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Updated `obi lcs` for the LCS alignment of two columns

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This commit is contained in:
Celine Mercier
2016-12-16 19:40:36 +01:00
parent d99447c12b
commit 857a5198e4
2 changed files with 49 additions and 14 deletions
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45
python/obitools3/commands/lcs.pyx
View File

@ -4,7 +4,8 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.obidms._obidms cimport OBIDMS # TODO cimport doesn't work
from obitools3.utils cimport str2bytes
from obitools3.obidms.capi.obialign cimport obi_lcs_align_one_column
from obitools3.obidms.capi.obialign cimport obi_lcs_align_one_column, \
obi_lcs_align_two_columns
import time
@ -161,19 +162,35 @@ cpdef align(str dms_n,
cdef OBIDMS d
d = OBIDMS(dms_n)
# Align 1 column (2 columns not implemented yet)
if obi_lcs_align_one_column(d._pointer, \
str2bytes(input_view_1_n), \
str2bytes(input_column_1_n), \
str2bytes(input_elt_1_n), \
str2bytes(id_column_1_n), \
str2bytes(output_view_n), \
str2bytes(comments), \
print_seq, \
print_count, \
threshold, normalize, reference, similarity_mode) < 0 :
raise Exception("Error aligning sequences")
if input_view_2_n == "" and input_column_2_n == "" :
if obi_lcs_align_one_column(d._pointer, \
str2bytes(input_view_1_n), \
str2bytes(input_column_1_n), \
str2bytes(input_elt_1_n), \
str2bytes(id_column_1_n), \
str2bytes(output_view_n), \
str2bytes(comments), \
print_seq, \
print_count, \
threshold, normalize, reference, similarity_mode) < 0 :
raise Exception("Error aligning sequences")
else :
if obi_lcs_align_two_columns(d._pointer, \
str2bytes(input_view_1_n), \
str2bytes(input_view_2_n), \
str2bytes(input_column_1_n), \
str2bytes(input_column_2_n), \
str2bytes(input_elt_1_n), \
str2bytes(input_elt_2_n), \
str2bytes(id_column_1_n), \
str2bytes(id_column_2_n), \
str2bytes(output_view_n), \
str2bytes(comments), \
print_seq, \
print_count, \
threshold, normalize, reference, similarity_mode) < 0 :
raise Exception("Error aligning sequences")
d.close()

18
python/obitools3/obidms/capi/obialign.pxd
View File

@ -20,3 +20,21 @@ cdef extern from "obi_align.h" nogil:
int reference,
bint similarity_mode)
int obi_lcs_align_two_columns(OBIDMS_p dms,
const_char_p seq1_view_name,
const_char_p seq2_view_name,
const_char_p seq1_column_name,
const_char_p seq2_column_name,
const_char_p seq1_elt_name,
const_char_p seq2_elt_name,
const_char_p id1_column_name,
const_char_p id2_column_name,
const_char_p output_view_name,
const_char_p output_view_comments,
bint print_seq,
bint print_count,
double threshold,
bint normalize,
int reference,
bint similarity_mode);