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OBITools
OBITools3
Commits
9d042f7b
Commit
9d042f7b
authored
Apr 13, 2016
by
Celine Mercier
Browse files
Options
Browse Files
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Plain Diff
Refactored and relocated the set and get functions of all column types,
both within and out of the context of a view
parent
5ec2d884
Changes
28
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Showing
28 changed files
with
1081 additions
and
1322 deletions
+1081
-1322
python/obitools3/obidms/_obidms.cfiles
python/obitools3/obidms/_obidms.cfiles
+12
-0
python/obitools3/obidms/_obidmscolumn_bool.pyx
python/obitools3/obidms/_obidmscolumn_bool.pyx
+2
-2
python/obitools3/obidms/_obidmscolumn_char.pyx
python/obitools3/obidms/_obidmscolumn_char.pyx
+2
-2
python/obitools3/obidms/_obidmscolumn_float.pyx
python/obitools3/obidms/_obidmscolumn_float.pyx
+2
-2
python/obitools3/obidms/_obidmscolumn_int.pyx
python/obitools3/obidms/_obidmscolumn_int.pyx
+2
-2
python/obitools3/obidms/_obidmscolumn_seq.pyx
python/obitools3/obidms/_obidmscolumn_seq.pyx
+2
-2
python/obitools3/obidms/_obidmscolumn_str.pyx
python/obitools3/obidms/_obidmscolumn_str.pyx
+11
-11
python/obitools3/obidms/capi/obidmscolumn.pxd
python/obitools3/obidms/capi/obidmscolumn.pxd
+22
-155
python/obitools3/obidms/capi/obiview.pxd
python/obitools3/obidms/capi/obiview.pxd
+136
-0
python/obitools3/obiimport.py
python/obitools3/obiimport.py
+24
-24
src/obidmscolumn.c
src/obidmscolumn.c
+47
-1
src/obidmscolumn.h
src/obidmscolumn.h
+9
-1
src/obidmscolumn_bool.c
src/obidmscolumn_bool.c
+7
-105
src/obidmscolumn_bool.h
src/obidmscolumn_bool.h
+0
-75
src/obidmscolumn_char.c
src/obidmscolumn_char.c
+7
-106
src/obidmscolumn_char.h
src/obidmscolumn_char.h
+0
-75
src/obidmscolumn_float.c
src/obidmscolumn_float.c
+7
-105
src/obidmscolumn_float.h
src/obidmscolumn_float.h
+0
-75
src/obidmscolumn_idx.c
src/obidmscolumn_idx.c
+3
-24
src/obidmscolumn_idx.h
src/obidmscolumn_idx.h
+1
-0
src/obidmscolumn_int.c
src/obidmscolumn_int.c
+7
-107
src/obidmscolumn_int.h
src/obidmscolumn_int.h
+0
-75
src/obidmscolumn_seq.c
src/obidmscolumn_seq.c
+12
-106
src/obidmscolumn_seq.h
src/obidmscolumn_seq.h
+4
-80
src/obidmscolumn_str.c
src/obidmscolumn_str.c
+15
-109
src/obidmscolumn_str.h
src/obidmscolumn_str.h
+2
-78
src/obiview.c
src/obiview.c
+294
-0
src/obiview.h
src/obiview.h
+451
-0
No files found.
python/obitools3/obidms/_obidms.cfiles
View file @
9d042f7b
...
...
@@ -37,3 +37,15 @@
../../../src/obiview.c
../../../src/utils.h
../../../src/utils.c
../../../src/obidmscolumn_bool.c
../../../src/obidmscolumn_bool.h
../../../src/obidmscolumn_char.c
../../../src/obidmscolumn_char.h
../../../src/obidmscolumn_float.c
../../../src/obidmscolumn_float.h
../../../src/obidmscolumn_int.c
../../../src/obidmscolumn_int.h
../../../src/obidmscolumn_seq.c
../../../src/obidmscolumn_seq.h
../../../src/obidmscolumn_str.c
../../../src/obidmscolumn_str.h
python/obitools3/obidms/_obidmscolumn_bool.pyx
View file @
9d042f7b
#cython: language_level=3
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
,
\
obi_column_get_obibool_with_elt_name_in_view
,
\
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
from
.capi.obiview
cimport
obi_column_get_obibool_with_elt_name_in_view
,
\
obi_column_get_obibool_with_elt_idx_in_view
,
\
obi_column_set_obibool_with_elt_name_in_view
,
\
obi_column_set_obibool_with_elt_idx_in_view
...
