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The new install version based on classical setup.py #1

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coissac merged 15 commits from pip-standard-orig-python into master 2019-03-29 15:25:03 +00:00
Conversation 2 Commits 15 Files Changed 40 +169 -98
3 changed files with 169 additions and 98 deletions
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2
python/obitools3/apps/temp.pxd
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@ -6,3 +6,5 @@ Created on 28 juillet 2017
@author: coissac
'''
from obitools3.dms.dms cimport DMS
from obitools3.utils cimport tobytes,tostr

3
python/obitools3/apps/temp.pyx
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@ -17,9 +17,6 @@ from obitools3.dms.dms import DMS
from obitools3.apps.config import getConfiguration
from obitools3.apps.config import logger
from obitools3.dms.dms cimport DMS
from obitools3.utils cimport tobytes,tostr
cpdef get_temp_dir():
"""
Returns a temporary directory object specific of this instance of obitools.

110
python/obitools3/dms/column/column.cfiles Normal file
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@ -0,0 +1,110 @@
../../../../src/obi_lcs.h
../../../../src/obi_lcs.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/utils.h
../../../../src/utils.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/libjson/json_utils.h
../../../../src/libjson/json_utils.c
../../../../src/libjson/cJSON.h
../../../../src/libjson/cJSON.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/linked_list.h
../../../../src/linked_list.c
../../../../src/obidmscolumn_array.h
../../../../src/obidmscolumn_array.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn_str.c
../../../../src/array_indexer.h
../../../../src/array_indexer.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.c
../../../../src/encode.h
../../../../src/uint8_indexer.c
../../../../src/uint8_indexer.h
../../../../src/build_reference_db.c
../../../../src/build_reference_db.h
../../../../src/kmer_similarity.c
../../../../src/kmer_similarity.h
../../../../src/obi_clean.c
../../../../src/obi_clean.h
../../../../src/obi_ecopcr.c
../../../../src/obi_ecopcr.h
../../../../src/obi_ecotag.c
../../../../src/obi_ecotag.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms_taxonomy.h
../../../../src/obilittlebigman.c
../../../../src/obilittlebigman.h
../../../../src/_sse.h
../../../../src/obidebug.h
../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../src/libecoPCR/libapat/apat_parse.c
../../../../src/libecoPCR/libapat/apat_search.c
../../../../src/libecoPCR/libapat/apat.h
../../../../src/libecoPCR/libapat/Gmach.h
../../../../src/libecoPCR/libapat/Gtypes.h
../../../../src/libecoPCR/libapat/libstki.c
../../../../src/libecoPCR/libapat/libstki.h
../../../../src/libecoPCR/libthermo/nnparams.h
../../../../src/libecoPCR/libthermo/nnparams.c
../../../../src/libecoPCR/ecoapat.c
../../../../src/libecoPCR/ecodna.c
../../../../src/libecoPCR/ecoError.c
../../../../src/libecoPCR/ecoMalloc.c
../../../../src/libecoPCR/ecoPCR.h

17
python/obitools3/dms/column/column.pxd
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@ -1,21 +1,14 @@
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t, \
name_data_type, \
obitype_t, \
obiversion_t, \
OBI_QUAL
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_header_p, \
obi_close_column, \
obi_get_elements_names, \
obi_column_write_comments
from ..capi.obitypes cimport index_t, \
obitype_t
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ..capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.view.view cimport View
from ..view.view cimport View
from obitools3.dms.object cimport OBIWrapper
from ..object cimport OBIWrapper
cdef dict __OBIDMS_COLUMN_CLASS__

