diff --git a/python/obitools3/apps/temp.pxd b/python/obitools3/apps/temp.pxd index 2c6c690..252e41d 100755 --- a/python/obitools3/apps/temp.pxd +++ b/python/obitools3/apps/temp.pxd @@ -6,3 +6,5 @@ Created on 28 juillet 2017 @author: coissac ''' +from obitools3.dms.dms cimport DMS +from obitools3.utils cimport tobytes,tostr \ No newline at end of file diff --git a/python/obitools3/apps/temp.pyx b/python/obitools3/apps/temp.pyx index 996189a..eb01da8 100755 --- a/python/obitools3/apps/temp.pyx +++ b/python/obitools3/apps/temp.pyx @@ -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. diff --git a/python/obitools3/dms/column/column.cfiles b/python/obitools3/dms/column/column.cfiles new file mode 100644 index 0000000..19f702c --- /dev/null +++ b/python/obitools3/dms/column/column.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/dms/column/column.pxd b/python/obitools3/dms/column/column.pxd index 2dd5e14..7e68906 100755 --- a/python/obitools3/dms/column/column.pxd +++ b/python/obitools3/dms/column/column.pxd @@ -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__ diff --git a/python/obitools3/dms/column/column.pyx b/python/obitools3/dms/column/column.pyx index fdc338d..aae7f71 100755 --- a/python/obitools3/dms/column/column.pyx +++ b/python/obitools3/dms/column/column.pyx @@ -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, \ diff --git a/python/obitools3/dms/column/column_idx.cfiles b/python/obitools3/dms/column/column_idx.cfiles new file mode 100644 index 0000000..19f702c --- /dev/null +++ b/python/obitools3/dms/column/column_idx.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/dms/column/column_idx.pxd b/python/obitools3/dms/column/column_idx.pxd index 2e2c63e..c07c9b7 100755 --- a/python/obitools3/dms/column/column_idx.pxd +++ b/python/obitools3/dms/column/column_idx.pxd @@ -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) : diff --git a/python/obitools3/dms/column/column_idx.pyx b/python/obitools3/dms/column/column_idx.pyx index 8ddd766..da1bb06 100755 --- a/python/obitools3/dms/column/column_idx.pyx +++ b/python/obitools3/dms/column/column_idx.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/bool.cfiles b/python/obitools3/dms/column/typed_column/bool.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/bool.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/dms/column/typed_column/bool.pxd b/python/obitools3/dms/column/typed_column/bool.pxd index 22cf51b..41209c0 100755 --- a/python/obitools3/dms/column/typed_column/bool.pxd +++ b/python/obitools3/dms/column/typed_column/bool.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/bool.pyx b/python/obitools3/dms/column/typed_column/bool.pyx index ae113b8..54377fd 100755 --- a/python/obitools3/dms/column/typed_column/bool.pyx +++ b/python/obitools3/dms/column/typed_column/bool.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/char.cfiles b/python/obitools3/dms/column/typed_column/char.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/char.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/dms/column/typed_column/char.pxd b/python/obitools3/dms/column/typed_column/char.pxd index 7614c4f..c67db85 100755 --- a/python/obitools3/dms/column/typed_column/char.pxd +++ b/python/obitools3/dms/column/typed_column/char.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/char.pyx b/python/obitools3/dms/column/typed_column/char.pyx index d4e8c39..1ba7e89 100755 --- a/python/obitools3/dms/column/typed_column/char.pyx +++ b/python/obitools3/dms/column/typed_column/char.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/float.cfiles b/python/obitools3/dms/column/typed_column/float.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/float.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/dms/column/typed_column/float.pxd b/python/obitools3/dms/column/typed_column/float.pxd index edd898e..07e9f7b 100755 --- a/python/obitools3/dms/column/typed_column/float.pxd +++ b/python/obitools3/dms/column/typed_column/float.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/float.pyx b/python/obitools3/dms/column/typed_column/float.pyx index f00e123..3a0702b 100755 --- a/python/obitools3/dms/column/typed_column/float.pyx +++ b/python/obitools3/dms/column/typed_column/float.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/int.cfiles b/python/obitools3/dms/column/typed_column/int.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/int.