New obi uniq: stores columns with too many elements per line as
character strings, and keeps a minimum of things in the memory
This commit is contained in:
Celine Mercier
@ -6,4 +6,4 @@ from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
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cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy)
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cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, list mergedKeys_list=*, Taxonomy taxonomy=*, bint mergeIds=*, list categories=*)
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cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, list mergedKeys_list=*, Taxonomy taxonomy=*, bint mergeIds=*, list categories=*, int max_elts=*)
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@ -11,9 +11,10 @@ from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t
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from obitools3.apps.optiongroups import addSequenceInputOption, addMinimalOutputOption, addTaxonomyInputOption
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from obitools3.uri.decode import open_uri
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from obitools3.apps.config import logger
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from obitools3.utils cimport tobytes
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__title__="Groups records together"
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__title__="Groups sequence records together"
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@ -60,79 +61,79 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
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cdef object fa_sn
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# Create columns
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if 'species' in o_view and o_view['species'].data_type_int != OBI_INT :
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o_view.delete_column('species')
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if 'species' not in o_view:
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if b"species" in o_view and o_view[b"species"].data_type_int != OBI_INT :
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o_view.delete_column(b"species")
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if b"species" not in o_view:
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Column.new_column(o_view,
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'species',
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b"species",
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OBI_INT
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)
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if 'genus' in o_view and o_view['genus'].data_type_int != OBI_INT :
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o_view.delete_column('genus')
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if 'genus' not in o_view:
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if b"genus" in o_view and o_view[b"genus"].data_type_int != OBI_INT :
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o_view.delete_column(b"genus")
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if b"genus" not in o_view:
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Column.new_column(o_view,
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'genus',
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b"genus",
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OBI_INT
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)
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if 'family' in o_view and o_view['family'].data_type_int != OBI_INT :
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o_view.delete_column('family')
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if 'family' not in o_view:
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if b"family" in o_view and o_view[b"family"].data_type_int != OBI_INT :
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o_view.delete_column(b"family")
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if b"family" not in o_view:
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Column.new_column(o_view,
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'family',
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b"family",
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OBI_INT
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)
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if 'species_name' in o_view and o_view['species_name'].data_type_int != OBI_STR :
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o_view.delete_column('species_name')
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if 'species_name' not in o_view:
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if b"species_name" in o_view and o_view[b"species_name"].data_type_int != OBI_STR :
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o_view.delete_column(b"species_name")
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if b"species_name" not in o_view:
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Column.new_column(o_view,
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'species_name',
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b"species_name",
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OBI_STR
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)
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if 'genus_name' in o_view and o_view['genus_name'].data_type_int != OBI_STR :
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o_view.delete_column('genus_name')
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if 'genus_name' not in o_view:
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if b"genus_name" in o_view and o_view[b"genus_name"].data_type_int != OBI_STR :
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o_view.delete_column(b"genus_name")
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if b"genus_name" not in o_view:
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Column.new_column(o_view,
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'genus_name',
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b"genus_name",
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OBI_STR
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)
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if 'family_name' in o_view and o_view['family_name'].data_type_int != OBI_STR :
