243 lines
9.9 KiB
Cython
Executable File
243 lines
9.9 KiB
Cython
Executable File
#cython: language_level=3
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.dms.dms cimport DMS
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from obitools3.dms.capi.obidms cimport OBIDMS_p
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from obitools3.dms.view import RollbackException
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from obitools3.dms.capi.obiecopcr cimport obi_ecopcr
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from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addTaxonomyOption, addNoProgressBarOption
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from obitools3.uri.decode import open_uri
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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.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
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from obitools3.dms.view import View
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from libc.stdlib cimport malloc, free
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from libc.stdint cimport int32_t
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import sys
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from io import BufferedWriter
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__title__="in silico PCR"
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# TODO: add option to output unique ids
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def addOptions(parser):
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addMinimalInputOption(parser)
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addTaxonomyOption(parser)
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addMinimalOutputOption(parser)
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addNoProgressBarOption(parser)
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group = parser.add_argument_group('obi ecopcr specific options')
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group.add_argument('--primer1', '-F',
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action="store", dest="ecopcr:primer1",
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metavar='<PRIMER>',
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type=str,
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required=True,
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help="Forward primer, length must be less than or equal to 32")
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group.add_argument('--primer2', '-R',
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action="store", dest="ecopcr:primer2",
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metavar='<PRIMER>',
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type=str,
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required=True,
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help="Reverse primer, length must be less than or equal to 32")
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group.add_argument('--error', '-e',
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action="store", dest="ecopcr:error",
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metavar='<ERROR>',
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default=0,
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type=int,
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help="Maximum number of errors (mismatches) allowed per primer. Default: 0.")
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group.add_argument('--min-length', '-l',
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action="store",
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dest="ecopcr:min-length",
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metavar="<MINIMUM LENGTH>",
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type=int,
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default=0,
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help="Minimum length of the in silico amplified DNA fragment, excluding primers.")
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group.add_argument('--max-length', '-L',
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action="store",
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dest="ecopcr:max-length",
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metavar="<MAXIMUM LENGTH>",
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type=int,
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default=0,
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help="Maximum length of the in silico amplified DNA fragment, excluding primers.")
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group.add_argument('--restrict-to-taxid', '-r',
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action="append",
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dest="ecopcr:restrict-to-taxid",
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metavar="<TAXID>",
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type=int,
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default=[],
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help="Only the sequence records corresponding to the taxonomic group identified "
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"by TAXID are considered for the in silico PCR. The TAXID is an integer "
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"that can be found in the NCBI taxonomic database.")
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group.add_argument('--ignore-taxid', '-i',
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action="append",
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dest="ecopcr:ignore-taxid",
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metavar="<TAXID>",
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type=int,
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default=[],
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help="The sequences of the taxonomic group identified by TAXID are not considered for the in silico PCR.")
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group.add_argument('--circular', '-c',
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action="store_true",
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dest="ecopcr:circular",
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default=False,
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help="Considers that the input sequences are circular (e.g. mitochondrial or chloroplastic DNA).")
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group.add_argument('--salt-concentration', '-a',
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action="store",
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dest="ecopcr:salt-concentration",
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metavar="<FLOAT>",
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type=float,
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default=0.05,
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help="Salt concentration used for estimating the Tm. Default: 0.05.")
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group.add_argument('--salt-correction-method', '-m',
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action="store",
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dest="ecopcr:salt-correction-method",
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metavar="<1|2>",
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type=int,
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default=1,
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help="Defines the method used for estimating the Tm (melting temperature) between the primers and their corresponding "
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"target sequences. SANTALUCIA: 1, or OWCZARZY: 2. Default: 1.")
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group.add_argument('--keep-primers', '-p',
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action="store_true",
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dest="ecopcr:keep-primers",
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default=False,
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help="Whether to keep the primers attached to the output sequences (default: the primers are cut out).")
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group.add_argument('--keep-nucs', '-D',
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action="store",
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dest="ecopcr:keep-nucs",
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metavar="<N>",
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type=int,
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default=0,
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help="Keeps N nucleotides on each side of the in silico amplified sequences, "
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"not including the primers (implying that primers are automatically kept if N > 0).")