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/dms/column/typed_column/int.pxd b/python/obitools3/dms/column/typed_column/int.pxd index 51be9f3..0cac022 100755 --- a/python/obitools3/dms/column/typed_column/int.pxd +++ b/python/obitools3/dms/column/typed_column/int.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/int.pyx b/python/obitools3/dms/column/typed_column/int.pyx index 2359d0a..5d9150e 100755 --- a/python/obitools3/dms/column/typed_column/int.pyx +++ b/python/obitools3/dms/column/typed_column/int.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/qual.cfiles b/python/obitools3/dms/column/typed_column/qual.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/qual.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/dms/column/typed_column/qual.pxd b/python/obitools3/dms/column/typed_column/qual.pxd index b0c0b47..3b8a20e 100755 --- a/python/obitools3/dms/column/typed_column/qual.pxd +++ b/python/obitools3/dms/column/typed_column/qual.pxd @@ -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) : diff --git a/python/obitools3/dms/column/typed_column/qual.pyx b/python/obitools3/dms/column/typed_column/qual.pyx index f45ed88..7670f3a 100755 --- a/python/obitools3/dms/column/typed_column/qual.pyx +++ b/python/obitools3/dms/column/typed_column/qual.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/seq.cfiles b/python/obitools3/dms/column/typed_column/seq.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/seq.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/dms/column/typed_column/seq.pxd b/python/obitools3/dms/column/typed_column/seq.pxd index 7ccf985..fcab9af 100755 --- a/python/obitools3/dms/column/typed_column/seq.pxd +++ b/python/obitools3/dms/column/typed_column/seq.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/seq.pyx b/python/obitools3/dms/column/typed_column/seq.pyx index 6c0679b..e77e076 100755 --- a/python/obitools3/dms/column/typed_column/seq.pyx +++ b/python/obitools3/dms/column/typed_column/seq.pyx @@ -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 diff --git a/python/obitools3/dms/column/typed_column/str.cfiles b/python/obitools3/dms/column/typed_column/str.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/str.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/dms/column/typed_column/str.pxd b/python/obitools3/dms/column/typed_column/str.pxd index 5bb75df..8f72b44 100755 --- a/python/obitools3/dms/column/typed_column/str.pxd +++ b/python/obitools3/dms/column/typed_column/str.pxd @@ -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 diff --git a/python/obitools3/dms/column/typed_column/str.pyx b/python/obitools3/dms/column/typed_column/str.pyx index 76e14a5..412d86b 100755 --- a/python/obitools3/dms/column/typed_column/str.pyx +++ b/python/obitools3/dms/column/typed_column/str.pyx @@ -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 diff --git a/python/obitools3/dms/dms.pxd b/python/obitools3/dms/dms.pxd index 25e4319..6fc3068 100755 --- a/python/obitools3/dms/dms.pxd +++ b/python/obitools3/dms/dms.pxd @@ -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): diff --git a/python/obitools3/dms/taxo/taxo.pxd b/python/obitools3/dms/taxo/taxo.pxd index e885897..0e4cbd0 100755 --- a/python/obitools3/dms/taxo/taxo.pxd +++ b/python/obitools3/dms/taxo/taxo.pxd @@ -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 - \ No newline at end of file + cdef Taxonomy _tax \ No newline at end of file diff --git a/python/obitools3/dms/taxo/taxo.pyx b/python/obitools3/dms/taxo/taxo.pyx index 2ff403b..758b7ac 100755 --- a/python/obitools3/dms/taxo/taxo.pyx +++ b/python/obitools3/dms/taxo/taxo.pyx @@ -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 = PyCapsule_GetPointer(taxon_capsule, NULL) + self._pointer = PyCapsule_GetPointer(taxon_capsule, NULL) if self._pointer == NULL : raise Exception("Error reading a taxon (NULL pointer)") self._tax = tax diff --git a/python/obitools3/utils.pxd b/python/obitools3/utils.pxd index 443bc73..53d3765 100755 --- a/python/obitools3/utils.pxd +++ b/python/obitools3/utils.pxd @@ -1,4 +1,4 @@ -# cython: language_level=3 +#cython: language_level=3 from obitools3.dms.capi.obitypes cimport obitype_t, index_t diff --git a/python/obitools3/utils.pyx b/python/obitools3/utils.pyx index 4d0a946..d3a1526 100755 --- a/python/obitools3/utils.pyx +++ b/python/obitools3/utils.pyx @@ -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, \