python cookbook3

1、算GC含量

def validate_base_sequence(base_sequence, RNAflag = False):      #判断序列是否只含有A、T、G、C、U
    seq = base_sequence.upper()
    return len(seq) == (seq.count('U' if RNAflag else 'T') +seq.count('C') +
               seq.count('A') +seq.count('G'))              
    
def gc_content(base_seq):                                #计算GC含量
    assert validate_base_sequence(base_seq), 'argument has invalid characters'
    seq = base_seq.upper()
    return (base_seq.count('G') +base_seq.count('C')) / len(base_seq)

def recognition_site(base_seq, recognition_seq):
    return base_seq.find(recognition_seq)

def test():
    assert validate_base_sequence('ACTG')
    assert validate_base_sequence('')
    assert not validate_base_sequence('ACUG')
    assert validate_base_sequence('ACUG', True)
    assert not validate_base_sequence('ACUG', False)
    assert validate_base_sequence('ACTG', False)
    assert .5 == gc_content('ACTG')
    assert 1.0 == gc_content('CCGG')
    assert .25 == gc_content('ACTT')
    print('All tests passed.')
test()

2、元组

>>> DNABases, RNABases = 'TCAG', 'UCAG'
>>> DNABases
'TCAG'
>>> RNABases
'UCAG'
>>> bases = 'TCAG', 'UCAG' # a two-element tuple
>>> bases
('TCAG', 'UCAG')

3、切割

def recognition_site(base_seq, recognition_seq):
    return base_seq.find(recognition_seq)

def restriction_cut(base_seq, recognition_seq, offset = 0):
    site = recognition_site(base_seq, recognition_seq)
    return base_seq[:site+offset], base_seq[site+offset:]

aseq1 = 'AAAAATCCCGAGGCGGCTATATAGGGCTCCGGAGGCGTAATATAAAA'
left, right = restriction_cut(aseq1, 'TCCGGA')

4、读取fasta序列，并取最长的序列

def read_FASTA(filename):
    with open(filename) as file:
        contents = file.read() 
    entries = contents.split('>')[1:] # skip blank first entry
    partitioned_entries = [entry.partition('\n') for entry in entries]
    result = [(entry[0], entry[2].replace('\n', '')) for entry in partitioned_entries]
    return result

def longest_sequence(filename):
    longest_seq = ''
    for info, seq in read_FASTA(filename):
        longest_seq = max(longest_seq, seq, key=len)
    return longest_seq