26
python/obitools3/dms/column/column.pyx
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@ -3,31 +3,27 @@
__OBIDMS_COLUMN_CLASS__ = {}
from obitools3.dms.object cimport OBIWrapper
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obitypes cimport index_t, \
name_data_type, \
obitype_t, \
obiversion_t, \
OBI_QUAL
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_header_p, \
from ..capi.obitypes cimport name_data_type, \
obitype_t, \
obiversion_t, \
OBI_QUAL
from ..capi.obidms cimport obi_import_column
from ..capi.obidmscolumn cimport OBIDMS_column_header_p, \
obi_close_column, \
obi_get_elements_names, \
obi_column_write_comments
from obitools3.dms.capi.obidms cimport obi_import_column
from obitools3.dms.view.view cimport View
from obitools3.dms.capi.obiutils cimport obi_format_date
from ..capi.obiutils cimport obi_format_date
from obitools3.dms.capi.obiview cimport obi_view_add_column, \
from ..capi.obiview cimport obi_view_add_column, \
obi_view_get_pointer_on_column_in_view, \
Obiview_p, \
NUC_SEQUENCE_COLUMN
from obitools3.dms.object cimport OBIDeactivatedInstanceError
from ..object cimport OBIDeactivatedInstanceError
from obitools3.utils cimport tobytes, \
bytes2str, \

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python/obitools3/dms/column/column_idx.cfiles Normal file
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@ -0,0 +1,110 @@
../../../../src/obi_lcs.h
../../../../src/obi_lcs.c
../../../../src/obierrno.h
../../../../src/obierrno.c
../../../../src/upperband.h
../../../../src/upperband.c
../../../../src/sse_banded_LCS_alignment.h
../../../../src/sse_banded_LCS_alignment.c
../../../../src/obiblob.h
../../../../src/obiblob.c
../../../../src/utils.h
../../../../src/utils.c
../../../../src/obidms.h
../../../../src/obidms.c
../../../../src/libjson/json_utils.h
../../../../src/libjson/json_utils.c
../../../../src/libjson/cJSON.h
../../../../src/libjson/cJSON.c
../../../../src/obiavl.h
../../../../src/obiavl.c
../../../../src/bloom.h
../../../../src/bloom.c
../../../../src/crc64.h
../../../../src/crc64.c
../../../../src/murmurhash2.h
../../../../src/murmurhash2.c
../../../../src/obidmscolumn.h
../../../../src/obidmscolumn.c
../../../../src/obitypes.h
../../../../src/obitypes.c
../../../../src/obidmscolumndir.h
../../../../src/obidmscolumndir.c
../../../../src/obiblob_indexer.h
../../../../src/obiblob_indexer.c
../../../../src/obiview.h
../../../../src/obiview.c
../../../../src/hashtable.h
../../../../src/hashtable.c
../../../../src/linked_list.h
../../../../src/linked_list.c
../../../../src/obidmscolumn_array.h
../../../../src/obidmscolumn_array.c
../../../../src/obidmscolumn_blob.h
../../../../src/obidmscolumn_blob.c
../../../../src/obidmscolumn_idx.h
../../../../src/obidmscolumn_idx.c
../../../../src/obidmscolumn_bool.h
../../../../src/obidmscolumn_bool.c
../../../../src/obidmscolumn_char.h
../../../../src/obidmscolumn_char.c
../../../../src/obidmscolumn_float.h
../../../../src/obidmscolumn_float.c
../../../../src/obidmscolumn_int.h
../../../../src/obidmscolumn_int.c
../../../../src/obidmscolumn_qual.h
../../../../src/obidmscolumn_qual.c
../../../../src/obidmscolumn_seq.h
../../../../src/obidmscolumn_seq.c
../../../../src/obidmscolumn_str.h
../../../../src/obidmscolumn_str.c
../../../../src/array_indexer.h
../../../../src/array_indexer.c
../../../../src/char_str_indexer.h
../../../../src/char_str_indexer.c
../../../../src/dna_seq_indexer.h
../../../../src/dna_seq_indexer.c
../../../../src/encode.c
../../../../src/encode.h
../../../../src/uint8_indexer.c
../../../../src/uint8_indexer.h
../../../../src/build_reference_db.c
../../../../src/build_reference_db.h
../../../../src/kmer_similarity.c
../../../../src/kmer_similarity.h
../../../../src/obi_clean.c
../../../../src/obi_clean.h
../../../../src/obi_ecopcr.c
../../../../src/obi_ecopcr.h
../../../../src/obi_ecotag.c
../../../../src/obi_ecotag.h
../../../../src/obidms_taxonomy.c
../../../../src/obidms_taxonomy.h
../../../../src/obilittlebigman.c
../../../../src/obilittlebigman.h
../../../../src/_sse.h
../../../../src/obidebug.h
../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../src/libecoPCR/libapat/apat_parse.c
../../../../src/libecoPCR/libapat/apat_search.c
../../../../src/libecoPCR/libapat/apat.h
../../../../src/libecoPCR/libapat/Gmach.h
../../../../src/libecoPCR/libapat/Gtypes.h
../../../../src/libecoPCR/libapat/libstki.c
../../../../src/libecoPCR/libapat/libstki.h
../../../../src/libecoPCR/libthermo/nnparams.h
../../../../src/libecoPCR/libthermo/nnparams.c
../../../../src/libecoPCR/ecoapat.c
../../../../src/libecoPCR/ecodna.c
../../../../src/libecoPCR/ecoError.c
../../../../src/libecoPCR/ecoMalloc.c
../../../../src/libecoPCR/ecoPCR.h

