New command: obi align, except it's called obi pouic for now because of
a Cython compilation bug
This commit is contained in:
Celine Mercier
@ -1,236 +0,0 @@
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#cython: language_level=3
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#
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# from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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# from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
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# from obitools3.utils cimport str2bytes
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#
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# from obitools3.dms.capi.obialign cimport obi_lcs_align_one_column, \
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# obi_lcs_align_two_columns
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#
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#
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# import time
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#
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# __title__="Aligns one sequence column with itself or two sequence columns"
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#
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#
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# default_config = { 'inputview' : None,
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# }
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#
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# def addOptions(parser):
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#
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# # TODO put this common group somewhere else but I don't know where.
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# # Also some options should probably be in another group
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# group=parser.add_argument_group('DMS and view options')
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#
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# group.add_argument('--default-dms', '-d',
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# action="store", dest="obi:defaultdms",
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# metavar='<DMS NAME>',
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# default=None,
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# type=str,
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# help="Name of the default DMS for reading and writing data.")
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#
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# group.add_argument('--input-view-1', '-i',
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# action="store", dest="obi:inputview1",
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# metavar='<INPUT VIEW NAME>',
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# default=None,
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# type=str,
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# help="Name of the (first) input view.")
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#
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# group.add_argument('--input-view-2', '-I',
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# action="store", dest="obi:inputview2",
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# metavar='<INPUT VIEW NAME>',
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# default="",
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# type=str,
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# help="Eventually, the name of the second input view.")
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#
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# group.add_argument('--input-column-1', '-c',
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# action="store", dest="obi:inputcolumn1",
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# metavar='<INPUT COLUMN NAME>',
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# default="",
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# type=str,
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# help="Name of the (first) input column. "
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# " Default: the default nucleotide sequence column of the view if there is one.")
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#
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# group.add_argument('--input-column-2', '-C',
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# action="store", dest="obi:inputcolumn2",
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# metavar='<INPUT COLUMN NAME>',
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# default="",
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# type=str,
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# help="Eventually, the name of the second input column.")
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#
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# group.add_argument('--input-elt-1', '-e',
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# action="store", dest="obi:inputelement1",
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# metavar='<INPUT ELEMENT NAME>',
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# default="",
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# type=str,
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# help="If the first input column has multiple elements per line, name of the element referring to the sequence to align. "
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# " Default: the first element of the line.")
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#
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# group.add_argument('--input-elt-2', '-E',
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# action="store", dest="obi:inputelement2",
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# metavar='<INPUT ELEMENT NAME>',
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# default="",
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# type=str,
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# help="If the second input column has multiple elements per line, name of the element referring to the sequence to align. "
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# " Default: the first element of the line.")
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#
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# group.add_argument('--id-column-1', '-f',
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# action="store", dest="obi:idcolumn1",
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# metavar='<ID COLUMN NAME>',
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# default="",
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# type=str,
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# help="Name of the (first) column containing the identifiers of the sequences to align. "
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# " Default: the default ID column of the view if there is one.")
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#
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# group.add_argument('--id-column-2', '-F',
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# action="store", dest="obi:idcolumn2",
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# metavar='<ID COLUMN NAME>',
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# default="",
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# type=str,
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# help="Eventually, the name of the second ID column.")
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#
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# group.add_argument('--output-view', '-o',
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# action="store", dest="obi:outputview",
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# metavar='<OUTPUT VIEW NAME>',
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# default=None,
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# type=str,
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# help="Name of the output view.")
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#
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#
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# group=parser.add_argument_group('obi lcs specific options')
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#
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# group.add_argument('--threshold','-t',
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# action="store", dest="align:threshold",
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# metavar='<THRESHOLD>',
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# default=0.0,
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# type=float,
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# help="Score threshold. If the score is normalized and expressed in similarity (default),"
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# " it is an identity, e.g. 0.95 for an identity of 95%%. If the score is normalized"
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# " and expressed in distance, it is (1.0 - identity), e.g. 0.05 for an identity of 95%%."
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# " If the score is not normalized and expressed in similarity, it is the length of the"
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# " Longest Common Subsequence. If the score is not normalized and expressed in distance,"
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# " it is (reference length - LCS length)."
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# " Only sequence pairs with a similarity above <THRESHOLD> are printed. Default: 0.00"
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# " (no threshold).")
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#
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# group.add_argument('--longest-length','-L',
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# action="store_const", dest="align:reflength",
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# default=0,
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# const=1,
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# help="The reference length is the length of the longest sequence."
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# " Default: the reference length is the length of the alignment.")
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#
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# group.add_argument('--shortest-length','-l',
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# action="store_const", dest="align:reflength",
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# default=0,
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# const=2,
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# help="The reference length is the length of the shortest sequence."
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# " Default: the reference length is the length of the alignment.")
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#
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# group.add_argument('--raw','-r',
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# action="store_false", dest="align:normalize",
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# default=True,
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# help="Raw score, not normalized. Default: score is normalized with the reference sequence length.")
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#
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# group.add_argument('--distance','-D',
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# action="store_false", dest="align:similarity",
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# default=True,
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# help="Score is expressed in distance. Default: score is expressed in similarity.")
