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Sequence alignment: added the possibility to specify the index of the

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sequences to align in a column containing multiple sequences per line (C
level for now)
This commit is contained in:
Celine Mercier
2016-11-29 16:15:02 +01:00
parent 5fb025f310
commit 98d0849653
6 changed files with 26 additions and 11 deletions
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2
python/obitools3/obidms/_obidms.pyx
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@ -581,7 +581,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
id1_col_p = id1_col_pp[0]
id2_col_p = id2_col_pp[0]
if obi_align_one_column(iview1_p, icol1_p, oview_p, id1_col_p, id2_col_p, ocol_p, threshold, normalize, reference, similarity_mode) < 0 :
if obi_align_one_column(iview1_p, icol1_p, NULL, oview_p, id1_col_p, id2_col_p, ocol_p, threshold, normalize, reference, similarity_mode) < 0 :
raise Exception("Error aligning sequences")

1
python/obitools3/obidms/capi/obialign.pxd
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@ -8,6 +8,7 @@ cdef extern from "obi_align.h" nogil:
int obi_align_one_column(Obiview_p seq_view,
OBIDMS_column_p seq_column,
const char* seq_name,
Obiview_p score_view,
OBIDMS_column_p id1_column,
OBIDMS_column_p id2_column,