8
python/obitools3/dms/column/column_idx.pxd
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@ -1,9 +1,11 @@
# #cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
from ..capi.obitypes cimport index_t
from .column cimport Column, \
Column_multi_elts
cdef class Column_idx(Column) :

11
python/obitools3/dms/column/column_idx.pyx
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@ -2,26 +2,23 @@
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.view.view cimport View
from ..view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from obitools3.dms.capi.obiview cimport obi_get_index_with_elt_name_and_col_p_in_view, \
from ..capi.obiview cimport obi_get_index_with_elt_name_and_col_p_in_view, \
obi_get_index_with_elt_idx_and_col_p_in_view, \
obi_set_index_with_elt_name_and_col_p_in_view, \
obi_set_index_with_elt_idx_and_col_p_in_view, \
Obiview_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ..capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obitypes cimport OBI_IDX, OBIIdx_NA, index_t
from ..capi.obitypes cimport OBI_IDX, OBIIdx_NA, index_t
from cpython.long cimport PyLong_FromLongLong
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
# TODO overwrite other functions from Column and Column_multi_elts

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python/obitools3/dms/column/typed_column/bool.cfiles Normal file
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@ -0,0 +1,110 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

4
python/obitools3/dms/column/typed_column/bool.pxd
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@ -1,9 +1,9 @@
# #cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from ...capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column, \
from ..column cimport Column, \
Column_multi_elts

16
python/obitools3/dms/column/typed_column/bool.pyx
View File

@ -2,20 +2,14 @@
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
from ..column cimport register_column_class
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column cimport register_column_class
from obitools3.dms.view.view cimport View
from ...view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from obitools3.dms.capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
from ...capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
obi_get_bool_with_elt_idx_and_col_p_in_view, \
obi_set_bool_with_elt_name_and_col_p_in_view, \
obi_set_bool_with_elt_idx_and_col_p_in_view, \
@ -23,9 +17,9 @@ from obitools3.dms.capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_
obi_set_array_with_col_p_in_view, \
Obiview_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
from ...capi.obitypes cimport OBI_BOOL, \
OBIBool_NA, \
OBITuple_NA, \
obibool_t

110
python/obitools3/dms/column/typed_column/char.cfiles Normal file
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@ -0,0 +1,110 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

4
python/obitools3/dms/column/typed_column/char.pxd
View File

@ -1,9 +1,9 @@
# #cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from ...capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column, \
from ..column cimport Column, \
Column_multi_elts

