Python get_subtype_reference_alignment_entropy_syn_filename Examples

Example #1

File: get_subtype_entropy_synonymous.py Project: iosonofabio/hivwholeseq

def get_subtype_reference_alignment_entropy_syn(region, subtype='B', VERBOSE=0,
                                                refname='HXB2',
                                                type='nuc'):
    '''Get the entropy of a large subtype reference alignment'''
    import cPickle as pickle

    fn = get_subtype_reference_alignment_entropy_syn_filename(region,
                                                              subtype=subtype,
                                                              refname=refname,
                                                              type=type,
                                                              VERBOSE=VERBOSE)

    with open(fn, 'r') as f:
        data = pickle.load(f)

    return data

Example #2

File: get_subtype_entropy_synonymous.py Project: 5l1v3r1/hivwholeseq

def get_subtype_reference_alignment_entropy_syn(region,
                                                subtype='B',
                                                VERBOSE=0,
                                                refname='HXB2',
                                                type='nuc'):
    '''Get the entropy of a large subtype reference alignment'''
    import cPickle as pickle

    fn = get_subtype_reference_alignment_entropy_syn_filename(region,
                                                              subtype=subtype,
                                                              refname=refname,
                                                              type=type,
                                                              VERBOSE=VERBOSE)

    with open(fn, 'r') as f:
        data = pickle.load(f)

    return data

Example #3

File: get_subtype_entropy_synonymous.py Project: iosonofabio/hivwholeseq

            if VERBOSE >= 2:
                print 'Get alignment'
            ali = get_subtype_reference_alignment(region, subtype=subtype,
                                                  refname=refname,
                                                  VERBOSE=VERBOSE)
            alim = np.array(ali, 'S1')

            if VERBOSE >= 2:
                print 'Compute entropy'
            S = get_ali_entropy_syn(alim, VERBOSE=VERBOSE)

            if VERBOSE >= 2:
                print 'Store to file'
            fn_out = get_subtype_reference_alignment_entropy_syn_filename(region,
                                                                      subtype=subtype,
                                                                      refname=refname,
                                                                      VERBOSE=VERBOSE)

            with open(fn_out, 'wb') as f:
                pickle.dump(S, f)

        else:
            if VERBOSE >= 2:
                print 'Get entropy from file'
            S = get_subtype_reference_alignment_entropy_syn(region,
                                                        subtype=subtype,
                                                        refname=refname,
                                                        VERBOSE=VERBOSE)

        Ss[region] = S

Example #4

File: get_subtype_entropy_synonymous.py Project: 5l1v3r1/hivwholeseq

            if VERBOSE >= 2:
                print 'Get alignment'
            ali = get_subtype_reference_alignment(region,
                                                  subtype=subtype,
                                                  refname=refname,
                                                  VERBOSE=VERBOSE)
            alim = np.array(ali, 'S1')

            if VERBOSE >= 2:
                print 'Compute entropy'
            S = get_ali_entropy_syn(alim, VERBOSE=VERBOSE)

            if VERBOSE >= 2:
                print 'Store to file'
            fn_out = get_subtype_reference_alignment_entropy_syn_filename(
                region, subtype=subtype, refname=refname, VERBOSE=VERBOSE)

            with open(fn_out, 'wb') as f:
                pickle.dump(S, f)

        else:
            if VERBOSE >= 2:
                print 'Get entropy from file'
            S = get_subtype_reference_alignment_entropy_syn(region,
                                                            subtype=subtype,
                                                            refname=refname,
                                                            VERBOSE=VERBOSE)

        Ss[region] = S