-05-27
Christop
h
er
L
ee
M
erge commit 're
m
o
t
es
/
mkszuba/ebuild
s
'
into mar
e
k_t
m
p
commit
|
commitdiff
|
tree
next