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#
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# group.add_argument('--print-seq','-s',
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# action="store_true", dest="align:printseq",
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# default=False,
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# help="The nucleotide sequences are written in the output view. Default: they are not written.")
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#
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# group.add_argument('--print-count','-n',
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# action="store_true", dest="align:printcount",
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# default=False,
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# help="Sequence counts are written in the output view. Default: they are not written.")
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#
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# group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
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# action="store", dest="align:threadcount",
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# metavar='<THREAD COUNT>',
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# default=1,
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# type=int,
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# help="Number of threads to use for the computation. Default: one.")
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#
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#
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# # cpdef align(str dms_n,
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# # str input_view_1_n, str output_view_n,
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# # str input_view_2_n="",
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# # str input_column_1_n="", str input_column_2_n="",
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# # str input_elt_1_n="", str input_elt_2_n="",
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# # str id_column_1_n="", str id_column_2_n="",
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# # double threshold=0.0, bint normalize=True,
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# # int reference=0, bint similarity_mode=True,
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# # bint print_seq=False, bint print_count=False,
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# # comments="",
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# # int thread_count=1) :
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# #
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# # cdef OBIDMS d
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# # d = OBIDMS(dms_n)
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# #
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# # if input_view_2_n == "" and input_column_2_n == "" :
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# # if obi_lcs_align_one_column(d._pointer, \
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# # str2bytes(input_view_1_n), \
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# # str2bytes(input_column_1_n), \
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# # str2bytes(input_elt_1_n), \
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# # str2bytes(id_column_1_n), \
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# # str2bytes(output_view_n), \
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# # str2bytes(comments), \
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# # print_seq, \
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# # print_count, \
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# # threshold, normalize, reference, similarity_mode,
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# # thread_count) < 0 :
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# # raise Exception("Error aligning sequences")
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# # else :
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# # if obi_lcs_align_two_columns(d._pointer, \
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# # str2bytes(input_view_1_n), \
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# # str2bytes(input_view_2_n), \
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# # str2bytes(input_column_1_n), \
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# # str2bytes(input_column_2_n), \
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# # str2bytes(input_elt_1_n), \
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# # str2bytes(input_elt_2_n), \
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# # str2bytes(id_column_1_n), \
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# # str2bytes(id_column_2_n), \
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# # str2bytes(output_view_n), \
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# # str2bytes(comments), \
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# # print_seq, \
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# # print_count, \
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# # threshold, normalize, reference, similarity_mode) < 0 :
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# # raise Exception("Error aligning sequences")
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# #
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# # d.close()
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# #
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# #
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def run(config):
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pass
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# TODO: Build formatted comments with all parameters etc
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# comments = "Obi align"
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#
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# # Call cython alignment function
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# align(config['obi']['defaultdms'], \
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# config['obi']['inputview1'], \
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# config['obi']['outputview'], \
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# input_view_2_n = config['obi']['inputview2'], \
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# input_column_1_n = config['obi']['inputcolumn1'], \
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# input_column_2_n = config['obi']['inputcolumn2'], \
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# input_elt_1_n = config['obi']['inputelement1'], \
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# input_elt_2_n = config['obi']['inputelement2'], \
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# id_column_1_n = config['obi']['idcolumn1'], \
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# id_column_2_n = config['obi']['idcolumn2'], \
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# threshold = config['align']['threshold'], \
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# normalize = config['align']['normalize'], \
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# reference = config['align']['reflength'], \
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# similarity_mode = config['align']['similarity'], \
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# print_seq = config['align']['printseq'], \
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# print_count = config['align']['printcount'], \
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# comments = comments, \
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# thread_count = config['align']['threadcount'])
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#
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# print("Done.")
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# #
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# #
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# #
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# #
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# #
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18
python/obitools3/commands/pouic.pxd
Normal file
18
python/obitools3/commands/pouic.pxd
Normal file
@ -0,0 +1,18 @@
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#cython: language_level=3
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cpdef align_columns(bytes dms_n,
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bytes input_view_1_n,
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bytes output_view_n,
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bytes input_view_2_n=*,
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bytes input_column_1_n=*,
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bytes input_column_2_n=*,
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bytes input_elt_1_n=*,
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bytes input_elt_2_n=*,
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bytes id_column_1_n=*,
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bytes id_column_2_n=*,
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double threshold=*, bint normalize=*,
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int reference=*, bint similarity_mode=*,
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bint print_seq=*, bint print_count=*,
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bytes comments=*,
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int thread_count=*)
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272
python/obitools3/commands/pouic.pyx
Normal file
272
python/obitools3/commands/pouic.pyx
Normal file
@ -0,0 +1,272 @@
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#cython: language_level=3
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.dms import DMS
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from obitools3.dms.view.view cimport View
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from obitools3.uri.decode import open_uri
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from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
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from obitools3.dms.view import RollbackException
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from obitools3.apps.config import logger
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from obitools3.utils cimport tobytes, str2bytes
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from obitools3.dms.capi.obialign cimport obi_lcs_align_one_column, \
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obi_lcs_align_two_columns
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import time
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import sys
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__title__="Aligns one sequence column with itself or two sequence columns"
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def addOptions(parser):
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addMinimalInputOption(parser)
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addMinimalOutputOption(parser)
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group=parser.add_argument_group('obi align specific options')
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group.add_argument('--input-2', '-I',
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action="store", dest="pouic:inputuri2",
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metavar='<INPUT URI>',
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default="",
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type=str,
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help="Eventually, the URI of the second input to align with the first one.")