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o_view.delete_column('family_name')
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if 'family_name' not in o_view:
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if b"family_name" in o_view and o_view[b"family_name"].data_type_int != OBI_STR :
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o_view.delete_column(b"family_name")
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if b"family_name" not in o_view:
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Column.new_column(o_view,
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'family_name',
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b"family_name",
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OBI_STR
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)
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if 'rank' in o_view and o_view['rank'].data_type_int != OBI_STR :
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o_view.delete_column('rank')
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if 'rank' not in o_view:
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if b"rank" in o_view and o_view[b"rank"].data_type_int != OBI_STR :
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o_view.delete_column(b"rank")
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if b"rank" not in o_view:
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Column.new_column(o_view,
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'rank',
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b"rank",
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OBI_STR
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)
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if 'scientific_name' in o_view and o_view['scientific_name'].data_type_int != OBI_STR :
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o_view.delete_column('scientific_name')
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if 'scientific_name' not in o_view:
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if b"scientific_name" in o_view and o_view[b"scientific_name"].data_type_int != OBI_STR :
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o_view.delete_column(b"scientific_name")
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if b"scientific_name" not in o_view:
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Column.new_column(o_view,
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'scientific_name',
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b"scientific_name",
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OBI_STR
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)
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for seq in o_view:
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if 'merged_taxid' in seq :
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if b"merged_taxid" in seq :
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m_taxids = []
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for k in seq['merged_taxid'].keys() :
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if seq['merged_taxid'][k] is not None:
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m_taxids_dict = seq[b"merged_taxid"]
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for k in m_taxids_dict.keys() :
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if m_taxids_dict[k] is not None:
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m_taxids.append(int(k))
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taxid = taxonomy.last_common_taxon(*m_taxids)
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seq['taxid'] = taxid
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seq[b"taxid"] = taxid
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tsp = taxonomy.get_species(taxid)
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tgn = taxonomy.get_genus(taxid)
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tfa = taxonomy.get_family(taxid)
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@ -155,72 +156,126 @@ cdef merge_taxonomy_classification(View_NUC_SEQS o_view, Taxonomy taxonomy) :
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fa_sn = None
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tfa = None
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seq['species'] = tsp
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seq['genus'] = tgn
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seq['family'] = tfa
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seq[b"species"] = tsp
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seq[b"genus"] = tgn
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seq[b"family"] = tfa
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seq['species_name'] = sp_sn
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seq['genus_name'] = gn_sn
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seq['family_name'] = fa_sn
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seq[b"species_name"] = sp_sn
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seq[b"genus_name"] = gn_sn
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seq[b"family_name"] = fa_sn
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seq['rank'] = taxonomy.get_rank(taxid)
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seq['scientific_name'] = taxonomy.get_scientific_name(taxid)
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seq[b"rank"] = taxonomy.get_rank(taxid)
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seq[b"scientific_name"] = taxonomy.get_scientific_name(taxid)
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cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, list mergedKeys_list=None, Taxonomy taxonomy=None, bint mergeIds=False, list categories=None) :
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cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, list mergedKeys_list=None, Taxonomy taxonomy=None, bint mergeIds=False, list categories=None, int max_elts=10000) :
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cdef int i
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cdef int k
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cdef int k_count
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cdef int o_idx
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cdef int u_idx
