repo.or.cz
/
pygr.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
basic database tutorial
2009-09-03
Christo
p
her Lee
basic database tutoria
l
commit
|
commitdiff
|
tree
2009-09-03
Ch
r
ist
o
pher Lee
added ba
c
k __len__
(
) to SQLTableBase
.
Ho
w
in heck
.
.
.
commit
|
commitdiff
|
tree
2009-09-03
Chr
i
sto
p
h
e
r Lee
added s
e
ction on PrefixUnionDic
t
commit
|
commitdiff
|
tree
2009-09-02
Chr
i
stopher Lee
added s
e
ction on
pluggi
n
g
i
n
y
o
u
r o
w
n seq
u
ence par
s
er
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
moved
old material out to
c
ompgenomics
.
rst
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
some minor sequence tutorial revisions
commit
|
commitdiff
|
tree
2009-09-02
Christopher Lee
added tut
o
r
ial se
c
tion
o
n
a
c
cessing sequence database
.
.
.
commit
|
commitdiff
|
tree
2009-09-02
Christopher L
e
e
s
p
l
it up bullet p
o
ints to in
t
egrate into th
e
co
d
e example
commit
|
commitdiff
|
tree
2009-09-02
Christopher L
e
e
revi
s
ed sequence
tutorial i
n
tr
o
(first part
)
commit
|
commitdiff
|
tree
2009-09-02
Christop
h
er Lee
Merge commit 'remotes/
c
tb
/
xmlrpc_t
u
torial' int
o
tu
t
orial
commit
|
commitdiff
|
tree
2009-09-02
C
hristopher
Lee
Merge commit 'remotes/ctb/do
c
_alignment' into tutorial
commit
|
commitdiff
|
tree
2009-09-02
C
h
ristop
h
er L
e
e
revised gff3
code
commit
|
commitdiff
|
tree
2009-09-02
C
h
ris
t
ophe
r
Lee
adde
d
GFF3 example
o
f gen
e
b
uild
i
ng
commit
|
commitdiff
|
tree
2009-09-01
Christoph
e
r Lee
Merge
commit 'remot
e
s/mkszuba
/
xmlrpc_tutor
i
al' into
.
.
.
commit
|
commitdiff
|
tree
2009-09-01
Chris
t
ophe
r
Lee
Merge co
m
mit
'remotes/ctb/doc_a
n
no
t
ations' into tutorial
commit
|
commitdiff
|
tree
2009-09-01
Ch
r
i
s
topher Lee
e
x
tracted material for
separate database tutor
i
a
l
commit
|
commitdiff
|
tree
2009-08-29
Christopher Lee
removed unnecessary stat
and shuti
l
import from setup
.
py
commit
|
commitdiff
|
tree
2009-08-14
C
hristopher Lee
fixed easy_in
s
tal
l
bug by protect
i
ng
coordinato
r
.
Reso
u
rceFil
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
ist
o
pher Lee
fixed blast_test:
renam
e
d tes
t
_seq_without_d
b
() to
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Christopher Le
e
Merge
commit 'remo
t
es/ct
b
/minor_fixe
s
'
i
nto mino
r
_
f
ixes
commit
|
commitdiff
|
tree
2009-08-04
Christopher
Lee
f
i
x port passing in testutil
.
TestX
M
LRPCS
e
rver
commit
|
commitdiff
|
tree
2009-08-04
Ch
r
istop
h
er Lee
use p
a
ir_
i
d
entity_tuple() for
blast_
t
e
st
f
ormat
t
i
ng
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
C
h
ristopher
L
ee
added BlastBase
.
tearDo
w
n() to close seqdbs as they
.
.