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group.add_argument('--threshold','-t',
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action="store", dest="pouic:threshold",
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metavar='<THRESHOLD>',
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default=0.0,
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type=float,
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help="Score threshold. If the score is normalized and expressed in similarity (default),"
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" it is an identity, e.g. 0.95 for an identity of 95%%. If the score is normalized"
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" and expressed in distance, it is (1.0 - identity), e.g. 0.05 for an identity of 95%%."
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" If the score is not normalized and expressed in similarity, it is the length of the"
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" Longest Common Subsequence. If the score is not normalized and expressed in distance,"
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" it is (reference length - LCS length)."
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" Only sequence pairs with a similarity above <THRESHOLD> are printed. Default: 0.00"
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" (no threshold).")
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group.add_argument('--longest-length','-L',
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action="store_const", dest="pouic:reflength",
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default=0,
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const=1,
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help="The reference length is the length of the longest sequence."
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" Default: the reference length is the length of the alignment.")
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group.add_argument('--shortest-length','-l',
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action="store_const", dest="pouic:reflength",
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default=0,
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const=2,
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help="The reference length is the length of the shortest sequence."
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" Default: the reference length is the length of the alignment.")
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group.add_argument('--raw','-r',
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action="store_false", dest="pouic:normalize",
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default=True,
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help="Raw score, not normalized. Default: score is normalized with the reference sequence length.")
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group.add_argument('--distance','-D',
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action="store_false", dest="pouic:similarity",
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default=True,
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help="Score is expressed in distance. Default: score is expressed in similarity.")
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group.add_argument('--print-seq','-s',
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action="store_true", dest="pouic:printseq",
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default=False,
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help="The nucleotide sequences are written in the output view. Default: they are not written.")
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group.add_argument('--print-count','-n',
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action="store_true", dest="pouic:printcount",
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default=False,
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help="Sequence counts are written in the output view. Default: they are not written.")
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group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
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action="store", dest="pouic:threadcount",
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metavar='<THREAD COUNT>',
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default=1,
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type=int,
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help="Number of threads to use for the computation. Default: one.")
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cpdef align_columns(bytes dms_n,
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bytes input_view_1_n,
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bytes output_view_n,
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bytes input_view_2_n=b"",
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bytes input_column_1_n=b"",
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bytes input_column_2_n=b"",
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bytes input_elt_1_n=b"",
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bytes input_elt_2_n=b"",
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bytes id_column_1_n=b"",
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bytes id_column_2_n=b"",
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double threshold=0.0, bint normalize=True,
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int reference=0, bint similarity_mode=True,
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bint print_seq=False, bint print_count=False,
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bytes comments=b"{}",
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int thread_count=1) :
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if input_view_2_n == b"" and input_column_2_n == b"" :
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if obi_lcs_align_one_column(dms_n, \
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input_view_1_n, \
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input_column_1_n, \
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input_elt_1_n, \
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id_column_1_n, \
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output_view_n, \
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comments, \
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print_seq, \
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print_count, \
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threshold, normalize, reference, similarity_mode,
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thread_count) < 0 :
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raise Exception("Error aligning sequences")
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else:
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if obi_lcs_align_two_columns(dms_n, \
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input_view_1_n, \
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input_view_2_n, \
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input_column_1_n, \
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input_column_2_n, \
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input_elt_1_n, \
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input_elt_2_n, \
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id_column_1_n, \
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id_column_2_n, \
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output_view_n, \
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comments, \
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print_seq, \
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print_count, \
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threshold, normalize, reference, similarity_mode) < 0 :
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raise Exception("Error aligning sequences")
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def run(config):
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DMS.obi_atexit()
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logger("info", "obi align")
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# Open the input: only the DMS
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input = open_uri(config['obi']['inputURI'],
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dms_only=True)
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if input is None:
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raise Exception("Could not read input")
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i_dms = input[0]
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i_dms_name = input[0].name
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i_uri = input[1]
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i_view_name = i_uri.split(b"/")[0]
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i_column_name = b""
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i_element_name = b""
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if len(i_uri.split(b"/")) == 2:
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i_column_name = i_uri.split(b"/")[1]
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if len(i_uri.split(b"/")) == 3:
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i_element_name = i_uri.split(b"/")[2]
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if len(i_uri.split(b"/")) > 3:
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raise Exception("Input URI contains too many elements:", config['obi']['inputURI'])
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# Open the second input if there is one
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i_dms_2 = None
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i_dms_name_2 = b""
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original_i_view_name_2 = b""
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i_view_name_2 = b""
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i_column_name_2 = b""
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i_element_name_2 = b""
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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()
|
||||
|
||||
@ -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
|
||||
|
||||
Reference in New Issue
Block a user