Пример #1
0
            validate_genelocustatsoptions
            )
    from abgpgenelocusdirectory import AbgpGeneLocusDirectory
    from lib_sequencerepetitiveness import annotatedproteinsequencerepetitivenesscheck

    # construct the command line option parser
    parser = abgpoptparser()
    genelocustatsoptions(parser)
    parser.remove_option('--explain')
    # parse the command line & validate
    (OPTIONS, args) = parser.parse_args()
    validate_genelocustatsoptions(parser,OPTIONS)

    # change directory to the one specified by optparse option
    os.chdir(OPTIONS.DIRECTORY)
    locus = AbgpGeneLocusDirectory(OPTIONS.DIRECTORY)
    input = locus.toinputdict()
 
    # do geneconfirmation
    input,gene_status = geneconfirmation(input,verbose=True)

    # do a protein sequence repetitiveness check
    IS_REPETITIVE = annotatedproteinsequencerepetitivenesscheck(input)

    # do a check on tiny/small exons
    HAS_SMALL_OR_TINY_EXONS = annotatedgeneexonsizeevaluation(input)

    # do check on noncannocical splice sites
    for org in input.keys():
        status, warnings = confirmcanonicalsplicesites(input[org]['genomeseq'],
                input[org]['gff-gene'],exon_fmethod=GFF_CDS_FMETHOD,verbose=False)
Пример #2
0
thisoption = parser.get_option('--dirwithloci')
thisoption.help = 'give statistics for all the AbfgpGeneLocusDirectories in this --dirwithloci'
thisoption = parser.get_option('--filewithloci')
thisoption.help = 'give statistics for all the AbfgpGeneLocusDirectories listed in this --filewithloci'
(OPTIONS, args) = parser.parse_args()
OPTIONS.target = None # dummy option
validate_abgpinputoptions(parser,OPTIONS)
validate_abgpoptions(parser,OPTIONS)

################################################################################
################################################################################

if OPTIONS.loci:
    input = {} # input data structure, empty
    for locusdir in OPTIONS.loci:
        locus = AbgpGeneLocusDirectory(locusdir)
        locuskey = locus._create_auto_key(
                identifier2organism=ABGP_LOCUS_IDENTIFIER2ORGANISM_MAPPING
                )
        if input.has_key(locuskey):
            for suffix in list('abcdefghijklmnopqrstuvwxyz'):
                if not input.has_key(locuskey+suffix):
                    input.update( locus.toinputdict(key=locuskey+suffix) )
                    break
        else:
            input.update( locus.toinputdict(key=locuskey) )
else:
    print "Exception.NoAbgpGeneLocusDirectoriesProvided"
    print ""
    parser.print_help()
    sysexit()