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cdef tuple u_id
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cdef int i_idx
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cdef int i_count
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cdef set mergedKeys
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cdef str key_str
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cdef bytes key
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cdef bytes mkey
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cdef bytes merged_col_name
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cdef bytes o_id
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cdef bytes i_id
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cdef set mergedKeys_set
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cdef tuple unique_id
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cdef list catl
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cdef list mergedKeys
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cdef list mergedKeys_list_b
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cdef list mergedKeys_m
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cdef list str_merged_cols
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cdef list merged_sequences
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cdef dict uniques
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cdef dict merged_infos
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cdef object iter_view
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cdef dict mkey_infos
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cdef dict merged_dict
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cdef dict mkey_cols
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cdef Line i_seq
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cdef Line o_seq
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cdef str key
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cdef bytes key_b
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cdef str mkey
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cdef str merged_col_name
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cdef Line u_seq
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cdef Column i_col
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cdef Column seq_col
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cdef object to_merge
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cdef Column_line mcol
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cdef Column i_seq_col
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cdef Column i_id_col
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cdef Column i_taxid_col
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cdef Column i_taxid_dist_col
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cdef Column o_id_col
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cdef Column o_taxid_dist_col
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cdef Column o_merged_col
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cdef Column_line i_mcol
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cdef list catl
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cdef dict merged_ids_dict
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cdef int nb_ids_max
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cdef set ids_list
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cdef bytes k
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cdef int n
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cdef dict taxid_dist_dict
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cdef object taxid_dist_dict
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cdef object iter_view
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cdef object mcol
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cdef object to_merge
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#print(categories)
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uniques = {}
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mergedKeys_list_b = []
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if mergedKeys_list is not None:
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mergedKeys=set(mergedKeys_list)
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for key_str in mergedKeys_list:
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mergedKeys_list_b.append(tobytes(key_str))
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mergedKeys_set=set(mergedKeys_list_b)
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else:
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mergedKeys=set()
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mergedKeys_set=set()
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if taxonomy is not None:
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mergedKeys.add('taxid')
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mergedKeys_set.add(b"taxid")
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mergedKeys = list(mergedKeys_set)
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k_count = len(mergedKeys)
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mergedKeys_m = []
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for k in range(k_count):
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mergedKeys_m.append(b"merged_" + mergedKeys[k])
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if categories is None:
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categories = []
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# Going through columns to merge a first time to create merged columns with the good number of elements per line and elemnts names
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# Keep columns that are going to be used a lot in variables
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i_seq_col = view[NUC_SEQUENCE_COLUMN]
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i_id_col = view[ID_COLUMN]
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i_taxid_col = view[b"taxid"]
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if b"taxid_dist" in view:
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i_taxid_dist_col = view[b"taxid_dist"]
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# First browsing
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i = 0
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o_idx = 0
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logger("info", "First browsing through the input")
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merged_infos = {}
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i = 0
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iter_view = iter(view)
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for i_seq in iter_view:
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for i_seq in iter_view :
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pb(i)
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for key in mergedKeys:
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mkey = "merged_%s" % key
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# This can't be done in the same line as the unique_id tuple creation because it generates a bug
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# where Cython (version 0.25.2) does not detect the reference to the categs_list variable and deallocates
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# it at the beginning of the function.
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# (Only happens if categs_list is an optional parameter, which it is).
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catl = []
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for x in categories :
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catl.append(i_seq[x])
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unique_id = tuple(catl) + (i_seq_col.get_line_idx(i),)
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#unique_id = tuple(i_seq[x] for x in categories) + (seq_col.get_line_idx(i),) # The line that cython can't read properly
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if unique_id in uniques:
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uniques[unique_id].append(i)
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else:
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uniques[unique_id] = [i]
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for k in range(k_count):
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key = mergedKeys[k]
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mkey = mergedKeys_m[k]
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if key in i_seq: # TODO what if mkey already in i_seq?
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if mkey not in merged_infos:
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merged_infos[mkey] = {}
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@ -234,166 +289,183 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
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mkey_infos['nb_elts'] += 1
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i+=1
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for key in mergedKeys:
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merged_col_name = "merged_%s" % key
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# Create merged columns
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str_merged_cols = []
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mkey_cols = {}
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for k in range(k_count):
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key = mergedKeys[k]
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merged_col_name = mergedKeys_m[k]
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i_col = view[key]
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Column.new_column(o_view,
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merged_col_name,
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OBI_INT,
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nb_elements_per_line=merged_infos[merged_col_name]['nb_elts'],
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elements_names=merged_infos[merged_col_name]['elt_names'],
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comments=i_col.comments,
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alias=merged_col_name # TODO what if it already exists
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)
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if merged_infos[merged_col_name]['nb_elts'] > max_elts:
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str_merged_cols.append(merged_col_name)
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Column.new_column(o_view,
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merged_col_name,
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OBI_STR,
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to_eval=True,
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comments=i_col.comments,
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alias=merged_col_name # TODO what if it already exists
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)
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else:
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Column.new_column(o_view,
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merged_col_name,
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OBI_INT,
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nb_elements_per_line=merged_infos[merged_col_name]['nb_elts'],
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elements_names=list(merged_infos[merged_col_name]['elt_names']),
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comments=i_col.comments,
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alias=merged_col_name # TODO what if it already exists
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)
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mkey_cols[merged_col_name] = o_view[merged_col_name]
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# taxid_dist column
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if mergeIds and b"taxid" in mergedKeys:
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if len(view) > max_elts: #The number of different IDs corresponds to the number of sequences in the view
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str_merged_cols.append(b"taxid_dist")
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Column.new_column(o_view,
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b"taxid_dist",
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OBI_STR,
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to_eval=True,
