diff --git a/python/obitools3/commands/uniq.pyx b/python/obitools3/commands/uniq.pyx index 24cfc0a..202c88a 100644 --- a/python/obitools3/commands/uniq.pyx +++ b/python/obitools3/commands/uniq.pyx @@ -2,7 +2,8 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport from obitools3.dms import DMS -from obitools3.dms.view.view cimport View, Line +from obitools3.dms.view.view cimport View +from obitools3.dms.obiseq cimport Nuc_Seq_Stored from obitools3.dms.view import RollbackException from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS from obitools3.dms.column.column cimport Column, Column_line @@ -49,16 +50,16 @@ def addOptions(parser): cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) : - cdef int taxid - cdef Line seq - cdef list m_taxids - cdef bytes k - cdef object tsp - cdef object tgn - cdef object tfa - cdef object sp_sn - cdef object gn_sn - cdef object fa_sn + cdef int taxid + cdef Nuc_Seq_Stored seq + cdef list m_taxids + cdef bytes k + cdef object tsp + cdef object tgn + cdef object tfa + cdef object sp_sn + cdef object gn_sn + cdef object fa_sn # Create columns if b"species" in o_view and o_view[b"species"].data_type_int != OBI_INT : @@ -196,9 +197,9 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li cdef dict mkey_infos cdef dict merged_dict cdef dict mkey_cols - cdef Line i_seq - cdef Line o_seq - cdef Line u_seq + cdef Nuc_Seq_Stored i_seq + cdef Nuc_Seq_Stored o_seq + cdef Nuc_Seq_Stored u_seq cdef Column i_col cdef Column i_seq_col cdef Column i_id_col