17
python/obitools3/dms/column/typed_column/char.pyx
View File

@ -1,20 +1,15 @@
#cython: language_level=3
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
from ..column cimport register_column_class
from obitools3.dms.column.column cimport register_column_class
from obitools3.dms.view.view cimport View
from ...view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from obitools3.dms.capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \
from ...capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_view, \
obi_get_char_with_elt_idx_and_col_p_in_view, \
obi_set_char_with_elt_name_and_col_p_in_view, \
obi_set_char_with_elt_idx_and_col_p_in_view, \
@ -22,9 +17,9 @@ from obitools3.dms.capi.obiview cimport obi_get_char_with_elt_name_and_col_p_in_
obi_set_array_with_col_p_in_view, \
Obiview_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obitypes cimport OBI_CHAR, \
from ...capi.obitypes cimport OBI_CHAR, \
OBIChar_NA, \
OBITuple_NA, \
obichar_t
@ -121,7 +116,7 @@ cdef class Column_multi_elts_char(Column_multi_elts):
cpdef set_item(self, index_t line_nb, object elt_id, object value) :
global obi_errno
cdef bytes elt_name
cdef bytes elt_name
cdef obichar_t value_b
if value is None :
value_b = OBIChar_NA

110
python/obitools3/dms/column/typed_column/float.cfiles Normal file
View File

@ -0,0 +1,110 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

4
python/obitools3/dms/column/typed_column/float.pxd
View File

@ -1,9 +1,9 @@
# #cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from ...capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column, \
from ..column cimport Column, \
Column_multi_elts

15
python/obitools3/dms/column/typed_column/float.pyx
View File

@ -1,20 +1,15 @@
#cython: language_level=3
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
from ..column cimport register_column_class
from obitools3.dms.column.column cimport register_column_class
from obitools3.dms.view.view cimport View
from ...view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from obitools3.dms.capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \
from ...capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in_view, \
obi_get_float_with_elt_idx_and_col_p_in_view, \
obi_set_float_with_elt_name_and_col_p_in_view, \
obi_set_float_with_elt_idx_and_col_p_in_view, \
@ -22,9 +17,9 @@ from obitools3.dms.capi.obiview cimport obi_get_float_with_elt_name_and_col_p_in
obi_set_array_with_col_p_in_view, \
Obiview_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obitypes cimport OBI_FLOAT, \
from ...capi.obitypes cimport OBI_FLOAT, \
OBIFloat_NA, \
OBITuple_NA, \
obifloat_t

110
python/obitools3/dms/column/typed_column/int.cfiles Normal file
View File

@ -0,0 +1,110 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

4
python/obitools3/dms/column/typed_column/int.pxd
View File

@ -1,9 +1,9 @@
# #cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from ...capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column, \
from ..column cimport Column, \
Column_multi_elts

14
python/obitools3/dms/column/typed_column/int.pyx
View File

@ -1,19 +1,15 @@
#cython: language_level=3
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column cimport Column, \
Column_multi_elts
from ..column cimport register_column_class
from obitools3.dms.column.column cimport register_column_class
from obitools3.dms.view.view cimport View
from ...view.view cimport View
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from obitools3.dms.capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \
from ...capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_view, \
obi_get_int_with_elt_idx_and_col_p_in_view, \
obi_set_int_with_elt_name_and_col_p_in_view, \
obi_set_int_with_elt_idx_and_col_p_in_view, \
@ -21,9 +17,9 @@ from obitools3.dms.capi.obiview cimport obi_get_int_with_elt_name_and_col_p_in_v
obi_set_array_with_col_p_in_view, \
Obiview_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obitypes cimport OBI_INT, \
from ...capi.obitypes cimport OBI_INT, \
OBIInt_NA, \
OBITuple_NA, \
obiint_t

110
python/obitools3/dms/column/typed_column/qual.cfiles Normal file
View File

@ -0,0 +1,110 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

6
python/obitools3/dms/column/typed_column/qual.pxd
View File

@ -1,10 +1,10 @@
# #cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from ...capi.obitypes cimport index_t
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx
from ..column_idx cimport Column_idx, \
Column_multi_elts_idx
cdef class Column_qual(Column_idx) :

