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add .qual file ext to file extension guessing in SeqIO. submitted by Paul Cantalupo.
2010-11-18
R
obe
r
t Buels
add
.
qu
a
l fil
e
ext to file exte
n
si
o
n guessing i
n
SeqIO
.
.
.
commit
|
commitdiff
|
tree
2010-07-30
Robert
B
u
e
ls
di
r
in maint
for working
on dy
n
amiting the mono
l
ith
commit
|
commitdiff
|
tree
2010-07-29
Robert Buels
strip keyword subst
i
tution f
r
om perl scripts
commit
|
commitdiff
|
tree
2010-07-29
Robert B
u
els
s
trip ke
y
word substitution f
r
om perl modules
commit
|
commitdiff
|
tree
2010-07-26
Robert Bu
e
ls
S
tand
A
loneBlast
.
t
s
hould allow dif
f
e
r
e
n
t
types of
quotin
g
commit
|
commitdiff
|
tree
2010-07-26
R
o
bert Buels
whitespace cleanup in Wrappe
r
Base
.
pm code
commit
|
commitdiff
|
tree
2010-07-20
Robert Buels
b
r
oke t/Assembl
y
/Assem
b
ly
.
t into 3 sane test f
i
le
s
commit
|
commitdiff
|
tree
2010-07-20
Ro
b
ert
B
uels
more
perltidy
commit
|
commitdiff
|
tree
2010-07-20
Robert Buels
ad
d
ed
'Region' interp
r
o type
.
recently-a
d
ded
t
est
.
.
.
commit
|
commitdiff
|
tree
2010-07-20
Robert Buel
s
more perltidy
commit
|
commitdiff
|
tree
2010-07-20
Robert
B
uels
more
p
e
rltidy
commit
|
commitdiff
|
tree
2010-07-20
R
obert
B
uels
add
e
d a litt
l
e
d
efensive e
r
r
or chec
k
ing when adding
.
.
.
commit
|
commitdiff
|
tree
2010-07-20
R
obert
Buel
s
i
n
ter
p
ro p
a
rser now throws an error w
h
e
n
it cannot
.
.
.
commit
|
commitdiff
|
tree
2010-07-20
Robert Buel
s
perlt
i
dy on Simpl
e
Ontol
o
gyEngine
.
pm using bioperl p
e
r
l
t
i
dy
.
.
.
commit
|
commitdiff
|
tree
2010-07-20
R
o
bert B
u
els
moved p
l
atf
o
rm detection out of in
n
er loop of B
i
o:
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
R
o
ber
t
Buels
M
e
rge bran
c
h 'master' of git
h
ub
.
com:biop
e
rl/b
i
operl
.
.
.
commit
|
commitdiff
|
tree
2010-06-07
Robert B
u
els
Merge
branch 't
o
p
i
c/longest_orf' into moster
commit
|
commitdiff
|
tree
2010-06-07
Robert Buels
Primar
y
Seq
I
.
pm whitespace
c
lea
n
up
commit
|
commitdiff
|
tree
2010-06-07
R
obert Bu
e
ls
c
larified
some tran
s
la
t
e() POD
commit
|
commitdiff
|
tree
2010-06-07
Rober
t
Buels
added comment (
n
o
t
p
o
d) b
l
oc
k
for internal _codon_i
s
.
.
.
commit
|
commitdiff
|
tree
2010-06-05
Robert B
u
els
cle
a
n up stray w
h
ite
s
pace in
A
ssembly
.
t
commit
|
commitdiff
|
tree
2010-06-05
R
obert Buels
added
more in
t
ensive
t
ests
f
o
r
l
o
nges
t
-orf-f
i
n
ding
.
.
.
commit
|
commitdiff
|
tree
2010-06-05
Robert Buels
tweaked
t
ranslate() a
r
g
s
f
ormat, r
e
moved -longest_orf
.
.
.
commit
|
commitdiff
|
tree
2010-06-05
Rob
e
rt Buels
ano
t
her tr
a
nslate() do
c
pat
c
h for
better
r
e
n
d
eri
n
g on
.
.
.
commit
|
commitdiff
|
tree
2010-06-05
Ro
b
ert Buels
more sane (maint
a
inable) format
f
o
r
tran
s
late() option
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
Robert Buels
test fix
:
if this
t
ransl
a
te() is supposed to die
,
it
.
.
.
commit
|
commitdiff
|
tree
2010-05-25
Robert Buels
docp
a
tch to e
x
a
mples/longor
f
.
pl
commit
|
commitdiff
|
tree
2010-05-21
Robert Bu
e
ls
added comment wi
t
h the
base
s
used in
the codon table
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
R
ober
t
Buels
fixed s
u
ppo
r
t for also
i
ncluding partial ORFs at the
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
Rober
t
Buels
test f
o
r partial
-
orf warning
s
hould require the ORF
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
Ro
b
e
r
t Buels
updated topic/lo
n
gest_orf from ma
s
ter
commit
|
commitdiff
|
tree
2010-05-21
Ro
b
ert Buels
orf find
e
r getting closer to passing
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
Rober
t
Bue
l
s
m
o
re t
e
sts for
t
he orf
find
e
r
commit
|
commitdiff
|
tree
2010-05-21
Robert
Buel
s
_find_orfs
now reco
g
ni
z
es orfs
that reach the end of
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
Robert Buels
test
f
or ORF
miss
i
ng-sto
p
-codon w
a
r
n
ing should
be more
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
Robert B
u
els
w
h
itespace cor
r
ecti
o
n
commit
|
commitdiff
|
tree
2010-05-21
Robe
r
t Buels
test fix: if this translat
e
(
) is sup
p
os
e
d
t
o die, it
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
Rober
t
Buels
re
f
a
c
tored ORF finding in Bio::PrimarySeq
I
, in order
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
R
obert Buels
tighten
e
d a
n
d cleane
d
up
p
e
rl
in Bio::
T
ools::CodonTab
l
e
.
.
.
commit
|
commitdiff
|
tree
2010-05-21
Robert Bue
l
s
Bio::Tools
:
:CodonTab
l
e whit
e
space cleanup
commit
|
commitdiff
|
tree
2010-05-20
Robe
r
t Bue
l
s
docpatch to examp
l
e
s
/
longor
f
.
pl
commit
|
commitdiff
|
tree
2010-05-20
Robert B
u
el
s
doc
p
atc
h
to ex
a
mple
s
/
longorf
.
pl
commit
|
commitdiff
|
tree
2010-05-20
R
obert Buels
i
f
B
io
:
:DB::
T
axonomy::entrez cannot
load XML::Twig
.
.
.
commit
|
commitdiff
|
tree