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group.add_argument('--kingdom-mode', '-k',
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action="store_true",
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dest="ecopcr:kingdom-mode",
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default=False,
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help="Print in the output the kingdom of the in silico amplified sequences (default: print the superkingdom).")
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def run(config):
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cdef int32_t* restrict_to_taxids_p = NULL
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cdef int32_t* ignore_taxids_p = NULL
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restrict_to_taxids_len = len(config['ecopcr']['restrict-to-taxid'])
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restrict_to_taxids_p = <int32_t*> malloc((restrict_to_taxids_len + 1) * sizeof(int32_t)) # +1 for the -1 flagging the end of the array
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for i in range(restrict_to_taxids_len) :
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restrict_to_taxids_p[i] = config['ecopcr']['restrict-to-taxid'][i]
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restrict_to_taxids_p[restrict_to_taxids_len] = -1
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ignore_taxids_len = len(config['ecopcr']['ignore-taxid'])
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ignore_taxids_p = <int32_t*> malloc((ignore_taxids_len + 1) * sizeof(int32_t)) # +1 for the -1 flagging the end of the array
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for i in range(ignore_taxids_len) :
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ignore_taxids_p[i] = config['ecopcr']['ignore-taxid'][i]
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ignore_taxids_p[ignore_taxids_len] = -1
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DMS.obi_atexit()
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logger("info", "obi ecopcr")
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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_view_name = input[1]
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# Open the output: only the DMS
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output = open_uri(config['obi']['outputURI'],
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input=False,
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dms_only=True)
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if output is None:
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raise Exception("Could not create output")
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o_dms = output[0]
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output_0 = output[0]
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o_dms_name = output[0].name
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o_view_name = output[1]
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# Open the taxonomy DMS
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taxdms = open_uri(config['obi']['taxoURI'],
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dms_only=True)
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if taxdms is None:
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raise Exception("Could not open taxonomy DMS")
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tax_dms = taxdms[0]
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tax_dms_name = taxdms[0].name
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# Read taxonomy name
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taxonomy_name = config['obi']['taxoURI'].split("/")[-1] # Robust in theory
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# If stdout output create a temporary view in the input dms that will be deleted afterwards.
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if type(output_0)==BufferedWriter:
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o_dms = i_dms
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o_view_name = b"temp"
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while o_view_name in i_dms: # Making sure view name is unique in input DMS
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o_view_name = o_view_name+b"_"+str2bytes(str(i))
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i+=1
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# Save command config in View comments
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command_line = " ".join(sys.argv[1:])
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input_dms_name=[i_dms_name]
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input_view_name= [i_view_name]
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input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
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input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
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comments = View.print_config(config, "ecopcr", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
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# TODO: primers in comments?
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if obi_ecopcr(i_dms.name_with_full_path, tobytes(i_view_name),
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tax_dms.name_with_full_path, tobytes(taxonomy_name), \
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o_dms.name_with_full_path, tobytes(o_view_name), comments, \
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tobytes(config['ecopcr']['primer1']), tobytes(config['ecopcr']['primer2']), \
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config['ecopcr']['error'], \
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config['ecopcr']['min-length'], config['ecopcr']['max-length'], \
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restrict_to_taxids_p, ignore_taxids_p, \
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config['ecopcr']['circular'], config['ecopcr']['salt-concentration'], config['ecopcr']['salt-correction-method'], \
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config['ecopcr']['keep-nucs'], config['ecopcr']['keep-primers'], config['ecopcr']['kingdom-mode']) < 0:
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raise Exception("Error running ecopcr")
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# Save command config in DMS comments
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o_dms.record_command_line(command_line)
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free(restrict_to_taxids_p)
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free(ignore_taxids_p)
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# stdout output: write to buffer
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if type(output_0)==BufferedWriter:
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logger("info", "Printing to output...")
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o_view = o_dms[o_view_name]
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o_view.print_to_output(output_0, noprogressbar=config['obi']['noprogressbar'])
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o_view.close()
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#print("\n\nOutput view:\n````````````", file=sys.stderr)
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#print(repr(o_dms[o_view_name]), file=sys.stderr)
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# If stdout output, delete the temporary result view in the input DMS
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if type(output_0)==BufferedWriter:
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View.delete_view(i_dms, o_view_name)
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i_dms.close(force=True)
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o_dms.close(force=True)
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logger("info", "Done.")
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