Question

我正在尝试解析一个大的fasta文件，我遇到内存不足错误。一些改进数据处理的建议将不胜感激。目前程序正确地打印出名称，但部分通过文件我得到一个MemoryError

这是发电机

def readFastaEntry( fp ):
    name = ""
    seq = ""
    for line in fp:
        if line.startswith( ">" ):
            tmp = []
            tmp.append( name )
            tmp.append( seq )
            name = line
            seq = ""
            yield tmp
        else:
            seq = seq.join( line )

这里是调用者存根，在此部分工作后将添加更多

fp = open( sys.argv[1], 'r' )

for seq in readFastaEntry( fp ) :
    print seq[0]

对于那些与fasta格式不相似的人，这里有一个例子

>1 (PB2)
AATATATTCAATATGGAGAGAATAAAAGAACTAAGAGATCTAATGTCACAGTCTCGCACTCGCGAGATAC
TCACCAAAACCACTGTGGACCACATGGCCATAATCAAAAAGTACACATCAGGAAGGCAAGAGAAGAACCC
TGCACTCAGGATGAAGTGGATGATG
>2 (PB1)
AACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTTCCAGCGCAAAATGCCATAAGCACC
ACATTTCCCTATACTGGAGACCCTCC

每个条目都以“＆gt;”开头说明名称等，然后接下来的N行是数据。除了具有“＆gt;”的下一行之外，没有定义的数据结尾。在开始。

Answer 1

您是否考虑过使用BioPython。他们有sequence reader可以读取fasta文件。如果您对自己编码感兴趣，可以查看BioPython's code。

修改：已添加代码

def read_fasta(fp):
    name, seq = None, []
    for line in fp:
        line = line.rstrip()
        if line.startswith(">"):
            if name: yield (name, ''.join(seq))
            name, seq = line, []
        else:
            seq.append(line)
    if name: yield (name, ''.join(seq))

with open('f.fasta') as fp:
    for name, seq in read_fasta(fp):
        print(name, seq)

Answer 2

此格式的pyparsing解析器只有几行。请参阅以下代码中的注释：

data = """>1 (PB2) 
AATATATTCAATATGGAGAGAATAAAAGAACTAAGAGATCTAATGTCACAGTCTCGCACTCGCGAGATAC 
TCACCAAAACCACTGTGGACCACATGGCCATAATCAAAAAGTACACATCAGGAAGGCAAGAGAAGAACCC 
TGCACTCAGGATGAAGTGGATGATG 
>2 (PB1) 
AACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTTCCAGCGCAAAATGCCATAAGCACC 
ACATTTCCCTATACTGGAGACCCTCC"""

from pyparsing import Word, nums, QuotedString, Combine, OneOrMore

# define some basic forms
integer = Word(nums)
key = QuotedString("(", endQuoteChar=")")

# sequences are "words" made up of the characters A, G, C, and T
# we want to match one or more of them, and have the parser combine
# them into a single string (Combine by default requires all of its
# elements to be adjacent within the input string, but we want to allow
# for the intervening end of lines, so we add adjacent=False)
sequence = Combine(OneOrMore(Word("AGCT")), adjacent=False)

# define the overall pattern to scan for - attach results names
# to each matched element
seqEntry = ">" + integer("index") + key("key") + sequence("sequence")

for seq,s,e in seqEntry.scanString(data):
    # just dump out the matched data
    print seq.dump()
    # could also access fields as seq.index, seq.key and seq.sequence

打印：

['>', '1', 'PB2', 'AATATATTCAATATGGAGAGAATAAAAGAACTAAGAGATCTAATGTCACAGTCTCGCACTCGCGAGATACTCACCAAAACCACTGTGGACCACATGGCCATAATCAAAAAGTACACATCAGGAAGGCAAGAGAAGAACCCTGCACTCAGGATGAAGTGGATGATG']
- index: 1
- key: PB2
- sequence: AATATATTCAATATGGAGAGAATAAAAGAACTAAGAGATCTAATGTCACAGTCTCGCACTCGCGAGATACTCACCAAAACCACTGTGGACCACATGGCCATAATCAAAAAGTACACATCAGGAAGGCAAGAGAAGAACCCTGCACTCAGGATGAAGTGGATGATG
['>', '2', 'PB1', 'AACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTTCCAGCGCAAAATGCCATAAGCACCACATTTCCCTATACTGGAGACCCTCC']
- index: 2
- key: PB1
- sequence: AACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTTCCAGCGCAAAATGCCATAAGCACCACATTTCCCTATACTGGAGACCCTCC

Answer 3

如果没有很好地理解你在做什么，我会编写这样的代码：

def readFastaEntry( fp ):
    name = ""
    while True:
        line = name or f.readline()
        if not line:
            break
        seq = []
        while True:
            name = f.readline()
            if not name or name.startswith(">"):
                break
            else:
                seq.append(name)
        yield (line, "".join(seq))

在起始行到下一个起始行之后收集数据。使seq数组意味着最小化字符串连接直到最后一刻。产生一个元组比列表更有意义。

Answer 4

def read_fasta(filename):
    name = None
    with open(filename) as file:
        for line in file:
            if line[0] == ">":
                if name:
                    yield (name, seq)
                name = line[1:-1].split("|")[0]
                seq = ""
            else:
                seq += line[:-1]
        yield (name, seq)

使用生成器解析fasta文件（python）

4 个答案: