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add test for leading whitespace before exonerate query, fix to work with old exonerat...
2011-03-17
Robert Buels
add test for leading whit
e
spa
c
e before e
x
onerate que
r
y
.
.
.
commit
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commitdiff
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tree
2011-03-17
Rob
e
rt B
u
els
fix bi
g
perfor
m
a
n
ce regress
i
o
n in
w
hich _load
_
modu
l
e
.
.
.
commit
|
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tree
2011-03-17
Rober
t
Buels
improved
B
io::SeqFeature::Generi
c
::has_tag performance
.
.
.
commit
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commitdiff
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tree
2011-03-17
Robert Buels
im
p
roved _
r
earrange performa
n
ce by 30%
commit
|
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tree
2011-03-08
R
obert Bue
l
s
bugfix to Bi
o
::Tools:
:
RepeatMasker, reverse ma
t
c
h
es
.
.
.
commit
|
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tree
2011-03-08
Rob
e
rt Buels
lo
c
alize $_
i
f you are
g
oing to modify it in a lib
.
.
.
commit
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tree
2011-02-24
Rob
e
rt
B
uels
add a
c
ou
p
le more tests
f
o
r new
p
has
e
acces
s
or
commit
|
commitdiff
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tree
2011-02-24
Robert Buels
add
p
hase
attr to Bio::Seq
F
eatureI,
t
o
match Bio::SeqFeature
.
.
.
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|
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tree
2010-11-22
Robert Bu
e
ls
add seq
(
) me
t
hod to PrimaryQual,
w
hic
h
is similar to
.
.
.
commit
|
commitdiff
|
tree
2010-11-18
Robert Buels
add
.
qual
file ext to file
extension
g
uessing in Se
q
IO
.
.
.
commit
|
commitdiff
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tree
2010-07-30
Robert Buels
dir in maint f
o
r working on dyn
a
miting the monolith
commit
|
commitdiff
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tree
2010-07-29
R
o
bert Buels
strip keyword
sub
s
tituti
o
n from perl scripts
commit
|
commitdiff
|
tree
2010-07-29
Robert Buels
strip keywor
d
su
b
stitution from perl modules
commit
|
commitdiff
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tree
2010-07-26
R
o
bert Buels
Stand
A
lo
n
eBlast
.
t should
a
ll
o
w
different t
y
pes
o
f q
u
o
ting
commit
|
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tree
2010-07-26
Robert Buels
whitesp
a
ce cleanup in
WrapperBase
.
p
m code
commit
|
commitdiff
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tree
2010-07-20
Robert Buels
broke t/Assembly/As
s
embly
.
t into 3 sane test files
commit
|
commitdiff
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tree
2010-07-20
Rob
e
rt Buels
more perltidy
commit
|
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tree
2010-07-20
Robert Buels
added
'R
e
gion' interpro
type
.
recently-adde
d
test
.
.
.
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|
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tree
2010-07-20
R
o
be
r
t Buels
more perltidy
commit
|
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tree
2010-07-20
Robert
B
uels
more p
e
rl
t
idy
commit
|
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tree
2010-07-20
Robert
Buels
added a
littl
e
defens
i
ve error checking when a
d
ding
.
.
.
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|
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|
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2010-07-20
Rob
e
rt Bue
l
s
interpro
parser
now thro
w
s a
n
er
r
or when it cann
o
t
.
.
.
commit
|
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2010-07-20
Robert Buels
perltidy on SimpleO
n
tologyEngine
.
pm using bioperl perltidy
.
.
.
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|
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|
tree
2010-07-20
Rob
e
rt Bue
l
s
m
oved platform dete
c
t
i
on
out of i
n
ner
loop of Bio:
.
.
.
commit
|
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|
tree
2010-06-07
R
ob
e
rt Bu
e
l
s
Me
r
ge br
a
nch 'master' of g
i
th
u
b
.
c
om:bioperl/biope
r
l
.
.
.