.
commit
|
commitdiff
|
tree
2009-08-04
Chr
i
s
t
ophe
r
L
ee
M
er
g
e
c
ommi
t
'remo
t
es/
m
ks
z
u
b
a/doc_make
'
commit
|
commitdiff
|
tree
2009-08-04
Christo
p
her
L
ee
Merge commit 'remot
e
s/mkszuba/rpm'
commit
|
commitdiff
|
tree
2009-07-29
Chri
s
topher Lee
go
t
rid o
f
B
l
ast
M
app
i
ng
.
w
a
r
n_about_self_matches()
commit
|
commitdiff
|
tree
2009-07-29
Christopher Le
e
change
d
NLMSA p
a
i
r
wiseMode to allow reporting
of s
e
lf
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
C
hristo
p
her L
e
e
Merge commit
'
remotes/mksz
u
ba/deb
i
an'
commit
|
commitdiff
|
tree
2009-07-29
Christopher
L
ee
re
t
r
y
re
a
d
i
ng port_file
i
n Tes
t
X
M
LRP
C
S
erve
r
sever
a
l
.
.
.
commit
|
commitdiff
|
tree
2009-07-29
Christopher
L
e
e
added comments to proces
s
_blast()
commit
|
commitdiff
|
tree
2009-07-29
Chri
s
top
h
er
L
e
e
f
ix
prob
l
em
i
ntroduced
i
n
p
r
o
c
e
s
s_blast() by
commit
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Ch
r
i
st
o
pher
L
ee
h
an
d
le mis
s
i
ng W
I
NDIR case on Windows
commit
|
commitdiff
|
tree
2009-07-28
Chris
t
ophe
r
Lee
added SeqTransl
a
tor
.
__repr__
(
)
commit
|
commitdiff
|
tree
2009-07-28
Chr
i
s
top
h
er Lee
Merge commit
'remotes
/
ctb/s
i
m
ple
f
rame_for
m
a
t
db_cleanu
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher
Lee
Merge br
a
nch 'm
a
ster'
i
nto s
i
mplef
r
ame
commit
|
commitdiff
|
tree
2009-07-28
Chri
s
tophe
r
L
e
e
added SeqT
r
a
n
slator
.
iter_frames() met
h
od
,
used in B
l
astxMapp
.
.
.
commit
|
commitdiff
|
tree
2009-07-28
Christopher Lee
Merge
commit '
r
e
m
o
tes/ctb
/
simple
f
ra
m
e_doc_align' i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher Le
e
protec
t
2 more tests
u
sing blas
t
_enabled() check
commit
|
commitdiff
|
tree
2009-07-27
Chri
s
toph
e
r Lee
fixed syn
t
ax
error
commit
|
commitdiff
|
tree
2009-07-27
Chr
i
stopher
L
e
e
added
p
ython 2
.
3 code for FilePopen t
o
d
e
t
ect
b
ad ex
i
t
.
.
.
commit
|
commitdiff
|
tree
2009-07-27
Christopher
Lee
Merge
branch 'no_
e
dg
e
_db'
commit
|
commitdiff
|
tree
2009-07-27
Christ
o
pher Lee
Merge branc
h
'sile
n
cio'
commit
|
commitdiff
|
tree
2009-07-27
Christopher
L
ee
added showFormat
d
bMessag
e
s op
t
ion to Bl
a
st
M
apping
commit
|
commitdiff
|
tree
2009-07-25
Christopher Lee
adde
d
support
f
o
r no
-
edgeDB case in mapping
.
Graph:
.
.
.
commit
|
commitdiff
|
tree
2009-07-23
Chr
i
s
topher Lee
a
d
de
d
o
p
t
ion for
latex o
u
tpu
t
of the refer
e
nce man
u
al
commit
|
commitdiff
|
tree
2009-07-16
Christop
h
er Lee
M
e
rg
e
com
m
it 'r
e
motes/
c
tb/b
l
as
t
_test_rc' into simplefr
a
me
commit
|
commitdiff
|
tree
2009-07-16
Christopher Lee
a
d
d
ed m
o
re
d
o
c
stri
n
gs for blast
.