18
python/obitools3/dms/column/typed_column/qual.pyx
View File

@ -1,21 +1,17 @@
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.view.view cimport View
from ..column cimport register_column_class
from obitools3.dms.column.column cimport Column, \
register_column_class
from ...view.view cimport View
from ..column cimport Column
from obitools3.utils cimport tobytes, bytes2str, \
obi_errno_to_exception
from obitools3.dms.capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \
from ...capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_p_in_view, \
obi_get_qual_char_with_elt_idx_and_col_p_in_view, \
obi_set_qual_char_with_elt_name_and_col_p_in_view, \
obi_set_qual_char_with_elt_idx_and_col_p_in_view, \
@ -25,9 +21,9 @@ from obitools3.dms.capi.obiview cimport obi_get_qual_char_with_elt_name_and_col_
obi_set_qual_int_with_elt_idx_and_col_p_in_view, \
Obiview_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obitypes cimport OBI_QUAL, OBIQual_char_NA, OBIQual_int_NA, const_char_p
from ...capi.obitypes cimport OBI_QUAL, OBIQual_char_NA, OBIQual_int_NA, const_char_p
from libc.stdlib cimport malloc, free
from libc.stdint cimport uint8_t

110
python/obitools3/dms/column/typed_column/seq.cfiles Normal file
View File

@ -0,0 +1,110 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

4
python/obitools3/dms/column/typed_column/seq.pxd
View File

@ -1,9 +1,9 @@
# #cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from ...capi.obitypes cimport index_t
from obitools3.dms.column.column_idx cimport Column_idx, \
from ..column_idx cimport Column_idx, \
Column_multi_elts_idx

17
python/obitools3/dms/column/typed_column/seq.pyx
View File

@ -1,20 +1,17 @@
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.column.column cimport Column, register_column_class
from ..column cimport register_column_class
from obitools3.dms.view.view cimport View
from ...view.view cimport View
from ..column cimport Column
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from obitools3.dms.capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
from ...capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_view, \
obi_get_seq_with_elt_idx_and_col_p_in_view, \
obi_set_seq_with_elt_name_and_col_p_in_view, \
obi_set_seq_with_elt_idx_and_col_p_in_view, \
@ -24,9 +21,9 @@ from obitools3.dms.capi.obiview cimport obi_get_seq_with_elt_name_and_col_p_in_v
obi_set_array_with_col_p_in_view, \
Obiview_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obitypes cimport OBI_SEQ, \
from ...capi.obitypes cimport OBI_SEQ, \
OBISeq_NA, \
OBITuple_NA

