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OBITools
OBITools
Commits
28dad843
Commit
28dad843
authored
Mar 14, 2015
by
Eric Coissac
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6 changed files
with
51 additions
and
5 deletions
+51
-5
MANIFEST.in
MANIFEST.in
+1
-0
sdist.py
distutils.ext/obidistutils/command/sdist.py
+42
-0
core.py
distutils.ext/obidistutils/core.py
+3
-1
setup.py
setup.py
+1
-1
bioseq.py
src/obitools/utils/bioseq.py
+3
-2
version.py
src/obitools/version.py
+1
-1
No files found.
MANIFEST.in
View file @
28dad843
...
...
@@ -2,6 +2,7 @@ include setup.py
recursive-include distutils.ext *.py *.c *.pem
recursive-include src *.pyx *.pxd *.c *.h *.cfiles
recursive-include doc/sphinx/source *.txt *.rst *.py
recursive-include doc/sphinx/sphinxext *.py
include doc/sphinx/make.bat
include doc/sphinx/Makefile
include README.txt
...
...
distutils.ext/obidistutils/command/sdist.py
0 → 100644
View file @
28dad843
'''
Created on 10 mars 2015
@author: coissac
'''
import
os.path
from
distutils.command.sdist
import
sdist
as
orig_sdist
from
distutils
import
dir_util
class
sdist
(
orig_sdist
):
def
make_distribution
(
self
):
"""Create the source distribution(s). First, we create the release
tree with 'make_release_tree()'; then, we create all required
archive files (according to 'self.formats') from the release tree.
Finally, we clean up by blowing away the release tree (unless
'self.keep_temp' is true). The list of archive files created is
stored so it can be retrieved later by 'get_archive_files()'.
"""
# Don't warn about missing meta-data here -- should be (and is!)
# done elsewhere.
base_dir
=
self
.
distribution
.
get_fullname
()
base_name
=
os
.
path
.
join
(
self
.
dist_dir
,
base_dir
)
self
.
make_release_tree
(
os
.
path
.
join
(
'tmp'
,
base_dir
),
self
.
filelist
.
files
)
archive_files
=
[]
# remember names of files we create
# tar archive must be created last to avoid overwrite and remove
if
'tar'
in
self
.
formats
:
self
.
formats
.
append
(
self
.
formats
.
pop
(
self
.
formats
.
index
(
'tar'
)))
for
fmt
in
self
.
formats
:
file
=
self
.
make_archive
(
base_name
,
fmt
,
root_dir
=
'tmp'
,
base_dir
=
base_dir
,
owner
=
self
.
owner
,
group
=
self
.
group
)
archive_files
.
append
(
file
)
self
.
distribution
.
dist_files
.
append
((
'sdist'
,
''
,
file
))
self
.
archive_files
=
archive_files
if
not
self
.
keep_temp
:
dir_util
.
remove_tree
(
os
.
path
.
join
(
'tmp'
,
base_dir
),
dry_run
=
self
.
dry_run
)
distutils.ext/obidistutils/core.py
View file @
28dad843
...
...
@@ -8,6 +8,7 @@ from os import path
import
os.path
import
glob
import
sys
from
obidistutils.command.sdist
import
sdist
try
:
...
...
@@ -127,7 +128,8 @@ COMMANDS = {'build':build,
'build_sphinx'
:
build_sphinx
,
'install_scripts'
:
install_scripts
,
'install_sphinx'
:
install_sphinx
,
'install'
:
install
}
'install'
:
install
,
'sdist'
:
sdist
}
CTOOLS
=
[]
CEXES
=
[]
...
...
setup.py
View file @
28dad843
...
...
@@ -19,7 +19,7 @@ from os import path
PACKAGE
=
"OBITools"
VERSION
=
"1.1.
3
"
VERSION
=
"1.1.
4
"
AUTHOR
=
'Eric Coissac'
EMAIL
=
'eric@coissac.eu'
URL
=
'metabarcoding.org/obitools'
...
...
src/obitools/utils/bioseq.py
View file @
28dad843
...
...
@@ -58,6 +58,7 @@ def uniqSequence(seqIterator,taxonomy=None,mergedKey=None,mergeIds=False,categor
s
[
'count'
]
+=
seq
[
'count'
]
else
:
s
[
'count'
]
+=
1
seq
[
'count'
]
=
1
# if taxonomy is not None and 'taxid' in seq:
# s['merged_taxid'][seq['taxid']]=
for
key
in
mergedKey
:
...
...
@@ -70,7 +71,7 @@ def uniqSequence(seqIterator,taxonomy=None,mergedKey=None,mergeIds=False,categor
mkey
=
"merged_
%
s"
%
key
#cas ou on met a jour les merged_keys mais il n'y a pas de merged_keys dans la sequence qui arrive
if
key
in
seq
:
s
[
mkey
][
seq
[
key
]]
=
s
[
mkey
]
.
get
(
seq
[
key
],
0
)
+
1
s
[
mkey
][
seq
[
key
]]
=
s
[
mkey
]
.
get
(
seq
[
key
],
0
)
+
seq
[
'count'
]
#cas ou merged_keys existe deja
else
:
if
mkey
in
seq
:
...
...
@@ -98,7 +99,7 @@ def uniqSequence(seqIterator,taxonomy=None,mergedKey=None,mergeIds=False,categor
if
mkey
not
in
seq
:
seq
[
mkey
]
=
{}
if
key
in
seq
:
seq
[
mkey
][
seq
[
key
]]
=
seq
[
mkey
]
.
get
(
seq
[
key
],
0
)
+
1
seq
[
mkey
][
seq
[
key
]]
=
seq
[
mkey
]
.
get
(
seq
[
key
],
0
)
+
seq
[
'count'
]
del
(
seq
[
key
])
if
'count'
not
in
seq
:
...
...
src/obitools/version.py
View file @
28dad843
major
=
1
minor
=
1
serial
=
'
3
'
serial
=
'
4
'
version
=
"
%2
d.
%02
d
%
s"
%
(
major
,
minor
,
serial
)
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