py
commit
|
commitdiff
|
tree
2009-07-16
Christopher
L
ee
remove
d
old BlastxMapping code
commit
|
commitdiff
|
tree
2009-07-16
C
hristophe
r
Lee
new, greatly s
i
m
plified BlastxMappin
g
commit
|
commitdiff
|
tree
2009-07-16
Chris
t
opher Le
e
switched test_bla
s
tx_server to us
e
new TranslationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Chr
i
stophe
r
Lee
ad
d
ed read_blast_al
i
gnment() transl
a
teDest
option
commit
|
commitdiff
|
tree
2009-07-16
Chri
s
topher Lee
added NLMSA
.
edg
e
s() method
commit
|
commitdiff
|
tree
2009-07-16
Christopher
Lee
switched test_tb
l
ast
n
_parser to use new Tran
s
lationDB
.
.
.
commit
|
commitdiff
|
tree
2009-07-16
Ch
r
istoph
e
r Lee
switc
h
t
blastn
to use new Tran
s
lation
D
B approach
commit
|
commitdiff
|
tree
2009-07-15
Christopher
L
e
e
added t
r
ans
l
atio
n
DB
.
py
commit
|
commitdiff
|
tree
2009-07-15
Christopher
L
ee
move
d
d
b
name default into g
e
t
_
bo
u
nd_subclass()
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
mak
e
CoordsTo
I
nt
e
rval
s
/ get_interval()
u
se seq
.
absolu
t
e
_
sli
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
C
h
r
istopher Lee
cleaned
u
p Seq
P
at
h
.
classy
S
li
c
e()
commit
|
commitdiff
|
tree
2009-07-15
Christ
o
pher
Lee
Merge commi
t
're
m
otes
/
m
kszuba/nlmsa_no_verbos
e
' i
n
to
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Chr
i
s
t
opher Lee
Mer
g
e com
m
it 'remotes/mkszuba/cn
e
stedlist_n
o
ti
c
e' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-15
Christophe
r
Lee
incomple
t
e
ne
w
code for Tr
a
nslatio
n
DB
commit
|
commitdiff
|
tree
2009-07-15
Chri
s
topher Lee
cleaned up rev
e
rsePath con
s
truction
commit
|
commitdiff
|
tree
2009-07-15
Christopher Lee
a
d
d absol
u
te_sl
i
c
e()
m
ethod t
o
S
e
qPat
h
commit
|
commitdiff
|
tree
2009-07-14
Christopher Lee
Mer
g
e commit 'r
e
motes/mksz
u
b
a/cnestedlist_lo
g
ger' into
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
Mare
k
Szuba
Given
e
xi
s
ting isolation problems between t
e
s
t
s
run
.
.
.
commit
|
commitdiff
|
tree
2009-07-14
C
hristoph
e
r Lee
Merg
e
branch
'master'
i
n
t
o me
g
atests
commit
|
commitdiff
|
tree
2009-07-03
Christopher L
e
e
M
e
r
g
e bra
n
ch 'formatdb_fail'
commit
|
commitdiff
|
tree
2009-07-03
C
hristopher Lee
improve
d
wh
i
tespace
path warning
commit
|
commitdiff
|
tree
2009-07-03
Christ
o
pher
L
ee
added warning
for whitespa
c
e in
p
ath
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
Merge commit 'remotes/mks
z
uba/m
e
g
a
t
ests'
commit
|
commitdiff
|
tree
2009-07-01
C
h
ristopher L
e
e
use g
l
ob
.
glob(
)
instead of os
.
li
s
t
d
ir(); cleaned
u
p
.
.
.
commit
|
commitdiff
|
tree
2009-07-01
Christopher Lee
Mer
g
e co
m
mit 'remotes/mk
s
zu
b
a/
m
im
e
text'
commit
|
commitdiff
|
tree
2009-07-01
C
h
r
istopher Lee
Mer
g
e commit 'remot
e
s
/mkszuba/docfixes'
commit
|
commitdiff
|
tree
2009-07-01
Christo
p
her Lee
M
er
g
e
c
o
mmit 'rem
o
tes
/
mk
s
zuba
/
h
ashlib'
commit
|
commitdiff
|
tree
2009-06-26
Ch
r
istop
h
er Lee
fixed
cach
i
ng
bug
i
n
trodu
c
ed in
c
ommit 8d
9
966 i
n
P
refixUnion
.