110
python/obitools3/dms/column/typed_column/str.cfiles Normal file
View File

@ -0,0 +1,110 @@
../../../../../src/obi_lcs.h
../../../../../src/obi_lcs.c
../../../../../src/obierrno.h
../../../../../src/obierrno.c
../../../../../src/upperband.h
../../../../../src/upperband.c
../../../../../src/sse_banded_LCS_alignment.h
../../../../../src/sse_banded_LCS_alignment.c
../../../../../src/obiblob.h
../../../../../src/obiblob.c
../../../../../src/utils.h
../../../../../src/utils.c
../../../../../src/obidms.h
../../../../../src/obidms.c
../../../../../src/libjson/json_utils.h
../../../../../src/libjson/json_utils.c
../../../../../src/libjson/cJSON.h
../../../../../src/libjson/cJSON.c
../../../../../src/obiavl.h
../../../../../src/obiavl.c
../../../../../src/bloom.h
../../../../../src/bloom.c
../../../../../src/crc64.h
../../../../../src/crc64.c
../../../../../src/murmurhash2.h
../../../../../src/murmurhash2.c
../../../../../src/obidmscolumn.h
../../../../../src/obidmscolumn.c
../../../../../src/obitypes.h
../../../../../src/obitypes.c
../../../../../src/obidmscolumndir.h
../../../../../src/obidmscolumndir.c
../../../../../src/obiblob_indexer.h
../../../../../src/obiblob_indexer.c
../../../../../src/obiview.h
../../../../../src/obiview.c
../../../../../src/hashtable.h
../../../../../src/hashtable.c
../../../../../src/linked_list.h
../../../../../src/linked_list.c
../../../../../src/obidmscolumn_array.h
../../../../../src/obidmscolumn_array.c
../../../../../src/obidmscolumn_blob.h
../../../../../src/obidmscolumn_blob.c
../../../../../src/obidmscolumn_idx.h
../../../../../src/obidmscolumn_idx.c
../../../../../src/obidmscolumn_bool.h
../../../../../src/obidmscolumn_bool.c
../../../../../src/obidmscolumn_char.h
../../../../../src/obidmscolumn_char.c
../../../../../src/obidmscolumn_float.h
../../../../../src/obidmscolumn_float.c
../../../../../src/obidmscolumn_int.h
../../../../../src/obidmscolumn_int.c
../../../../../src/obidmscolumn_qual.h
../../../../../src/obidmscolumn_qual.c
../../../../../src/obidmscolumn_seq.h
../../../../../src/obidmscolumn_seq.c
../../../../../src/obidmscolumn_str.h
../../../../../src/obidmscolumn_str.c
../../../../../src/array_indexer.h
../../../../../src/array_indexer.c
../../../../../src/char_str_indexer.h
../../../../../src/char_str_indexer.c
../../../../../src/dna_seq_indexer.h
../../../../../src/dna_seq_indexer.c
../../../../../src/encode.c
../../../../../src/encode.h
../../../../../src/uint8_indexer.c
../../../../../src/uint8_indexer.h
../../../../../src/build_reference_db.c
../../../../../src/build_reference_db.h
../../../../../src/kmer_similarity.c
../../../../../src/kmer_similarity.h
../../../../../src/obi_clean.c
../../../../../src/obi_clean.h
../../../../../src/obi_ecopcr.c
../../../../../src/obi_ecopcr.h
../../../../../src/obi_ecotag.c
../../../../../src/obi_ecotag.h
../../../../../src/obidms_taxonomy.c
../../../../../src/obidms_taxonomy.h
../../../../../src/obilittlebigman.c
../../../../../src/obilittlebigman.h
../../../../../src/_sse.h
../../../../../src/obidebug.h
../../../../../src/libecoPCR/libapat/CODES/dft_code.h
../../../../../src/libecoPCR/libapat/CODES/dna_code.h
../../../../../src/libecoPCR/libapat/CODES/prot_code.h
../../../../../src/libecoPCR/libapat/apat_parse.c
../../../../../src/libecoPCR/libapat/apat_search.c
../../../../../src/libecoPCR/libapat/apat.h
../../../../../src/libecoPCR/libapat/Gmach.h
../../../../../src/libecoPCR/libapat/Gtypes.h
../../../../../src/libecoPCR/libapat/libstki.c
../../../../../src/libecoPCR/libapat/libstki.h
../../../../../src/libecoPCR/libthermo/nnparams.h
../../../../../src/libecoPCR/libthermo/nnparams.c
../../../../../src/libecoPCR/ecoapat.c
../../../../../src/libecoPCR/ecodna.c
../../../../../src/libecoPCR/ecoError.c
../../../../../src/libecoPCR/ecoMalloc.c
../../../../../src/libecoPCR/ecoPCR.h

4
python/obitools3/dms/column/typed_column/str.pxd
View File

@ -1,9 +1,9 @@
# #cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from ...capi.obitypes cimport index_t
from obitools3.dms.column.column_idx cimport Column_idx, \
from ..column_idx cimport Column_idx, \
Column_multi_elts_idx

36
python/obitools3/dms/column/typed_column/str.pyx
View File

@ -1,34 +1,30 @@
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport index_t
from obitools3.dms.column.column_idx cimport Column_idx, \
Column_multi_elts_idx
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.dms.column.column cimport Column, register_column_class
from ..column cimport register_column_class
from obitools3.dms.view.view cimport View
from ...view.view cimport View
from ..column cimport Column
from obitools3.utils cimport tobytes, \
obi_errno_to_exception
from obitools3.dms.capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \
obi_get_str_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_name_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view, \
obi_get_array_with_col_p_in_view, \
obi_set_array_with_col_p_in_view, \
Obiview_p
from ...capi.obiview cimport obi_get_str_with_elt_name_and_col_p_in_view, \
obi_get_str_with_elt_idx_and_col_p_in_view, \
obi_set_str_with_elt_name_and_col_p_in_view, \
obi_set_str_with_elt_idx_and_col_p_in_view, \
obi_get_array_with_col_p_in_view, \
obi_set_array_with_col_p_in_view, \
Obiview_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
from ...capi.obidmscolumn cimport OBIDMS_column_p
from obitools3.dms.capi.obitypes cimport OBI_STR, \
OBIStr_NA, \
OBITuple_NA, \
const_char_p
from ...capi.obitypes cimport OBI_STR, \
OBIStr_NA, \
OBITuple_NA, \
const_char_p
from libc.stdint cimport int32_t
from libc.stdlib cimport calloc, free