...
python/obitools3/obidms/_obidmscolumn_char.pyx
View file @
9d042f7b
#cython: language_level=3
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
,
\
obi_column_get_obichar_with_elt_name_in_view
,
\
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
from
.capi.obiview
cimport
obi_column_get_obichar_with_elt_name_in_view
,
\
obi_column_get_obichar_with_elt_idx_in_view
,
\
obi_column_set_obichar_with_elt_name_in_view
,
\
obi_column_set_obichar_with_elt_idx_in_view
...
...
python/obitools3/obidms/_obidmscolumn_float.pyx
View file @
9d042f7b
#cython: language_level=3
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
,
\
obi_column_get_obifloat_with_elt_name_in_view
,
\
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
from
.capi.obiview
cimport
obi_column_get_obifloat_with_elt_name_in_view
,
\
obi_column_get_obifloat_with_elt_idx_in_view
,
\
obi_column_set_obifloat_with_elt_name_in_view
,
\
obi_column_set_obifloat_with_elt_idx_in_view
...
...
python/obitools3/obidms/_obidmscolumn_int.pyx
View file @
9d042f7b
#cython: language_level=3
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
,
\
obi_column_get_obiint_with_elt_name_in_view
,
\
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
from
.capi.obiview
cimport
obi_column_get_obiint_with_elt_name_in_view
,
\
obi_column_get_obiint_with_elt_idx_in_view
,
\
obi_column_set_obiint_with_elt_name_in_view
,
\
obi_column_set_obiint_with_elt_idx_in_view
...
...
python/obitools3/obidms/_obidmscolumn_seq.pyx
View file @
9d042f7b
#cython: language_level=3
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
,
\
obi_column_get_obiseq_with_elt_name_in_view
,
\
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
from
.capi.obiview
cimport
obi_column_get_obiseq_with_elt_name_in_view
,
\
obi_column_get_obiseq_with_elt_idx_in_view
,
\
obi_column_set_obiseq_with_elt_name_in_view
,
\
obi_column_set_obiseq_with_elt_idx_in_view
...
...
python/obitools3/obidms/_obidmscolumn_str.pyx
View file @
9d042f7b
#cython: language_level=3
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
,
\
obi_column_get_obistr_with_elt_name_in_view
,
\
from
.capi.obidmscolumn
cimport
obi_truncate_and_close_column
from
.capi.obiview
cimport
obi_column_get_obistr_with_elt_name_in_view
,
\
obi_column_get_obistr_with_elt_idx_in_view
,
\
obi_column_set_obistr_with_elt_name_in_view
,
\
obi_column_set_obistr_with_elt_idx_in_view
...
...
@@ -16,8 +16,8 @@ from libc.string cimport strcmp
cdef
class
OBIDMS_column_str
(
OBIDMS_column
):
cpdef
object
get_line
(
self
,
index_t
line_nb
):
cdef
c
har
*
value
cdef
object
result
cdef
c
onst_char_p
value
cdef
object
result
value
=
obi_column_get_obistr_with_elt_idx_in_view
(
self
.
view
,
(
self
.
pointer
)[
0
],
line_nb
,
0
)
if
obi_errno
>
0
:
raise
IndexError
(
line_nb
)
...
...
@@ -41,8 +41,8 @@ cdef class OBIDMS_column_str(OBIDMS_column):
cdef
class
OBIDMS_column_multi_elts_str
(
OBIDMS_column_multi_elts
):
cpdef
object
get_item
(
self
,
index_t
line_nb
,
str
element_name
):
cdef
c
har
*
value
cdef
object
result
cdef
c
onst_char_p
value
cdef
object
result
value
=
obi_column_get_obistr_with_elt_name_in_view
(
self
.
view
,
(
self
.
pointer
)[
0
],
line_nb
,
str2bytes
(
element_name
))
if
obi_errno
>
0
:
raise
IndexError
(
line_nb
,
element_name
)
...
...
@@ -54,11 +54,11 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
return
result
cpdef
object
get_line
(
self
,
index_t
line_nb
)
:
cdef
c
har
*
value
cdef
object
value_in_result
cdef
dict
result
cdef
index_t
i
cdef
bint
all_NA
cdef
c
onst_char_p
value
cdef
object
value_in_result
cdef
dict
result
cdef
index_t
i
cdef
bint
all_NA
result
=
{}
all_NA
=
True
for
i
in
range
(
self
.
nb_elements_per_line
)
:
...
...
python/obitools3/obidms/capi/obidmscolumn.pxd
View file @
9d042f7b
...
...
