コード例 #1
0
ファイル: biopsy_test.py プロジェクト: JohnReid/biopsy
def test_analyse():
    sequences = {
            'mouse'         : 'TCTCAGTATGCGCACCTCTCCCGAGACACCTTTGAAGTCCTGGGTCCTTTGATGTGAGTGGGGAATGCGGTTTGCGGGGAGATCCTGAGACCCCTGTGGTCAGTGGCCCATAGAGCATGGGTGCTTGCTG',
            'dog'           : 'GCCAGGTATGTGCATCTCCCCTCAATCTGCCTTTGAAGCCCGGGGCCCTTTGATGTGAGTGGGGGATGCACCAGCCTGGGATCTTGCCAGCCTTGTGGTCAGTAGCCAACAGGGCACGGGGCTTGGTGGAGTTTGGAAATAAGAG',
            'human'         : 'TATGGGGTATGTGCATCTTCCTCACCTGCCTTTGAAGCCTGGGGCCCTTTGATGTTAGTGGGGAATGCACCAGCCTGGGGCTCTTGAGAGCTCTGCGGTCAGTGGCCAACAAGGAACAGGGACTGGGGAG',
    }

    print 'Analysing'
    hits = { }
    for name, seq in sequences.iteritems():
        hits[ name ] = biopsy.analyse( seq, 0.01 )

        print name, 'had', len( hits[ name ] ), 'hit(s)'
        print hits[ name ]



    for keys in [
                    [ 'mouse', 'dog' ],
                    [ 'mouse', 'human' ],
                    [ 'human', 'dog' ],
                    [ 'mouse', 'human', 'dog' ],
            ]:
        print keys
        seq, score = \
                biopsy.LCS(
                        [ hits[ key ] for key in keys ],
                        biopsy.get_char_for_hit,
                        biopsy.get_score_for_hit ).get_best()
        print score
        print ",".join( seq )
        print
コード例 #2
0
ファイル: biopsy_test.py プロジェクト: pombredanne/biopsy
def test_analyse():
    sequences = {
        'mouse':
        'TCTCAGTATGCGCACCTCTCCCGAGACACCTTTGAAGTCCTGGGTCCTTTGATGTGAGTGGGGAATGCGGTTTGCGGGGAGATCCTGAGACCCCTGTGGTCAGTGGCCCATAGAGCATGGGTGCTTGCTG',
        'dog':
        'GCCAGGTATGTGCATCTCCCCTCAATCTGCCTTTGAAGCCCGGGGCCCTTTGATGTGAGTGGGGGATGCACCAGCCTGGGATCTTGCCAGCCTTGTGGTCAGTAGCCAACAGGGCACGGGGCTTGGTGGAGTTTGGAAATAAGAG',
        'human':
        'TATGGGGTATGTGCATCTTCCTCACCTGCCTTTGAAGCCTGGGGCCCTTTGATGTTAGTGGGGAATGCACCAGCCTGGGGCTCTTGAGAGCTCTGCGGTCAGTGGCCAACAAGGAACAGGGACTGGGGAG',
    }

    print 'Analysing'
    hits = {}
    for name, seq in sequences.iteritems():
        hits[name] = biopsy.analyse(seq, 0.01)

        print name, 'had', len(hits[name]), 'hit(s)'
        print hits[name]

    for keys in [
        ['mouse', 'dog'],
        ['mouse', 'human'],
        ['human', 'dog'],
        ['mouse', 'human', 'dog'],
    ]:
        print keys
        seq, score = \
                biopsy.LCS(
                        [ hits[ key ] for key in keys ],
                        biopsy.get_char_for_hit,
                        biopsy.get_score_for_hit ).get_best()
        print score
        print ",".join(seq)
        print
コード例 #3
0
ファイル: biopsy_test.py プロジェクト: JohnReid/biopsy
def test_lcs():
    seqs = [
            # 'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagca',
            # 'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagca',
            'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagcagactgcatgcggacgggaccgcggatcgcgcggtgcgcctcagtgtacttccgaacgaatgagtcattaatagagcgctatatcgtaactgtctttgacgaagtataccgaaaccgtgcagccagacgtgatccgggcgttgtaaaggcgatcagcgccctaggagtaccatttttgccgtaggcttgcgtctcaaagaccagctggggcgtggtatcactcgtcagtacgatttctgccagatagatagcatagactgaaccttaggcccaatagggacacaattacccgagtgactgactggtctaaggggagtccccccttaaaacgttttacgtaatagcgggctccagaagcaaagcatcggtttgagccccagtactaaacgtttgagtgtttgctctcgtctgataggtaaaccgacaagagaaccaagctcaaggcgcggtaggtgcgccttgcgaactgttgatgccgtgagcgccaccatcccgtgcatcataggcagggagagaagaccacatggccttgcgaccgtatgagctgtttcagattaaatgccaacgggcatggtcggtgtccagcattttttgcagtcagctggtggtacacagtggggacaagaacgcctctggtagatgtcttctgaaggagtaactcatttcgttgaatcgaccttcccttgcgcttgaacgcggacctctagtctctctcgcagactggggtcgaaaatcaaggtagatatggaatgttccgcatgagggtagcgaccggatcgggcgtcaagtatatcctccctgctacgtccccctactagcctcagtccgcctcgaacctaggaagattggccacatcagcttggtggatgcctggtccatacttcagacccgagaatgttagacaggaccccatttggctcctttacgtacgatctatgtagacgcagtga',
            'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagcagactgcatgcggacgggaccgcggatcgcgcggtgcgcctcagtgtacttccgaacgaatgagtcattaatagagcgctatatcgtaactgtctttgacgaagtataccgaaaccgtgcagccagacgtgatccgggcgttgtaaaggcgatcagcgccctaggagtaccatttttgccgtaggcttgcgtctcaaagaccagctggggcgtggtatcactcgtcagtacgatttctgccagatagatagcatagactgaaccttaggcccaatagggacacaattacccgagtgactgactggtctaaggggagtccccccttaaaacgttttacgtaatagcgggctccagaagcaaagcatcggtttgagccccagtactaaacgtttgagtgtttgctctcgtctgataggtaaaccgacaagagaaccaagctcaaggcgcggtaggtgcgccttgcgaactgttgatgccgtgagcgccaccatcccgtgcatcataggcagggagagaagaccacatggccttgcgaccgtatgagctgtttcagattaaatgccaacgggcatggtcggtgtccagcattttttgcagtcagctggtggtacacagtggggacaagaacgcctctggtagatgtcttctgaaggagtaactcatttcgttgaatcgaccttcccttgcgcttgaacgcggacctctagtctctctcgcagactggggtcgaaaatcaaggtagatatggaatgttccgcatgagggtagcgaccggatcgggcgtcaagtatatcctccctgctacgtccccctactagcctcagtccgcctcgaacctaggaagattggccacatcagcttggtggatgcctggtccatacttcagacccgagaatgttagacaggaccccatttggctcctttacgtacgatctatgtagacgcagtga',
            # 'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagcagactgcatgcggacgggaccgcggatcgcgcggtgcgcctcagtgtacttccgaacgaatgagtcattaatagagcgctatatcgtaactgtctttgacgaagtataccgaaaccgtgcagccagacgtgatccgggcgttgtaaaggcgatcagcgccctaggagtaccatttttgccgtaggcttgcgtctcaaagaccagctggggcgtggtatcactcgtcagtacgatttctgccagatagatagcatagactgaaccttaggcccaatagggacacaattacccgagtgactgactggtctaaggggagtccccccttaaaacgttttacgtaatagcgggctccagaagcaaagcatcggtttgagccccagtactaaacgtttgagtgtttgctctcgtctgataggtaaaccgacaagagaaccaagctcaaggcgcggtaggtgcgccttgcgaactgttgatgccgtgagcgccaccatcccgtgcatcataggcagggagagaagaccacatggccttgcgaccgtatgagctgtttcagattaaatgccaacgggcatggtcggtgtccagcattttttgcagtcagctggtggtacacagtggggacaagaacgcctctggtagatgtcttctgaaggagtaactcatttcgttgaatcgaccttcccttgcgcttgaacgcggacctctagtctctctcgcagactggggtcgaaaatcaaggtagatatggaatgttccgcatgagggtagcgaccggatcgggcgtcaagtatatcctccctgctacgtccccctactagcctcagtccgcctcgaacctaggaagattggccacatcagcttggtggatgcctggtccatacttcagacccgagaatgttagacaggaccccatttggctcctttacgtacgatctatgtagacgcagtga',
            ]
    hits = biopsy.HitsVec()
    for s in seqs:
        hits.append( biopsy.analyse( s, 0.03 ) )
    lcs = biopsy.longest_common_subsequence( hits )
    print lcs
コード例 #4
0
ファイル: biopsy_test.py プロジェクト: pombredanne/biopsy
def test_lcs():
    seqs = [
        # 'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagca',
        # 'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagca',
        'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagcagactgcatgcggacgggaccgcggatcgcgcggtgcgcctcagtgtacttccgaacgaatgagtcattaatagagcgctatatcgtaactgtctttgacgaagtataccgaaaccgtgcagccagacgtgatccgggcgttgtaaaggcgatcagcgccctaggagtaccatttttgccgtaggcttgcgtctcaaagaccagctggggcgtggtatcactcgtcagtacgatttctgccagatagatagcatagactgaaccttaggcccaatagggacacaattacccgagtgactgactggtctaaggggagtccccccttaaaacgttttacgtaatagcgggctccagaagcaaagcatcggtttgagccccagtactaaacgtttgagtgtttgctctcgtctgataggtaaaccgacaagagaaccaagctcaaggcgcggtaggtgcgccttgcgaactgttgatgccgtgagcgccaccatcccgtgcatcataggcagggagagaagaccacatggccttgcgaccgtatgagctgtttcagattaaatgccaacgggcatggtcggtgtccagcattttttgcagtcagctggtggtacacagtggggacaagaacgcctctggtagatgtcttctgaaggagtaactcatttcgttgaatcgaccttcccttgcgcttgaacgcggacctctagtctctctcgcagactggggtcgaaaatcaaggtagatatggaatgttccgcatgagggtagcgaccggatcgggcgtcaagtatatcctccctgctacgtccccctactagcctcagtccgcctcgaacctaggaagattggccacatcagcttggtggatgcctggtccatacttcagacccgagaatgttagacaggaccccatttggctcctttacgtacgatctatgtagacgcagtga',
        'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagcagactgcatgcggacgggaccgcggatcgcgcggtgcgcctcagtgtacttccgaacgaatgagtcattaatagagcgctatatcgtaactgtctttgacgaagtataccgaaaccgtgcagccagacgtgatccgggcgttgtaaaggcgatcagcgccctaggagtaccatttttgccgtaggcttgcgtctcaaagaccagctggggcgtggtatcactcgtcagtacgatttctgccagatagatagcatagactgaaccttaggcccaatagggacacaattacccgagtgactgactggtctaaggggagtccccccttaaaacgttttacgtaatagcgggctccagaagcaaagcatcggtttgagccccagtactaaacgtttgagtgtttgctctcgtctgataggtaaaccgacaagagaaccaagctcaaggcgcggtaggtgcgccttgcgaactgttgatgccgtgagcgccaccatcccgtgcatcataggcagggagagaagaccacatggccttgcgaccgtatgagctgtttcagattaaatgccaacgggcatggtcggtgtccagcattttttgcagtcagctggtggtacacagtggggacaagaacgcctctggtagatgtcttctgaaggagtaactcatttcgttgaatcgaccttcccttgcgcttgaacgcggacctctagtctctctcgcagactggggtcgaaaatcaaggtagatatggaatgttccgcatgagggtagcgaccggatcgggcgtcaagtatatcctccctgctacgtccccctactagcctcagtccgcctcgaacctaggaagattggccacatcagcttggtggatgcctggtccatacttcagacccgagaatgttagacaggaccccatttggctcctttacgtacgatctatgtagacgcagtga',
        # 'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagcagactgcatgcggacgggaccgcggatcgcgcggtgcgcctcagtgtacttccgaacgaatgagtcattaatagagcgctatatcgtaactgtctttgacgaagtataccgaaaccgtgcagccagacgtgatccgggcgttgtaaaggcgatcagcgccctaggagtaccatttttgccgtaggcttgcgtctcaaagaccagctggggcgtggtatcactcgtcagtacgatttctgccagatagatagcatagactgaaccttaggcccaatagggacacaattacccgagtgactgactggtctaaggggagtccccccttaaaacgttttacgtaatagcgggctccagaagcaaagcatcggtttgagccccagtactaaacgtttgagtgtttgctctcgtctgataggtaaaccgacaagagaaccaagctcaaggcgcggtaggtgcgccttgcgaactgttgatgccgtgagcgccaccatcccgtgcatcataggcagggagagaagaccacatggccttgcgaccgtatgagctgtttcagattaaatgccaacgggcatggtcggtgtccagcattttttgcagtcagctggtggtacacagtggggacaagaacgcctctggtagatgtcttctgaaggagtaactcatttcgttgaatcgaccttcccttgcgcttgaacgcggacctctagtctctctcgcagactggggtcgaaaatcaaggtagatatggaatgttccgcatgagggtagcgaccggatcgggcgtcaagtatatcctccctgctacgtccccctactagcctcagtccgcctcgaacctaggaagattggccacatcagcttggtggatgcctggtccatacttcagacccgagaatgttagacaggaccccatttggctcctttacgtacgatctatgtagacgcagtga',
    ]
    hits = biopsy.HitsVec()
    for s in seqs:
        hits.append(biopsy.analyse(s, 0.03))
    lcs = biopsy.longest_common_subsequence(hits)
    print lcs
コード例 #5
0
ファイル: biopsy_test.py プロジェクト: pombredanne/biopsy
def test_score_pssms():
    # 'V$AP1_Q2'