4
python/obitools3/dms/dms.pxd
View File

@ -1,8 +1,8 @@
#cython: language_level=3
from obitools3.dms.object cimport OBIWrapper
from .object cimport OBIWrapper
from obitools3.dms.capi.obidms cimport OBIDMS_p
from .capi.obidms cimport OBIDMS_p
cdef class DMS(OBIWrapper):

11
python/obitools3/dms/taxo/taxo.pxd
View File

@ -1,10 +1,10 @@
# cython: language_level=3
#cython: language_level=3
from obitools3.dms.capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
from ..capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
from obitools3.dms.dms cimport DMS
from ..dms cimport DMS
from obitools3.dms.object cimport OBIWrapper
from ..object cimport OBIWrapper
cdef class Taxonomy(OBIWrapper) :
@ -28,5 +28,4 @@ cdef class Taxonomy(OBIWrapper) :
cdef class Taxon :
cdef ecotx_t* _pointer
cdef Taxonomy _tax
cdef Taxonomy _tax

19
python/obitools3/dms/taxo/taxo.pyx
View File

@ -1,13 +1,8 @@
#cython: language_level=3
from obitools3.utils cimport str2bytes, bytes2str, tobytes, tostr
from obitools3.dms.capi.obitaxonomy cimport ecotx_t, OBIDMS_taxonomy_p
from obitools3.dms.dms cimport DMS
from obitools3.dms.object cimport OBIWrapper
from obitools3.dms.capi.obitaxonomy cimport obi_taxonomy_exists, \
from ..capi.obitaxonomy cimport obi_taxonomy_exists, \
obi_read_taxonomy, \
obi_read_taxdump, \
obi_write_taxonomy, \
@ -20,9 +15,7 @@ from obitools3.dms.capi.obitaxonomy cimport obi_taxonomy_exists, \
obi_taxo_get_genus, \
obi_taxo_get_family, \
ecotx_t
from obitools3.dms.capi.obidms cimport OBIDMS_p
from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
import tarfile
@ -227,11 +220,7 @@ cdef class Taxonomy(OBIWrapper) :
cpdef write(self, object prefix) :
cdef DMS dms
cdef OBIDMS_p dms_p
dms = self._dms
dms_p = dms.pointer()
if obi_write_taxonomy(dms_p, self.pointer(), tobytes(prefix)) < 0 :
if obi_write_taxonomy(self._dms.pointer(), self.pointer(), tobytes(prefix)) < 0 :
raise Exception("Error writing the taxonomy to binary files")
@ -320,7 +309,7 @@ cdef class Taxonomy(OBIWrapper) :
cdef class Taxon : # TODO dict subclass?
def __init__(self, object taxon_capsule, Taxonomy tax) :
self._pointer = <ecotx_t*>PyCapsule_GetPointer(taxon_capsule, NULL)
self._pointer = <ecotx_t*> PyCapsule_GetPointer(taxon_capsule, NULL)
if self._pointer == NULL :
raise Exception("Error reading a taxon (NULL pointer)")
self._tax = tax

2
python/obitools3/utils.pxd
View File

@ -1,4 +1,4 @@
# cython: language_level=3
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport obitype_t, index_t

3
python/obitools3/utils.pyx
View File

@ -1,5 +1,4 @@
# cython: language_level=3
# distutils: include_dirs = src
#cython: language_level=3
from obitools3.dms.capi.obitypes cimport is_a_DNA_seq, \
OBI_VOID, \