Cython API: updated the test command for the new API and deactivated the
other commands for now
This commit is contained in:
Celine Mercier
@ -1,130 +1,133 @@
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.files.universalopener cimport uopen
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from obitools3.parsers.fasta import fastaIterator
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from obitools3.parsers.fastq import fastqIterator
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from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
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# from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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# from obitools3.files.universalopener cimport uopen
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# from obitools3.parsers.fasta import fastaIterator
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# from obitools3.parsers.fastq import fastqIterator
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# from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
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#
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# import time
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#
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import time
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__title__="Counts sequences in a sequence set"
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default_config = { 'destview' : None,
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'skip' : 0,
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'only' : None,
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'skiperror' : False,
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'seqinformat' : None,
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'moltype' : 'nuc',
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'filename' : None
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}
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def addOptions(parser):
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parser.add_argument(dest='import:filename',
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metavar='<FILENAME>',
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nargs='?',
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default=None,
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help='sequence file name to be imported' )
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group=parser.add_argument_group('obi import specific options')
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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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group.add_argument('--destination-view','-v',
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action="store", dest="import:destview",
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metavar='<VIEW NAME>',
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default=None,
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type=str,
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required=True,
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help="Name of the default DMS for reading and writing data")
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group.add_argument('--skip',
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action="store", dest="import:skip",
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metavar='<N>',
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default=None,
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type=int,
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help="skip the N first sequences")
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group.add_argument('--only',
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action="store", dest="import:only",
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metavar='<N>',
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default=None,
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type=int,
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help="treat only N sequences")
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group.add_argument('--skip-on-error',
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action="store_true", dest="import:skiperror",
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default=None,
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help="Skip sequence entries with parse error")
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group.add_argument('--fasta',
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action="store_const", dest="import:seqinformat",
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default=None,
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const='fasta',
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help="Input file is in fasta nucleic format (including obitools fasta extentions)")
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group.add_argument('--fastq',
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action="store_const", dest="import:seqinformat",
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default=None,
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const='fastq',
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help="Input file is in sanger fastq nucleic format (standard fastq)")
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group.add_argument('--nuc',
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action="store_const", dest="import:moltype",
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default=None,
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const='nuc',
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help="Input file contains nucleic sequences")
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group.add_argument('--prot',
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action="store_const", dest="import:moltype",
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default=None,
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const='pep',
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help="Input file contains protein sequences")
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# TODO: Handling of NA values
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def run(config):
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pb = ProgressBar(35000000, config, seconde=5) # TODO should be number of records in file
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inputs = uopen(config['import']['filename'])
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get_quality = False
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if config['import']['seqinformat']=='fasta':
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iseq = fastaIterator(inputs)
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view_type="NUC_SEQS_VIEW"
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elif config['import']['seqinformat']=='fastq':
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iseq = fastqIterator(inputs)
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view_type="NUC_SEQS_VIEW"
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get_quality = True
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else:
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raise RuntimeError('No file format specified')
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# Create DMS
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d = OBIDMS(config['obi']['defaultdms'])
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# Create view
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# view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
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pass
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# __title__="Counts sequences in a sequence set"
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#
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#
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# default_config = { 'destview' : None,
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# 'skip' : 0,
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# 'only' : None,
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# 'skiperror' : False,
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# 'seqinformat' : None,
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# 'moltype' : 'nuc',
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# 'filename' : None
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# }
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#
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# def addOptions(parser):
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# parser.add_argument(dest='import:filename',
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# metavar='<FILENAME>',
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# nargs='?',
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# default=None,
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# help='sequence file name to be imported' )
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#
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# group=parser.add_argument_group('obi import specific 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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# i = 0
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# for seq in iseq:
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# pb(i)
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# view[i].id = seq['id']
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# view[i].definition = seq['definition']
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# view[i].nuc_seq = seq['sequence']
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# if get_quality :
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# view[i].quality = seq['quality']
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# for tag in seq['tags'] :
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# view[i][tag] = seq['tags'][tag]
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# i+=1
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# group.add_argument('--destination-view','-v',
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# action="store", dest="import:destview",
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# metavar='<VIEW NAME>',
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# default=None,
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# type=str,
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# required=True,
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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('--skip',
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# action="store", dest="import:skip",
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# metavar='<N>',
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# default=None,
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# type=int,
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# help="skip the N first sequences")
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#
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# #print(view.__repr__())
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# group.add_argument('--only',
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# action="store", dest="import:only",
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# metavar='<N>',
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# default=None,
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# type=int,
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# help="treat only N sequences")
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#
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# view.close()
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d.close()
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# group.add_argument('--skip-on-error',
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# action="store_true", dest="import:skiperror",
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# default=None,
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# help="Skip sequence entries with parse error")
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#
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# group.add_argument('--fasta',
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# action="store_const", dest="import:seqinformat",
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# default=None,
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# const='fasta',
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# help="Input file is in fasta nucleic format (including obitools fasta extentions)")
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#
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# group.add_argument('--fastq',
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# action="store_const", dest="import:seqinformat",
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# default=None,
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# const='fastq',
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# help="Input file is in sanger fastq nucleic format (standard fastq)")
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#
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# group.add_argument('--nuc',
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# action="store_const", dest="import:moltype",
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# default=None,
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# const='nuc',
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# help="Input file contains nucleic sequences")
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#
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# group.add_argument('--prot',
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# action="store_const", dest="import:moltype",
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# default=None,
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# const='pep',
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# help="Input file contains protein sequences")
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#
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#
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#
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# # TODO: Handling of NA values
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# def run(config):
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# pb = ProgressBar(35000000, config, seconde=5) # TODO should be number of records in file
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#
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# inputs = uopen(config['import']['filename'])
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#
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# get_quality = False
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# if config['import']['seqinformat']=='fasta':
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# iseq = fastaIterator(inputs)
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# view_type="NUC_SEQS_VIEW"
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# elif config['import']['seqinformat']=='fastq':
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# iseq = fastqIterator(inputs)
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# view_type="NUC_SEQS_VIEW"
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# get_quality = True
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# else:
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# raise RuntimeError('No file format specified')
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#
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# # Create DMS
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# d = OBIDMS(config['obi']['defaultdms'])
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#
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# # Create view
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# # view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
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# #
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# # i = 0
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# # for seq in iseq:
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# # pb(i)
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# # view[i].id = seq['id']
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# # view[i].definition = seq['definition']
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# # view[i].nuc_seq = seq['sequence']
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# # if get_quality :
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# # view[i].quality = seq['quality']
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# # for tag in seq['tags'] :
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# # view[i][tag] = seq['tags'][tag]
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# # i+=1
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# #
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# # #print(view.__repr__())
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# #
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# # view.close()
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# d.close()
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#
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