Commit b0da36cb authored by Celine Mercier's avatar Celine Mercier

New command: obi align, except it's called obi pouic for now because of

a Cython compilation bug
parent d1f1fd43
#cython: language_level=3
#
# from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
# from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
# from obitools3.utils cimport str2bytes
#
# from obitools3.dms.capi.obialign cimport obi_lcs_align_one_column, \
# obi_lcs_align_two_columns
#
#
# import time
#
# __title__="Aligns one sequence column with itself or two sequence columns"
#
#
# default_config = { 'inputview' : None,
# }
#
# def addOptions(parser):
#
# # TODO put this common group somewhere else but I don't know where.
# # Also some options should probably be in another group
# group=parser.add_argument_group('DMS and view options')
#
# group.add_argument('--default-dms', '-d',
# action="store", dest="obi:defaultdms",
# metavar='<DMS NAME>',
# default=None,
# type=str,
# help="Name of the default DMS for reading and writing data.")
#
# group.add_argument('--input-view-1', '-i',
# action="store", dest="obi:inputview1",
# metavar='<INPUT VIEW NAME>',
# default=None,
# type=str,
# help="Name of the (first) input view.")
#
# group.add_argument('--input-view-2', '-I',
# action="store", dest="obi:inputview2",
# metavar='<INPUT VIEW NAME>',
# default="",
# type=str,
# help="Eventually, the name of the second input view.")
#
# group.add_argument('--input-column-1', '-c',
# action="store", dest="obi:inputcolumn1",
# metavar='<INPUT COLUMN NAME>',
# default="",
# type=str,
# help="Name of the (first) input column. "
# " Default: the default nucleotide sequence column of the view if there is one.")
#
# group.add_argument('--input-column-2', '-C',
# action="store", dest="obi:inputcolumn2",
# metavar='<INPUT COLUMN NAME>',
# default="",
# type=str,
# help="Eventually, the name of the second input column.")
#
# group.add_argument('--input-elt-1', '-e',
# action="store", dest="obi:inputelement1",
# metavar='<INPUT ELEMENT NAME>',
# default="",
# type=str,
# help="If the first input column has multiple elements per line, name of the element referring to the sequence to align. "
# " Default: the first element of the line.")
#
# group.add_argument('--input-elt-2', '-E',
# action="store", dest="obi:inputelement2",
# metavar='<INPUT ELEMENT NAME>',
# default="",
# type=str,
# help="If the second input column has multiple elements per line, name of the element referring to the sequence to align. "