    transfac_pssms = biopsy.get_transfac_pssm_accessions(
        biopsy.get_default_transfac_pssm_filter())
    print 'Got', len(transfac_pssms), 'pssms'
    seq = 'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagcagactgcatgcggacgggaccgcggatcgcgcggtgcgcctcagtgtacttccgaacgaatgagtcattaatagagcgctatatcgtaactgtctttgacgaagtataccgaaaccgtgcagccagacgtgatccgggcgttgtaaaggcgatcagcgccctaggagtaccatttttgccgtaggcttgcgtctcaaagaccagctggggcgtggtatcactcgtcagtacgatttctgccagatagatagcatagactgaaccttaggcccaatagggacacaattacccgagtgactgactggtctaaggggagtccccccttaaaacgttttacgtaatagcgggctccagaagcaaagcatcggtttgagccccagtactaaacgtttgagtgtttgctctcgtctgataggtaaaccgacaagagaaccaagctcaaggcgcggtaggtgcgccttgcgaactgttgatgccgtgagcgccaccatcccgtgcatcataggcagggagagaagaccacatggccttgcgaccgtatgagctgtttcagattaaatgccaacgggcatggtcggtgtccagcattttttgcagtcagctggtggtacacagtggggacaagaacgcctctggtagatgtcttctgaaggagtaactcatttcgttgaatcgaccttcccttgcgcttgaacgcggacctctagtctctctcgcagactggggtcgaaaatcaaggtagatatggaatgttccgcatgagggtagcgaccggatcgggcgtcaagtatatcctccctgctacgtccccctactagcctcagtccgcctcgaacctaggaagattggccacatcagcttggtggatgcctggtccatacttcagacccgagaatgttagacaggaccccatttggctcctttacgtacgatctatgtagacgcagtga'
    # seq = 'acatcat'
    # seq = 'gat'
    # hits = biopsy.HitVec()
    hits = biopsy.score_pssms_on_sequence(transfac_pssms, seq, 0.05)
    print hits
    print 'score_pssm_on_sequence: Got', len(hits), 'hits from', len(
        seq), 'bases'
    hits = biopsy.analyse(seq, 0.05)
    # print hits
    print 'analyse: Got', len(hits), 'hits from', len(seq), 'bases'
コード例 #6
0
ファイル: biopsy_test.py プロジェクト: JohnReid/biopsy
def test_score_pssms():
    # 'V$AP1_Q2'
    transfac_pssms = biopsy.get_transfac_pssm_accessions( biopsy.get_default_transfac_pssm_filter() )
    print 'Got', len( transfac_pssms ), 'pssms'
    seq = 'tacatcatctgtctgcagtagtctaaccgaccccccccagttttagaagcagactgcatgcggacgggaccgcggatcgcgcggtgcgcctcagtgtacttccgaacgaatgagtcattaatagagcgctatatcgtaactgtctttgacgaagtataccgaaaccgtgcagccagacgtgatccgggcgttgtaaaggcgatcagcgccctaggagtaccatttttgccgtaggcttgcgtctcaaagaccagctggggcgtggtatcactcgtcagtacgatttctgccagatagatagcatagactgaaccttaggcccaatagggacacaattacccgagtgactgactggtctaaggggagtccccccttaaaacgttttacgtaatagcgggctccagaagcaaagcatcggtttgagccccagtactaaacgtttgagtgtttgctctcgtctgataggtaaaccgacaagagaaccaagctcaaggcgcggtaggtgcgccttgcgaactgttgatgccgtgagcgccaccatcccgtgcatcataggcagggagagaagaccacatggccttgcgaccgtatgagctgtttcagattaaatgccaacgggcatggtcggtgtccagcattttttgcagtcagctggtggtacacagtggggacaagaacgcctctggtagatgtcttctgaaggagtaactcatttcgttgaatcgaccttcccttgcgcttgaacgcggacctctagtctctctcgcagactggggtcgaaaatcaaggtagatatggaatgttccgcatgagggtagcgaccggatcgggcgtcaagtatatcctccctgctacgtccccctactagcctcagtccgcctcgaacctaggaagattggccacatcagcttggtggatgcctggtccatacttcagacccgagaatgttagacaggaccccatttggctcctttacgtacgatctatgtagacgcagtga'
    # seq = 'acatcat'
    # seq = 'gat'
    # hits = biopsy.HitVec()
    hits = biopsy.score_pssms_on_sequence(
            transfac_pssms,
            seq,
            0.05 )
    print hits
    print 'score_pssm_on_sequence: Got', len( hits ), 'hits from', len( seq ), 'bases'
    hits = biopsy.analyse(
            seq,
            0.05)
    # print hits
    print 'analyse: Got', len( hits ), 'hits from', len( seq ), 'bases'