@@ -76,30 +76,7 @@ cdef extern from "obidmscolumn.h" nogil:
int
obi_select
(
OBIDMS_column_p
line_selection_column
,
index_t
line_to_grep
)
from
..capi.obiview
cimport
Obiview_p
# TODO
cdef
extern
from
"obidmscolumn_int.h"
nogil
:
int
obi_column_set_obiint_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
obiint_t
value
)
int
obi_column_set_obiint_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
obiint_t
value
)
obiint_t
obi_column_get_obiint_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
obiint_t
obi_column_get_obiint_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obiint_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
...
...
@@ -121,28 +98,6 @@ cdef extern from "obidmscolumn_int.h" nogil:
cdef
extern
from
"obidmscolumn_bool.h"
nogil
:
int
obi_column_set_obibool_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
obibool_t
value
)
int
obi_column_set_obibool_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
obibool_t
value
)
obibool_t
obi_column_get_obibool_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
obibool_t
obi_column_get_obibool_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obibool_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
...
...
@@ -163,28 +118,6 @@ cdef extern from "obidmscolumn_bool.h" nogil:
cdef
extern
from
"obidmscolumn_char.h"
nogil
:
int
obi_column_set_obichar_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
obichar_t
value
)
int
obi_column_set_obichar_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
obichar_t
value
)
obichar_t
obi_column_get_obichar_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
obichar_t
obi_column_get_obichar_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obichar_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
...
...
@@ -205,83 +138,39 @@ cdef extern from "obidmscolumn_char.h" nogil:
cdef
extern
from
"obidmscolumn_float.h"
nogil
:
int
obi_column_set_obifloat_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
obifloat_t
value
)
int
obi_column_set_obifloat_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
obifloat_t
value
)
obifloat_t
obi_column_get_obifloat_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
obifloat_t
obi_column_get_obifloat_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obifloat_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
obifloat_t
value
)
index_t
line_nb
,
const_char_p
element_name
,
obifloat_t
value
)
int
obi_column_set_obifloat_with_elt_idx
(
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
obifloat_t
value
)
index_t
line_nb
,
index_t
element_idx
,
obifloat_t
value
)
obifloat_t
obi_column_get_obifloat_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
index_t
line_nb
,
const_char_p
element_name
)
obifloat_t
obi_column_get_obifloat_with_elt_idx
(
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
cdef
extern
from
"obidmscolumn_str.h"
nogil
:
int
obi_column_set_obistr_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
char
*
value
)
index_t
element_idx
)
int
obi_column_set_obistr_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
char
*
value
)
const_char_p
obi_column_get_obistr_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
const_char_p
obi_column_get_obistr_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
cdef
extern
from
"obidmscolumn_str.h"
nogil
:
int
obi_column_set_obistr_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
c
har
*
value
)
c
onst_char_p
value
)
int
obi_column_set_obistr_with_elt_idx
(
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
c
har
*
value
)
c
onst_char_p
value
)
const_char_p
obi_column_get_obistr_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
char
*
element_name
)
index_t
line_nb
,
const_char_p
element_name
)
const_char_p
obi_column_get_obistr_with_elt_idx
(
OBIDMS_column_p
column
,
index_t
line_nb
,
...
...
@@ -289,43 +178,21 @@ cdef extern from "obidmscolumn_str.h" nogil:
cdef
extern
from
"obidmscolumn_seq.h"
nogil
:
int
obi_column_set_obiseq_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
char
*
value
)
int
obi_column_set_obiseq_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
char
*
value
)
const_char_p
obi_column_get_obiseq_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
const_char_p
obi_column_get_obiseq_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obiseq_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
c
har
*
value
)
c
onst_char_p
value
)
int
obi_column_set_obiseq_with_elt_idx
(
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
c
har
*
value
)
c
onst_char_p
value
)
c
onst_char_p
obi_column_get_obiseq_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
char
*
element_name
)
c
har
*
obi_column_get_obiseq_with_elt_name
(
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
c
onst_char_p
obi_column_get_obiseq_with_elt_idx
(
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
c
har
*
obi_column_get_obiseq_with_elt_idx
(
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
python/obitools3/obidms/capi/obiview.pxd
View file @
9d042f7b
...
...
@@ -3,6 +3,10 @@
from
.obitypes
cimport
const_char_p
,
\
OBIType_t
,
\
obiversion_t
,
\
obiint_t
,
\
obibool_t
,
\
obichar_t
,
\
obifloat_t
,
\
index_t
,
\
time_t
from
..capi.obidms
cimport
OBIDMS_p
...
...