# " Default: the first element of the line.")
#
# group.add_argument('--id-column-1', '-f',
# action="store", dest="obi:idcolumn1",
# metavar='<ID COLUMN NAME>',
# default="",
# type=str,
# help="Name of the (first) column containing the identifiers of the sequences to align. "
# " Default: the default ID column of the view if there is one.")
#
# group.add_argument('--id-column-2', '-F',
# action="store", dest="obi:idcolumn2",
# metavar='<ID COLUMN NAME>',
# default="",
# type=str,
# help="Eventually, the name of the second ID column.")
#
# group.add_argument('--output-view', '-o',
# action="store", dest="obi:outputview",
# metavar='<OUTPUT VIEW NAME>',
# default=None,
# type=str,
# help="Name of the output view.")
#
#
# group=parser.add_argument_group('obi lcs specific options')
#
# group.add_argument('--threshold','-t',
# action="store", dest="align:threshold",
# metavar='<THRESHOLD>',
# default=0.0,
# type=float,
# help="Score threshold. If the score is normalized and expressed in similarity (default),"
# " it is an identity, e.g. 0.95 for an identity of 95%%. If the score is normalized"
# " and expressed in distance, it is (1.0 - identity), e.g. 0.05 for an identity of 95%%."
# " If the score is not normalized and expressed in similarity, it is the length of the"
# " Longest Common Subsequence. If the score is not normalized and expressed in distance,"
# " it is (reference length - LCS length)."
# " Only sequence pairs with a similarity above <THRESHOLD> are printed. Default: 0.00"
# " (no threshold).")
#
# group.add_argument('--longest-length','-L',
# action="store_const", dest="align:reflength",
# default=0,
# const=1,
# help="The reference length is the length of the longest sequence."
# " Default: the reference length is the length of the alignment.")
#
# group.add_argument('--shortest-length','-l',
# action="store_const", dest="align:reflength",
# default=0,
# const=2,
# help="The reference length is the length of the shortest sequence."
# " Default: the reference length is the length of the alignment.")
#
# group.add_argument('--raw','-r',
# action="store_false", dest="align:normalize",
# default=True,
# help="Raw score, not normalized. Default: score is normalized with the reference sequence length.")
#
# group.add_argument('--distance','-D',
# action="store_false", dest="align:similarity",
# default=True,
# help="Score is expressed in distance. Default: score is expressed in similarity.")
#
# group.add_argument('--print-seq','-s',
# action="store_true", dest="align:printseq",
# default=False,
# help="The nucleotide sequences are written in the output view. Default: they are not written.")
#
# group.add_argument('--print-count','-n',
# action="store_true", dest="align:printcount",
# default=False,
# help="Sequence counts are written in the output view. Default: they are not written.")
#
# group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
# action="store", dest="align:threadcount",
# metavar='<THREAD COUNT>',
# default=1,
# type=int,
# help="Number of threads to use for the computation. Default: one.")
#
#
# # cpdef align(str dms_n,
# # str input_view_1_n, str output_view_n,
# # str input_view_2_n="",
# # str input_column_1_n="", str input_column_2_n="",
# # str input_elt_1_n="", str input_elt_2_n="",
# # str id_column_1_n="", str id_column_2_n="",
# # double threshold=0.0, bint normalize=True,
# # int reference=0, bint similarity_mode=True,
# # bint print_seq=False, bint print_count=False,
# # comments="",
# # int thread_count=1) :
# #
# # cdef OBIDMS d
# # d = OBIDMS(dms_n)
# #
# # 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,
# # thread_count) < 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()
# #
# #
def run(config):
pass
# TODO: Build formatted comments with all parameters etc
# comments = "Obi align"
#
# # Call cython alignment function
# align(config['obi']['defaultdms'], \
# config['obi']['inputview1'], \
# config['obi']['outputview'], \
# input_view_2_n = config['obi']['inputview2'], \
# input_column_1_n = config['obi']['inputcolumn1'], \
# input_column_2_n = config['obi']['inputcolumn2'], \
# input_elt_1_n = config['obi']['inputelement1'], \
# input_elt_2_n = config['obi']['inputelement2'], \
# id_column_1_n = config['obi']['idcolumn1'], \
# id_column_2_n = config['obi']['idcolumn2'], \
# threshold = config['align']['threshold'], \
# normalize = config['align']['normalize'], \
# reference = config['align']['reflength'], \
# similarity_mode = config['align']['similarity'], \
# print_seq = config['align']['printseq'], \
# print_count = config['align']['printcount'], \
# comments = comments, \
# thread_count = config['align']['threadcount'])
#
# print("Done.")
# #
# #
# #
# #
# #
\ No newline at end of file
#cython: language_level=3
cpdef align_columns(bytes dms_n,
bytes input_view_1_n,
bytes output_view_n,
bytes input_view_2_n=*,
bytes input_column_1_n=*,
bytes input_column_2_n=*,
bytes input_elt_1_n=*,
bytes input_elt_2_n=*,
bytes id_column_1_n=*,
bytes id_column_2_n=*,
double threshold=*, bint normalize=*,
int reference=*, bint similarity_mode=*,
bint print_seq=*, bint print_count=*,
bytes comments=*,
int thread_count=*)
\ No newline at end of file
#cython: language_level=3
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms import DMS
from obitools3.dms.view.view cimport View
from obitools3.uri.decode import open_uri
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
from obitools3.dms.view import RollbackException
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes, str2bytes
from obitools3.dms.capi.obialign cimport obi_lcs_align_one_column, \
obi_lcs_align_two_columns
import time
import sys
__title__="Aligns one sequence column with itself or two sequence columns"
def addOptions(parser):
addMinimalInputOption(parser)
addMinimalOutputOption(parser)
group=parser.add_argument_group('obi align specific options')
group.add_argument('--input-2', '-I',
action="store", dest="pouic:inputuri2",
metavar='<INPUT URI>',
default="",
type=str,
help="Eventually, the URI of the second input to align with the first one.")
group.add_argument('--threshold','-t',
action="store", dest="pouic:threshold",
metavar='<THRESHOLD>',
default=0.0,
type=float,
help="Score threshold. If the score is normalized and expressed in similarity (default),"
" it is an identity, e.g. 0.95 for an identity of 95%%. If the score is normalized"
" and expressed in distance, it is (1.0 - identity), e.g. 0.05 for an identity of 95%%."
" If the score is not normalized and expressed in similarity, it is the length of the"
" Longest Common Subsequence. If the score is not normalized and expressed in distance,"
" it is (reference length - LCS length)."