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comments=b"obi uniq taxid dist, stored as character strings to be read as dict",
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alias=b"taxid_dist" # TODO what if it already exists
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)
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else:
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Column.new_column(o_view,
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b"taxid_dist",
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OBI_INT,
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nb_elements_per_line=len(view),
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elements_names=[id for id in i_id_col],
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comments=b"obi uniq taxid dist",
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alias=b"taxid_dist" # TODO what if it already exists
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)
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del(merged_infos)
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# Merged ids column
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if mergeIds :
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Column.new_column(o_view,
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b"merged",
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OBI_STR,
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tuples=True,
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comments=b"obi uniq merged ids",
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alias=b"merged" # TODO what if it already exists
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)
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# Keep columns that are going to be used a lot in variables
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o_id_col = o_view[ID_COLUMN]
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if b"taxid_dist" in o_view:
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o_taxid_dist_col = o_view[b"taxid_dist"]
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if b"merged" in o_view:
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o_merged_col = o_view[b"merged"]
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logger("info", "Second browsing through the input")
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merged_ids_dict = {}
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taxid_dist_dict = {}
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i = 0
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# Initialize the progress bar
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pb = ProgressBar(len(uniques), seconde=5)
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o_idx = 0
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seq_col = view[NUC_SEQUENCE_COLUMN]
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iter_view = iter(view)
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for i_seq in iter_view :
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pb(i)
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for unique_id in uniques :
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pb(o_idx)
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# This can't be done in the same line as the u_id tuple creation because it generates a bug
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# where Cython (version 0.25.2) does not detect the reference to the categs_list variable and deallocates
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# it at the beginning of the function.
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# (Only happens if categs_list is an optional parameter, which it is).
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catl = []
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for x in categories :
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catl.append(i_seq[x])
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merged_sequences = uniques[unique_id]
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u_id = tuple(catl) + (seq_col.get_line_idx(i),)
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#u_id = tuple(i_seq[x] for x in categories) + (seq_col.get_line_idx(i),) # The line that cython can't read properly
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u_idx = uniques[unique_id][0]
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u_seq = view[u_idx]
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o_view[o_idx] = u_seq
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o_seq = o_view[o_idx]
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o_id = o_seq.id
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if u_id in uniques:
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if mergeIds:
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o_merged_col[o_idx] = [view[idx].id for idx in merged_sequences]
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if COUNT_COLUMN not in o_seq or o_seq[COUNT_COLUMN] is None:
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o_seq[COUNT_COLUMN] = 1
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if b"taxid_dist" in u_seq and i_taxid_dist_col[u_idx] is not None:
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taxid_dist_dict = i_taxid_dist_col[u_idx]
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else:
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taxid_dist_dict = {}
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for i_idx in merged_sequences:
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i_id = i_id_col[i_idx]
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i_seq = view[i_idx]
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if COUNT_COLUMN not in i_seq or i_seq[COUNT_COLUMN] is None:
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i_count = 1
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else:
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i_count = i_seq[COUNT_COLUMN]
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u_idx = uniques[u_id]
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||||
o_seq = o_view[u_idx]
|
||||
o_seq[COUNT_COLUMN] += i_count
|
||||
|
||||
for key in mergedKeys:
|
||||
if key=='taxid' and mergeIds:
|
||||
if 'taxid_dist' in i_seq:
|
||||
taxid_dist_dict[o_seq.id].update(i_seq["taxid_dist"])
|
||||
if 'taxid' in i_seq:
|
||||
