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obi uniq: better typing

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Celine Mercier
2018-02-12 14:38:07 +01:00
parent c8097e14e1
commit 370fb9272c
1 changed files with 15 additions and 14 deletions
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29
python/obitools3/commands/uniq.pyx
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@ -2,7 +2,8 @@
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms import DMS 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 import RollbackException
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.column.column cimport Column, Column_line 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 merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
cdef int taxid cdef int taxid
cdef Line seq cdef Nuc_Seq_Stored seq
cdef list m_taxids cdef list m_taxids
cdef bytes k cdef bytes k
cdef object tsp cdef object tsp
cdef object tgn cdef object tgn
cdef object tfa cdef object tfa
cdef object sp_sn cdef object sp_sn
cdef object gn_sn cdef object gn_sn
cdef object fa_sn cdef object fa_sn
# Create columns # Create columns
if b"species" in o_view and o_view[b"species"].data_type_int != OBI_INT : 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 mkey_infos
cdef dict merged_dict cdef dict merged_dict
cdef dict mkey_cols cdef dict mkey_cols
cdef Line i_seq cdef Nuc_Seq_Stored i_seq
cdef Line o_seq cdef Nuc_Seq_Stored o_seq
cdef Line u_seq cdef Nuc_Seq_Stored u_seq
cdef Column i_col cdef Column i_col
cdef Column i_seq_col cdef Column i_seq_col
cdef Column i_id_col cdef Column i_id_col