" Only sequence pairs with a similarity above <THRESHOLD> are printed. Default: 0.00"
" (no threshold).")
group.add_argument('--longest-length','-L',
action="store_const", dest="pouic:reflength",
default=0,
const=1,
help="The reference length is the length of the longest sequence."
" Default: the reference length is the length of the alignment.")
group.add_argument('--shortest-length','-l',
action="store_const", dest="pouic:reflength",
default=0,
const=2,
help="The reference length is the length of the shortest sequence."
" Default: the reference length is the length of the alignment.")
group.add_argument('--raw','-r',
action="store_false", dest="pouic:normalize",
default=True,
help="Raw score, not normalized. Default: score is normalized with the reference sequence length.")
group.add_argument('--distance','-D',
action="store_false", dest="pouic:similarity",
default=True,
help="Score is expressed in distance. Default: score is expressed in similarity.")
group.add_argument('--print-seq','-s',
action="store_true", dest="pouic:printseq",
default=False,
help="The nucleotide sequences are written in the output view. Default: they are not written.")
group.add_argument('--print-count','-n',
action="store_true", dest="pouic:printcount",
default=False,
help="Sequence counts are written in the output view. Default: they are not written.")
group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
action="store", dest="pouic:threadcount",
metavar='<THREAD COUNT>',
default=1,
type=int,
help="Number of threads to use for the computation. Default: one.")
cpdef align_columns(bytes dms_n,
bytes input_view_1_n,
bytes output_view_n,
bytes input_view_2_n=b"",
bytes input_column_1_n=b"",
bytes input_column_2_n=b"",
bytes input_elt_1_n=b"",
bytes input_elt_2_n=b"",
bytes id_column_1_n=b"",
bytes id_column_2_n=b"",
double threshold=0.0, bint normalize=True,
int reference=0, bint similarity_mode=True,
bint print_seq=False, bint print_count=False,
bytes comments=b"{}",
int thread_count=1) :
if input_view_2_n == b"" and input_column_2_n == b"" :
if obi_lcs_align_one_column(dms_n, \
input_view_1_n, \
input_column_1_n, \
input_elt_1_n, \
id_column_1_n, \
output_view_n, \
comments, \
print_seq, \
print_count, \
threshold, normalize, reference, similarity_mode,
thread_count) < 0 :
raise Exception("Error aligning sequences")
else:
if obi_lcs_align_two_columns(dms_n, \
input_view_1_n, \
input_view_2_n, \
input_column_1_n, \
input_column_2_n, \
input_elt_1_n, \
input_elt_2_n, \
id_column_1_n, \
id_column_2_n, \
output_view_n, \
comments, \
print_seq, \
print_count, \
threshold, normalize, reference, similarity_mode) < 0 :
raise Exception("Error aligning sequences")
def run(config):
DMS.obi_atexit()
logger("info", "obi align")
# Open the input: only the DMS
input = open_uri(config['obi']['inputURI'],
dms_only=True)
if input is None:
raise Exception("Could not read input")
i_dms = input[0]
i_dms_name = input[0].name
i_uri = input[1]
i_view_name = i_uri.split(b"/")[0]
i_column_name = b""
i_element_name = b""
if len(i_uri.split(b"/")) == 2:
i_column_name = i_uri.split(b"/")[1]
if len(i_uri.split(b"/")) == 3:
i_element_name = i_uri.split(b"/")[2]
if len(i_uri.split(b"/")) > 3:
raise Exception("Input URI contains too many elements:", config['obi']['inputURI'])
# Open the second input if there is one
i_dms_2 = None
i_dms_name_2 = b""
original_i_view_name_2 = b""
i_view_name_2 = b""
i_column_name_2 = b""
i_element_name_2 = b""
if config['pouic']['inputuri2']:
input_2 = open_uri(config['pouic']['inputuri2'],
dms_only=True)
if input_2 is None:
raise Exception("Could not read second input")
i_dms_2 = input_2[0]
i_dms_name_2 = i_dms_2.name
i_uri_2 = input_2[1]
original_i_view_name_2 = i_uri_2.split(b"/")[0]
if len(i_uri_2.split(b"/")) == 2:
i_column_name_2 = i_uri_2.split(b"/")[1]
if len(i_uri_2.split(b"/")) == 3:
i_element_name_2 = i_uri_2.split(b"/")[2]
if len(i_uri_2.split(b"/")) > 3:
raise Exception("Input URI contains too many elements:", config['pouic']['inputuri2'])
# If the 2 input DMS are not the same, temporarily import 2nd input view in first input DMS
if i_dms != i_dms_2:
temp_i_view_name_2 = original_i_view_name_2
i=0
while temp_i_view_name_2 in i_dms: # Making sure view name is unique in input DMS
temp_i_view_name_2 = original_i_view_name_2+b"_"+str2bytes(str(i))
i+=1
i_view_name_2 = temp_i_view_name_2
View.import_view(i_dms_2.full_path[:-7], i_dms.full_path[:-7], original_i_view_name_2, i_view_name_2)
# Open the output: only the DMS
output = open_uri(config['obi']['outputURI'],
input=False,
dms_only=True)
if output is None:
raise Exception("Could not create output")
o_dms = output[0]
o_dms_name = o_dms.name
final_o_view_name = output[1]
# If the input and output DMS are not the same, align creating a temporary view in the input dms that will be exported to