taxid_dist_dict[o_seq.id][i_seq.id] = i_seq['taxid']
|
||||
merged_dict = {}
|
||||
for mkey in mergedKeys_m:
|
||||
merged_dict[mkey] = {}
|
||||
|
||||
for k in range(k_count):
|
||||
|
||||
key = mergedKeys[k]
|
||||
mkey = mergedKeys_m[k]
|
||||
|
||||
if key==b"taxid" and mergeIds:
|
||||
if b"taxid_dist" in i_seq:
|
||||
taxid_dist_dict.update(i_taxid_dist_col[i_idx])
|
||||
if b"taxid" in i_seq:
|
||||
taxid_dist_dict[i_id] = i_taxid_col[i_idx]
|
||||
|
||||
mkey = "merged_%s" % key
|
||||
#cas ou on met a jour les merged_keys mais il n'y a pas de merged_keys dans la sequence qui arrive
|
||||
if key in i_seq:
|
||||
to_merge = i_seq[key]
|
||||
if type(to_merge) != bytes :
|
||||
to_merge = str(to_merge)
|
||||
mcol = o_seq[mkey]
|
||||
if mcol[to_merge] is None:
|
||||
mcol[to_merge] = i_count
|
||||
else:
|
||||
mcol[to_merge] = mcol[to_merge] + i_count
|
||||
if to_merge is not None:
|
||||
if type(to_merge) != bytes :
|
||||
to_merge = tobytes(str(to_merge))
|
||||
mcol = merged_dict[mkey]
|
||||
if to_merge not in mcol or mcol[to_merge] is None:
|
||||
mcol[to_merge] = i_count
|
||||
else:
|
||||
mcol[to_merge] = mcol[to_merge] + i_count
|
||||
o_seq[key] = None
|
||||
#cas ou merged_keys existe deja
|
||||
else: # TODO is this a good else
|
||||
if mkey in i_seq:
|
||||
mcol = o_seq[mkey]
|
||||
mcol = merged_dict[mkey]
|
||||
i_mcol = i_seq[mkey]
|
||||
for key_b in i_mcol:
|
||||
if mcol[key_b] is None:
|
||||
mcol[key_b] = i_mcol[key_b]
|
||||
else:
|
||||
mcol[key_b] = mcol[key_b] + i_mcol[key_b]
|
||||
if i_mcol is not None:
|
||||
for key2 in i_mcol:
|
||||
if mcol[key2] is None:
|
||||
mcol[key2] = i_mcol[key2]
|
||||
else:
|
||||
mcol[key2] = mcol[key2] + i_mcol[key2]
|
||||
|
||||
for key_b in i_seq.keys():
|
||||
# Merger proprement l'attribut merged s'il existe
|
||||
# Write taxid_dist
|
||||
if mergeIds and b"taxid" in mergedKeys:
|
||||
if b"taxid_dist" in str_merged_cols:
|
||||
o_taxid_dist_col[o_idx] = str(taxid_dist_dict)
|
||||
else:
|
||||
o_taxid_dist_col[o_idx] = taxid_dist_dict
|
||||
|
||||
# Write merged dicts
|
||||
for mkey in merged_dict:
|
||||
if mkey in str_merged_cols:
|
||||
mkey_cols[mkey][o_idx] = str(merged_dict[mkey])
|
||||
else:
|
||||
mkey_cols[mkey][o_idx] = merged_dict[mkey]
|
||||
|
||||
for key in i_seq.keys():
|
||||
# Delete informations that differ between the merged sequences
|
||||
# TODO make special columns list?
|
||||
if key_b != COUNT_COLUMN and key_b != ID_COLUMN and key_b != NUC_SEQUENCE_COLUMN and key_b in o_seq and o_seq[key_b] != i_seq[key_b] :
|
||||
o_seq[key_b] = None
|
||||
if key != COUNT_COLUMN and key != ID_COLUMN and key != NUC_SEQUENCE_COLUMN and key in o_seq and o_seq[key] != i_seq[key] :
|
||||
o_seq[key] = None
|
||||
|
||||
if mergeIds :
|
||||
merged_ids_dict[o_seq.id].append(i_seq.id)
|
||||
|
||||
else:
|
||||
o_view[o_idx] = i_seq
|
||||
o_seq = o_view[o_idx]
|
||||
uniques[u_id] = o_idx
|
||||
o_idx += 1
|
||||
|
||||
if COUNT_COLUMN not in o_seq or o_seq[COUNT_COLUMN] is None:
|
||||
o_seq[COUNT_COLUMN] = 1
|
||||
|
||||
for key in mergedKeys:
|
||||
if key=='taxid' and mergeIds:
|
||||
if 'taxid' in o_seq and 'taxid_dist' not in o_seq:
|
||||
taxid_dist_dict[i_seq.id] = {}
|
||||
if 'taxid' in o_seq:
|
||||
taxid_dist_dict[i_seq.id][o_seq.id] = o_seq['taxid']
|
||||
mkey = "merged_%s" % key
|
||||
if key in o_seq:
|
||||
to_merge = o_seq[key]
|
||||
if type(to_merge) != bytes :
|
||||
to_merge = str(to_merge)
|
||||
mcol = o_seq[mkey]
|
||||
if to_merge in mcol and mcol[to_merge] is not None:
|
||||
mcol[to_merge] = mcol[to_merge] + o_seq[COUNT_COLUMN]
|
||||
else:
|
||||
mcol[to_merge] = o_seq[COUNT_COLUMN]
|
||||
o_seq[key] = None # TODO delete column eventually -> make C function that deletes 'empty' columns
|
||||
|
||||
if mergeIds:
|
||||
merged_ids_dict[o_seq.id] = [o_seq.id]
|
||||
|
||||
i+=1
|
||||
|
||||
# Merged ids column
|
||||
if mergeIds :
|
||||
logger("info", "Building merged ids column")
|
||||
nb_ids_max = 0
|
||||
ids_list = set()
|
||||
for k in merged_ids_dict :
|
||||
ids_list = set(list(ids_list) + merged_ids_dict[k])
|
||||
n = len(merged_ids_dict[k])
|
||||
if n > nb_ids_max :
|
||||
nb_ids_max = n
|
||||
|
||||
Column.new_column(o_view,
|
||||
"merged",
|
||||
OBI_STR,
|
||||
nb_elements_per_line=nb_ids_max,
|
||||
elements_names=None,
|
||||
comments="obi uniq merged ids",
|
||||
alias="merged" # TODO what if it already exists
|
||||
)
|
||||
|
||||
for o_seq in o_view:
|
||||
o_seq['merged'] = merged_ids_dict[o_seq.id]
|
||||
|
||||
if mergeIds and 'taxid' in mergedKeys:
|
||||
logger("info", "Building taxid dist column")
|
||||
Column.new_column(o_view,
|
||||
"taxid_dist",
|
||||
OBI_INT,
|
||||
nb_elements_per_line=len(ids_list),
|
||||
elements_names=list(ids_list),
|
||||
comments="obi uniq taxid dist",
|
||||
alias="taxid_dist" # TODO what if it already exists
|
||||
)
|
||||
|
||||
for o_seq in o_view:
|
||||
if o_seq.id in taxid_dist_dict :
|
||||
o_seq['taxid_dist'] = taxid_dist_dict[o_seq.id]
|
||||
o_idx += 1
|
||||
|
||||
if taxonomy is not None:
|
||||
logger("info", "Merging taxonomy classification")
|
||||
merge_taxonomy_classification(o_view, taxonomy)
|
||||
|
||||
|
||||
|
||||
def run(config):
|
||||
|
||||
cdef tuple input
|
||||
@ -417,12 +489,16 @@ def run(config):
|
||||
input=False,
|
||||
newviewtype=View_NUC_SEQS)
|
||||
|
||||
# TODO exceptions not handled like they should be
|
||||
if output is None:
|
||||
raise Exception("Could not create output view")
|
||||
|
||||
entries = input[1]
|
||||
o_view = output[1]
|
||||
|
||||
if 'taxoURI' in config['obi'] : # TODO default None problem
|
||||
taxo_uri = open_uri(config['obi']['taxoURI'])
|
||||
if taxo_uri is None:
|
||||
raise RollbackException("Couldn't open taxonomy, rollbacking view", o_view)
|
||||
taxo = taxo_uri[1]
|
||||
else :
|
||||
taxo = None
|
||||
@ -431,9 +507,9 @@ def run(config):
|
||||
pb = ProgressBar(len(entries), config, seconde=5)
|
||||
|
||||
try:
|
||||
uniq_sequences(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'])
|
||||
except:
|
||||
raise RollbackException("obi uniq error, rollbacking view", o_view)
|
||||
uniq_sequences(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'], max_elts=config['obi']['maxelts'])
|
||||
except Exception, e:
|
||||
raise RollbackException("obi uniq error, rollbacking view: "+str(e), o_view)
|
||||
|
||||
print("\n")
|
||||
print(repr(o_view))
|
||||
|
||||
Reference in New Issue
Block a user