Esempio n. 1
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def find_saschas_pairs():
    pair_dists = biopsy.pair_analysis(
            'c:/data/remos/0/0.cleaned',
            'c:/data/remos/0/0.analysis',
            45,
            pair_filter = saschas_pair_filter,
            location_filter = biopsy.get_default_pair_filter(
                    family_file = 'C:/Data/Ensembl/mouse_families.txt',
                    paralog_file = 'C:/Data/Ensembl/mouse_paralogs.txt',
                    subtypes = [
                            # 'Fungi/Metazoa group',
                            # 'Coelomata',
                            # 'Bilateria',
                            # 'Chordata',
                            # 'Amniota',
                            # 'Tetrapoda',
                            'Euteleostomi',
                            'Theria',
                            'Eutheria',
                            'Euarchontoglires',
                            'Murinae',
                            'Mus musculus',
                    ]
            )
    )
    biopsy.save( pair_dists, 'saschas.pairs' )
Esempio n. 2
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def test_pair_analysis():
    import webbrowser
    remome_threshold = 100
    remome_file = 'c:/data/remos/%d/%d.cleaned' % ( remome_threshold, remome_threshold )
    analysis_file = 'c:/data/remos/%d/%d.analysis' % ( remome_threshold, remome_threshold )
    location_filter = biopsy.get_default_pair_filter()
    hits = biopsy.pair_analysis(
            remome_file,
            analysis_file,
            max_distance = 45,
            distance_filter = lambda d: d == 25,
            pair_filter = lambda p: p == ( 'M00471', 'M00791', False, False ),
            location_filter = location_filter
    )
    for k, v in hits.iteritems():
        print k
        print v
        for g in location_filter.filter2.genes_for_pair[ k ]:
            print g
            webbrowser.open( biopsy.ensembl_url( g ) )
        print