# the right DMS and deleted in the other afterwards.
if i_dms != o_dms:
temporary_view_name = final_o_view_name
i=0
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
i+=1
o_view_name = temporary_view_name
else:
o_view_name = final_o_view_name
# Save command config in View comments
command_line = " ".join(sys.argv[1:])
i_dms_list = [i_dms_name]
if i_dms_name_2 and i_dms_name != i_dms_name_2:
i_dms_list.append(i_dms_name_2)
i_view_list = [i_view_name]
if original_i_view_name_2 and i_view_name != original_i_view_name_2:
i_view_list.append(original_i_view_name_2)
comments = View.print_config(config, "pouic", command_line, input_dms_name=i_dms_list, input_view_name=i_view_list)
# Call cython alignment function
# Using default ID columns of the view. TODO discuss adding option
align_columns(i_dms_name, \
i_view_name, \
o_view_name, \
input_view_2_n = i_view_name_2, \
input_column_1_n = i_column_name, \
input_column_2_n = i_column_name_2, \
input_elt_1_n = i_element_name, \
input_elt_2_n = i_element_name_2, \
id_column_1_n = b"", \
id_column_2_n = b"", \
threshold = config['pouic']['threshold'], \
normalize = config['pouic']['normalize'], \
reference = config['pouic']['reflength'], \
similarity_mode = config['pouic']['similarity'], \
print_seq = config['pouic']['printseq'], \
print_count = config['pouic']['printcount'], \
comments = comments, \
thread_count = config['pouic']['threadcount'])
# If the input and output DMS are not the same, export result view to output DMS
if i_dms != o_dms:
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
# Save command config in output DMS comments
o_dms.record_command_line(command_line)
print("\n")
print(repr(o_dms[final_o_view_name]))
# If the two input DMS are different, delete the temporary input view in the first input DMS
if i_dms_2 and i_dms != i_dms_2:
View.delete_view(i_dms, i_view_name_2)
i_dms_2.close()
# If the input and the output DMS are different, delete the temporary result view in the input DMS
if i_dms != o_dms:
View.delete_view(i_dms, o_view_name)
o_dms.close()
i_dms.close()
\ No newline at end of file
......@@ -4,13 +4,13 @@ from obitools3.dms.capi.obidms cimport OBIDMS_p
from obitools3.dms.capi.obitypes cimport const_char_p
cdef extern from "obi_align.h" nogil:
cdef extern from "obi_lcs.h" nogil:
int obi_lcs_align_one_column(OBIDMS_p dms,
int obi_lcs_align_one_column(const_char_p dms_name,
const_char_p seq_view_name,
const_char_p seq_column_name,
const_char_p seq_elt_name,
const_char_p id_column_name,
const_char_p id_column_name,
const_char_p output_view_name,
const_char_p output_view_comments,
bint print_seq,
......@@ -22,7 +22,7 @@ cdef extern from "obi_align.h" nogil:
int thread_count)
int obi_lcs_align_two_columns(OBIDMS_p dms,
int obi_lcs_align_two_columns(const_char_p dms_name,
const_char_p seq1_view_name,
const_char_p seq2_view_name,
const_char_p seq1_column_name,
......
......@@ -7,7 +7,7 @@
../../../src/hashtable.c
../../../src/linked_list.c
../../../src/murmurhash2.c
../../../src/obi_align.c
../../../src/obi_lcs.c
../../../src/obi_clean.c
../../../src/obi_ecopcr.c
../../../src/libecoPCR/libthermo/nnparams.c
......
......@@ -7,7 +7,7 @@
../../src/hashtable.c
../../src/linked_list.c
../../src/murmurhash2.c
../../src/obi_align.c
../../src/obi_lcs.c
../../src/obi_clean.c
../../src/obi_ecopcr.c
../../src/libecoPCR/libthermo/nnparams.c
......
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