.
.
commit
|
commitdiff
|
tree
2009-06-20
Christophe
r
Lee
deprecated
cursor argum
e
nt to SQLTable
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
fi
x
ed issue 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
added
test for issue 99
commit
|
commitdiff
|
tree
2009-06-20
Christopher Lee
cleaned
up SQLi
t
eServerIn
f
o
commit
|
commitdiff
|
tree
2009-06-20
Christoph
e
r Lee
ad
d
ed DBServerInf
o
.
new_c
u
rsor() method
commit
|
commitdiff
|
tree
2009-06-13
Christopher Lee
Me
r
g
e
co
m
mit 'remotes/mkszub
a
/issue
9
7_test' i
n
to is
s
ue97_test
commit
|
commitdiff
|
tree
2009-06-13
Christopher
L
ee
removed
r
e
dunda
n
t and buggy rst
r
ip("
.
py"
)
call fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2009-06-12
Christopher Lee
fix
p
yrex cdef
commit
|
commitdiff
|
tree
2009-06-12
Chris
t
opher Lee
fi
x
issue97
commit
|
commitdiff
|
tree
2009-06-12
Christ
o
pher Lee
raised
m
i
nim
u
m identity for relaxed blast tests to 60%
commit
|
commitdiff
|
tree
2009-06-09
C
h
rist
o
p
h
er Lee
replaced
a
f
e
w remain
i
ng
refs in the docs
t
o pyg
r
.
Dat
a
.
.
.
commit
|
commitdiff
|
tree
2009-06-09
Christo
p
her Lee
Me
r
ge comm
i
t
'
r
e
mote
s
/mkszuba/deb
'
commit
|
commitdiff
|
tree
2009-06-09
Christ
o
pher Lee
M
erge commit 'r
e
m
otes/mkszub
a
/ren
a
mes'
commit
|
commitdiff
|
tree
2009-06-09
Christopher Lee
Merge branch 'interval_filt
e
rs' int
o
bla
s
t_te
s
ts
commit
|
commitdiff
|
tree
2009-06-09
Christopher Le
e
relaxed-tes
t
s had a bug that made
them pass the comparison
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christop
h
er
L
ee
must
c
l
o
se FileP
o
pen object before
e
xiting BlastxMapping
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Chr
i
stopher Lee
m
e
r
g
ed
i
n ct
b
/blastx_da
t
a
b
a
se
commit
|
commitdiff
|
tree
2009-06-04
Chris
t
opher Le
e
Merge commit 'remot
e
s
/ctb/
b
l
a
st
x
_generator' into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-04
Christop
h
er Lee
P
E
P8 and whi
t
espace f
i
xes to
nlm
s
a_utils
.
py; no functi
o
nalit
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
Christopher Lee
conve
r
t
ed add_al
i
gned_intervals functiona
l
ity into
.
.
.
commit
|
commitdiff
|
tree
2009-06-04
C
h
r
i
s
t
opher Lee
clean up Attribu
t
eInterface a
c
c
o
r
d
ing to
Titus suggestions
commit
|
commitdiff
|
tree
2009-06-04
Christopher Le
e
Merge commit 'r
e
mot
e
s/ctb/ctb_intervals' into int
e
rv
a
l_filters
commit
|
commitdiff
|
tree
2009-06-03
Chri
s
t
opher L
e
e
Merge com
m
i
t
'r
e
motes/
c
tb
/
ctb_blast2' into ctb_t
m
p
commit
|
commitdiff
|
tree
2009-06-03
Christopher L
e
e
Mer
g
e commit
'r
e
motes/ctb/min
o
r_doc_fixes'
into ctb_tmp
commit
|
commitdiff
|
tree
2009-06-03
Christopher Lee
me
r
ged in ctb
/
a
nnot
a
tion
commit
|
commitdiff
|
tree
next