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|
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|
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2010-06-07
Ro
b
ert Buels
M
e
rge
branch 'topic/
l
ongest_orf' into moster
commit
|
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2010-06-07
Robert Buels
PrimarySe
q
I
.
pm
whitespac
e
cleanup
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|
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2010-06-07
Robert
B
uels
clarified some
t
ranslate() POD
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|
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2010-06-07
Robert B
u
els
added comment (not po
d
) b
l
o
c
k for internal _codo
n
_i
s
.
.
.
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|
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|
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2010-06-05
R
o
bert Buels
clean up s
t
ray whitespace
i
n Assembly
.
t
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|
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2010-06-05
R
o
b
ert
B
uels
added m
o
re intensive te
s
t
s for longest-orf-finding
.
.
.
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|
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2010-06-05
Robert Bue
l
s
tw
e
a
ked tra
n
slate() a
r
gs
for
m
at,
removed -longest_orf
.
.
.
commit
|
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2010-06-05
Rob
e
r
t Buels
anoth
e
r transl
a
te() do
c
patch fo
r
better r
e
nder
i
n
g
o
n
.
.
.
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|
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2010-06-05
Robert Buels
m
ore sa
n
e
(maintainab
l
e)
format for translate() opti
o
n
.
.
.
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|
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2010-05-25
Ro
b
ert
Buels
test
f
ix: if t
h
is translate(
)
is
su
p
posed to di
e
,
i
t
.
.
.
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|
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2010-05-25
Robe
r
t B
u
e
ls
docpatch to examples/long
o
rf
.
p
l
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|
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2010-05-21
Robert Bue
l
s
added comment with the bases used in th
e
codo
n
t
a
ble
.
.
.
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|
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2010-05-21
Rob
e
rt Bu
e
l
s
f
ixed suppo
r
t
for al
s
o includ
i
ng pa
r
t
ial
O
RFs
at the
.
.
.
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|
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2010-05-21
Robert Bue
l
s
test for partial-orf warning
should
re
q
ui
r
e t
h
e ORF
.
.
.
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|
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2010-05-21
Rob
e
rt
Buels
updated topic/longe
s
t_orf from mas
t
er
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|
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2010-05-21
Robert Bu
e
ls
orf finde
r
gett
i
ng
c
loser
t
o passing
.
.
.
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|
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2010-05-21
Robert Bu
e
ls
m
ore tests for th
e
o
rf f
i
nder
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|
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|
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2010-05-21
R
o
bert
B
uels
_find_orfs now r
e
cognizes orfs that reach th
e
e
n
d
of
.
.
.
commit
|
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|
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2010-05-21
Rober
t
Buels
test for
ORF missing-sto
p
-codon
wa
r
n
ing should be m
o
r
e
.
.
.
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|
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|
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2010-05-21
Rob
e
rt B
u
els
whitespace corr
e
ction
commit
|
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|
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2010-05-21
R
o
bert Buels
te
s
t fix: if
this
tr
a
nsl
a
te() is s
u
pposed to
die, it
.
.
.
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|
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2010-05-21
R
o
bert Bu
e
ls
r
efactored ORF finding
i
n Bio::Pr
i
m
aryS
e
qI, in order
.
.
.
commit
|
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|
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2010-05-21
Ro
b
e
rt Buels
tig
h
tened an
d
clean
e
d up perl in Bio::Tools::CodonTable
.
.
.
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|
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2010-05-21
Robert Bu
e
l
s
B
i
o
:
:
T
o
ols::C
o
do
n
Table whitespac
e
cleanu
p
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|
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|
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2010-05-20
Robe
r
t Buels
docpatch to ex
a
mples/longo
r
f
.
pl
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|
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|
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2010-05-20
Robert
Buel
s
docpatch to
examples/lo
n
gorf
.
pl
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|
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|
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2010-05-20
R
obert Bu
e
ls
if Bio
:
:DB
:
:Taxonomy::entrez cannot load XML::
T
w
i
g
.
.
.
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