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#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, addNoProgressBarOption
from obitools3.dms.view import RollbackException
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes, str2bytes
from obitools3.dms.capi.obilcsalign cimport obi_lcs_align_one_column, \
obi_lcs_align_two_columns
from io import BufferedWriter
from cpython.exc cimport PyErr_CheckSignals
import time
import sys
__title__="Align one sequence column with itself or two sequence columns"
def addOptions(parser):
addMinimalInputOption(parser)
addMinimalOutputOption(parser)
addNoProgressBarOption(parser)
group=parser.add_argument_group('obi align specific options')
group.add_argument('--input-2', '-I',
action="store", dest="align: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="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_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['align']['inputuri2']:
input_2 = open_uri(config['align']['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['align']['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]
output_0 = output[0]
o_dms_name = o_dms.name
final_o_view_name = output[1]
o_view_name = final_o_view_name
# If stdout output or 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 or type(output_0)==BufferedWriter:
if type(output_0)==BufferedWriter:
o_dms = i_dms
o_view_name = b"temp"
while o_view_name in i_dms: # Making sure view name is unique in input DMS
o_view_name = o_view_name+b"_"+str2bytes(str(i))
i+=1
# Save command config in View comments
command_line = " ".join(sys.argv[1:])
i_dms_list = [i_dms_name]
if i_dms_name_2:
i_dms_list.append(i_dms_name_2)
i_view_list = [i_view_name]
if original_i_view_name_2:
i_view_list.append(original_i_view_name_2)
comments = View.print_config(config, "align", 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_with_full_path, \
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['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'])
# 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\nOutput view:\n````````````", file=sys.stderr)
#print(repr(o_dms[final_o_view_name]), file=sys.stderr)
# 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()
# stdout output: write to buffer
if type(output_0)==BufferedWriter:
logger("info", "Printing to output...")
o_view = o_dms[o_view_name]
o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
o_view.close()
# If the input and the output DMS are different, delete the temporary result view in the input DMS
if i_dms != o_dms or type(output_0)==BufferedWriter:
View.delete_view(i_dms, o_view_name)
o_dms.close(force=True)
i_dms.close(force=True)
logger("info", "Done.")
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