@@ -111,4 +115,136 @@ cdef extern from "obiview.h" nogil:
int
obi_close_view
(
Obiview_p
view
)
int
obi_save_and_close_view
(
Obiview_p
view
)
int
obi_column_set_obiint_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
obiint_t
value
)
int
obi_column_set_obiint_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
obiint_t
value
)
obiint_t
obi_column_get_obiint_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
obiint_t
obi_column_get_obiint_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obibool_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
obibool_t
value
)
int
obi_column_set_obibool_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
obibool_t
value
)
obibool_t
obi_column_get_obibool_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
obibool_t
obi_column_get_obibool_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obichar_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
obichar_t
value
)
int
obi_column_set_obichar_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
obichar_t
value
)
obichar_t
obi_column_get_obichar_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
obichar_t
obi_column_get_obichar_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obifloat_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
obifloat_t
value
)
int
obi_column_set_obifloat_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
obifloat_t
value
)
obifloat_t
obi_column_get_obifloat_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
obifloat_t
obi_column_get_obifloat_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obistr_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
const_char_p
value
)
int
obi_column_set_obistr_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
const_char_p
value
)
const_char_p
obi_column_get_obistr_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
const_char_p
obi_column_get_obistr_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
int
obi_column_set_obiseq_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
,
const_char_p
value
)
int
obi_column_set_obiseq_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
,
const_char_p
value
)
char
*
obi_column_get_obiseq_with_elt_name_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
const_char_p
element_name
)
char
*
obi_column_get_obiseq_with_elt_idx_in_view
(
Obiview_p
view
,
OBIDMS_column_p
column
,
index_t
line_nb
,
index_t
element_idx
)
python/obitools3/obiimport.py
View file @
9d042f7b
...
...
@@ -26,16 +26,16 @@ if __name__ == '__main__':
view
=
d
.
new_view
(
'uniq view'
,
view_type
=
"NUC_SEQS_VIEW"
)
for
i
in
range
(
35000000
)
:
if
(
not
(
i
%
500000
))
:
print
(
str
(
time
.
time
())
+
'
\t
'
+
str
(
i
))
id
=
"@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"
+
str
(
i
)
view
[
i
].
set_id
(
id
)
if
id
!=
view
[
i
][
"ID"
]
:
print
(
"nope"
,
id
,
view
[
i
][
"ID"
])
#
for i in range(35000000) :
#
if (not (i%500000)) :
#
print(str(time.time())+'\t'+str(i))
#
id = "@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"+str(i)
#
view[i].set_id(id)
#
if id != view[i]["ID"] :
#
print("nope", id, view[i]["ID"])
#
input_file = open(args.input_file, 'r')
#
input_file_buffered = bufferedRead(input_file)
input_file
=
open
(
args
.
input_file
,
'r'
)
input_file_buffered
=
bufferedRead
(
input_file
)
#
# if args.input_file[-1:] == "a" :
...
...
@@ -113,32 +113,32 @@ if __name__ == '__main__':
# l = 0
# next = False
#
#
l=0
#
i=0
l
=
0
i
=
0
# while (True):
# l+=1
# line = input_file.readline()
# if line=="":
# break
#
for line in input_file_buffered :
for
line
in
input_file_buffered
:
#
#
#if i > 1E7 :
#if i > 1E7 :
# # print('hmm?')
#
# if i == 6000000 :
# break
#
#
if l%4 == 0 :
if
l
%
4
==
0
:
#
#
if (not (i%500000)) :
#
print(str(time.time())+'\t'+str(i))
if
(
not
(
i
%
500000
))
:
print
(
str
(
time
.
time
())
+
'
\t
'
+
str
(
i
))
# #
# # #print("header", line)
# #
#
id = line.split(" ", 1)[0][1:]
id
=
line
.
split
(
" "
,
1
)[
0
][
1
:]
# print(id)
# # #rest = (line[:-1].split(" ", 1)[1]).split(";")
#
view[i].set_id(id)
view
[
i
].
set_id
(
id
)
# print(view[i]["ID"])
#
# i+=1
...
...
@@ -178,17 +178,17 @@ if __name__ == '__main__':
# # description = description.strip()
# # view[i].set_description(description)
#
# #
elif l%4 == 1 :
elif
l
%
4
==
1
:
# #
# #
seq = line[:-1]
seq
=
line
[:
-
1
]
# #print("seq", seq)
# #
view[i].set_sequence(seq)
# #
i+=1
view
[
i
].
set_sequence
(
seq
)
i
+=
1
#
#
l+=1
l
+=
1
#
#
#
input_file.close()
input_file
.
close
()
#print(view)
print
(
view
.
__repr__
())
...
...
src/obidmscolumn.c
View file @
9d042f7b
...
...
@@ -1418,7 +1418,53 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
}
char
*
obi_column_format_date
(
time_t
date